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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/lefse">Debian Med / lefse</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/lefse/commit/3295faf2f0be49bff623d39f6bf6d3efadbcab90">3295faf2</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-09-11T14:19:31Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Include an autopkgtest
Simple comparative tests to see if installed files return an expected output
</pre>
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<h4>2 changed files:</h4>
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<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
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+
debian/tests/control
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+
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="83223a554d33ba7e1888274ff8ac43adb8147ba0">
<a href="https://salsa.debian.org/med-team/lefse/commit/3295faf2f0be49bff623d39f6bf6d3efadbcab90#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/lefse/commit/3295faf2f0be49bff623d39f6bf6d3efadbcab90#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Run comparative tests to see if we get an expected default output. Test installed files so no need to move them.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># run_lefse</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="si" style="color: #d14;">$(</span>run_lefse 2>&1<span class="si" style="color: #d14;">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"usage: run_lefse [-h]"</span><span class="k" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"run_lefse comparative pass"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"run_lefse comparative fail"</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># format_input</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="si" style="color: #d14;">$(</span>format_input 2>&1<span class="si" style="color: #d14;">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"usage: format_input [-h]"</span><span class="k" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"format_input comparative pass"</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"format_input comparative fail"</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span> </span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># lefse2circlader</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="si" style="color: #d14;">$(</span>lefse2circlader <span class="nt" style="color: #000080;">-h</span> 2>&1<span class="si" style="color: #d14;">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"usage: lefse2circlader [-h]"</span><span class="k" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"lefse2circlader comparative pass"</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"lefse2circlader comparative fail"</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># plot_cladogram</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="si" style="color: #d14;">$(</span>plot_cladogram 2>&1<span class="si" style="color: #d14;">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"usage: plot_cladogram [-h]"</span><span class="k" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"plot_cladogram comparative pass"</span></span>
</pre>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"plot_cladogram comparative fail"</span></span>
</pre>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># plot_features</span></span>
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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="si" style="color: #d14;">$(</span>plot_features 2>&1<span class="si" style="color: #d14;">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"usage: plot_features [-h]"</span><span class="k" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"plot_features comparative pass"</span></span>
</pre>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"plot_features comparative fail"</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># plo_res</span></span>
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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="si" style="color: #d14;">$(</span>plot_res 2>&1<span class="si" style="color: #d14;">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"usage: plot_res [-h]"</span><span class="k" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"plot_res comparative pass"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num new new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"plot_res comparative fail"</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># qiime2lefse</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="si" style="color: #d14;">$(</span>qiime2lefse <span class="nt" style="color: #000080;">-h</span> 2>&1<span class="si" style="color: #d14;">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"usage: qiime2lefse [-h]"</span><span class="k" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"qiime2lefse comparative pass"</span></span>
</pre>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"qiime2lefse comparative fail"</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span></pre>
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