[med-svn] [python-pbh5tools] 05/05: Save help information from standalone executables as draft manpages

[Afif Elghraoui]

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commit fb30749bf6780b197ed99f5e16f6169c3ba56677
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Thu Aug 13 01:52:11 2015 -0700

    Save help information from standalone executables as draft manpages
---
 debian/bash5tools.md | 34 ++++++++++++++++++++++++++++++++++
 debian/cmph5tools.md | 26 ++++++++++++++++++++++++++
 2 files changed, 60 insertions(+)

diff --git a/debian/bash5tools.md b/debian/bash5tools.md
new file mode 100644
index 0000000..8e3d99b
--- /dev/null
+++ b/debian/bash5tools.md
@@ -0,0 +1,34 @@
+usage: bash5tools [-h] [--verbose] [--version] [--profile] [--debug]
+                  [--outFilePrefix OUTFILEPREFIX]
+                  [--readType {ccs,subreads,unrolled}] [--outType OUTTYPE]
+                  [--minLength MINLENGTH] [--minReadScore MINREADSCORE]
+                  [--minPasses MINPASSES]
+                  input.bas.h5
+
+Tool for extracting data from .bas.h5 files
+
+positional arguments:
+  input.bas.h5          input .bas.h5 filename
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --verbose, -v         Set the verbosity level (default: None)
+  --version             show program's version number and exit
+  --profile             Print runtime profile at exit (default: False)
+  --debug               Catch exceptions in debugger (requires ipdb) (default:
+                        False)
+  --outFilePrefix OUTFILEPREFIX
+                        output filename prefix [None]
+  --readType {ccs,subreads,unrolled}
+                        read type (ccs, subreads, or unrolled) []
+  --outType OUTTYPE     output file type (fasta, fastq) [fasta]
+
+Read filtering arguments:
+  --minLength MINLENGTH
+                        min read length [0]
+  --minReadScore MINREADSCORE
+                        min read score, valid only with
+                        --readType={unrolled,subreads} [0]
+  --minPasses MINPASSES
+                        min number of CCS passes, valid only with
+                        --readType=ccs [0]
diff --git a/debian/cmph5tools.md b/debian/cmph5tools.md
new file mode 100644
index 0000000..32c3abc
--- /dev/null
+++ b/debian/cmph5tools.md
@@ -0,0 +1,26 @@
+usage: cmph5tools [-h] [--verbose] [--version] [--profile] [--debug]
+                  {select,merge,sort,equal,summarize,stats,listMetrics,validate}
+                  ...
+
+Toolkit for command-line tools associated with cmp.h5 file processing. Notes:
+For all command-line arguments, default values are listed in [].
+
+positional arguments:
+  {select,merge,sort,equal,summarize,stats,listMetrics,validate}
+    select              Create new cmp.h5 files from selections of
+                        input.cmp.h5
+    merge               Merge input.cmp.h5 files into out.cmp.h5
+    sort                Sort input.cmp.h5 file
+    equal               Compare two cmp.h5 files for equivalence
+    summarize           Summarize contents of cmp.h5 files
+    stats               Compute statistics from input.cmp.h5
+    listMetrics         List available metrics
+    validate            Validate input.cmp.h5
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --verbose, -v         Set the verbosity level (default: None)
+  --version             show program's version number and exit
+  --profile             Print runtime profile at exit (default: False)
+  --debug               Catch exceptions in debugger (requires ipdb) (default:
+                        False)

-- 
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