[med-svn] [pbsim] 01/05: switch man page building to asciidoctor

[Sascha Steinbiss]

This is an automated email from the git hooks/post-receive script.

sascha-guest pushed a commit to branch master
in repository pbsim.

commit 486bc1e1ef1cf9f83532798f847d5e5bbbccf885
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Thu Mar 17 11:17:49 2016 +0000

    switch man page building to asciidoctor
---
 debian/control                        |  5 ++--
 debian/{pbsim.1.ronn => pbsim.1.adoc} | 47 +++++++++++++++++++----------------
 debian/rules                          |  3 +--
 3 files changed, 29 insertions(+), 26 deletions(-)

diff --git a/debian/control b/debian/control
index 0d14275..c62d16d 100644
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,8 @@ Section: science
 Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Sascha Steinbiss <sascha at steinbiss.name>
-Build-Depends: debhelper (>= 9), ruby-ronn
+Build-Depends: debhelper (>= 9),
+               asciidoctor
 Standards-Version: 3.9.6
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/pbsim.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/pbsim.git
@@ -18,4 +19,4 @@ Description: simulator for PacBio sequencing reads
  which could be useful for de novo assembly of genomes. PBSIM simulates
  those PacBio reads from a reference sequence by using either a model-based
  or sampling-based simulation. Simulated reads are useful, for example, when
- developing or evaluating sequence assemblers targeted at PacBio data.
\ No newline at end of file
+ developing or evaluating sequence assemblers targeted at PacBio data.
diff --git a/debian/pbsim.1.ronn b/debian/pbsim.1.adoc
similarity index 77%
rename from debian/pbsim.1.ronn
rename to debian/pbsim.1.adoc
index 349f871..8b852e9 100644
--- a/debian/pbsim.1.ronn
+++ b/debian/pbsim.1.adoc
@@ -1,9 +1,12 @@
-pbsim(1) -- simulator for PacBio sequencing reads
-=================================================
+# pbsim(1) 
+
+## NAME
+
+pbsim - simulator for PacBio sequencing reads
 
 ## SYNOPSIS
 
-`pbsim` [options] <reference.fasta>
+*pbsim* [options] <reference.fasta>
 
 ## DESCRIPTION
 
@@ -17,61 +20,61 @@ The options for pbsim can be divided into general, sampling-based and model-base
 
 ### General options
 
-  * `--prefix`:
+  *--prefix*::
     prefix of output files (sd).
 
-  * `--data-type`:
+  *--data-type*::
     data type. CLR or CCS (CLR).
 
-  * `--depth`:
+  *--depth*::
     depth of coverage (CLR: 20.0, CCS: 50.0).
 
-  * `--length-min`:
+  *--length-min*::
     minimum length (100).
 
-  * `--length-max`:
+  *--length-max*::
     maximum length (CLR: 25000, CCS: 2500).
 
-  * `--accuracy-min`:
+  *--accuracy-min*::
     minimum accuracy (CLR: 0.75, CCS: fixed as 0.75).
     This option can be used only in case of CLR.
 
-  * `--accuracy-max`:
+  *--accuracy-max*::
     maximum accuracy (CLR: 1.00, CCS: fixed as 1.00).
     This option can be used only in case of CLR.
 
-  * `--difference-ratio`:
+  *--difference-ratio*::
     ratio of differences. substitution:insertion:deletion.
     Each value up to 1000 (CLR: 10:60:30, CCS:6:21:73).
 
-  * `--seed`:
+  *--seed*::
     for a pseudorandom number generator (Unix time).
 
 ### Options for sampling-based simulation
 
-  * `--sample-fastq`:
+  *--sample-fastq*::
     FASTQ format file to sample.
 
-  * `--sample-profile-id`:
-    sample-fastq (filtered) profile ID. When using `--sample-fastq`, profile is stored. `sample_profile_<ID>.fastq`, and `sample_profile_<ID>_.stats` are created.
-    When not using `--sample-fastq`, profile is re-used. Note that when profile is used, `--length-min,max`, `--accuracy-min,max` would be the same as the profile.
+  *--sample-profile-id*::
+    sample-fastq (filtered) profile ID. When using *--sample-fastq*, profile is stored. `sample_profile_<ID>.fastq`, and `sample_profile_<ID>_.stats` are created.
+    When not using *--sample-fastq*, profile is re-used. Note that when profile is used, *--length-min,max*, *--accuracy-min,max* would be the same as the profile.
 
 ### Options for model-based simulation
 
-  * `--model_qc`:
+  *--model_qc*::
     model of quality code.
 
-  * `--length-mean`:
+  *--length-mean*::
     mean of length model (CLR: 3000.0, CCS:450.0).
 
-  * `--length-sd`:
+  *--length-sd*::
     standard deviation of length model (CLR: 2300.0, CCS: 170.0).
 
-  * `--accuracy-mean`:
+  *--accuracy-mean*::
     mean of accuracy model (CLR: 0.78, CCS: fixed as 0.98).
     This option can be used only in case of CLR.
 
-  * `--accuracy-sd`:
+  *--accuracy-sd*::
     standard deviation of accuracy model (CLR: 0.02, CCS: fixed as 0.02).
     This option can be used only in case of CLR.
 
@@ -115,4 +118,4 @@ pbsim is available under the terms of the GNU General Public License, version 2
 
 ## AUTHORS
 
-Michiaki Hamada (mhamada at k.u-tokyo.ac.jp), Yukiteru Ono
\ No newline at end of file
+Michiaki Hamada (mhamada at k.u-tokyo.ac.jp), Yukiteru Ono
diff --git a/debian/rules b/debian/rules
index ffc2581..46ca188 100755
--- a/debian/rules
+++ b/debian/rules
@@ -5,11 +5,10 @@
 
 override_dh_auto_clean:
 	rm -f debian/pbsim.1
-	rm -f debian/pbsim.1.html
 	dh_auto_clean --
 
 override_dh_installman:
-	ronn debian/pbsim.1.ronn
+	asciidoctor -a docdate='' -b manpage debian/pbsim.1.adoc
 	dh_installman --
 
 override_dh_auto_install:

-- 
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