[med-svn] r14460 - trunk/packages/python-biom-format/trunk/debian

[Andreas Tille]

Author: tille
Date: 2013-08-16 23:32:01 +0000 (Fri, 16 Aug 2013)
New Revision: 14460

Removed:
   trunk/packages/python-biom-format/trunk/debian/biom_validator.1
   trunk/packages/python-biom-format/trunk/debian/convert_biom.1
Modified:
   trunk/packages/python-biom-format/trunk/debian/rules
Log:
Create manpages at package build time


Deleted: trunk/packages/python-biom-format/trunk/debian/biom_validator.1
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/biom_validator.1	2013-08-15 20:06:03 UTC (rev 14459)
+++ trunk/packages/python-biom-format/trunk/debian/biom_validator.1	2013-08-16 23:32:01 UTC (rev 14460)
@@ -1,44 +0,0 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.10.
-.TH BIOM_VALIDATOR "1" "August 2012" "biom_validator 1.0.0" "User Commands"
-.SH NAME
-biom_validator \- Test a biom file for adherence to the format specification
-.SH SYNOPSIS
-.B biom_validator
-[\fIoptions\fR] \fI{-i/--biom_fp BIOM_FP}\fR
-.SH DESCRIPTION
-[] indicates optional input (order unimportant)
-{} indicates required input (order unimportant)
-.PP
-Test a biom file for adherence to the format specification. This specification is defined at http://www.qiime.org/...
-.PP
-Example usage:
-Print help message and exit
-.IP
-biom_validator \fB\-h\fR
-.PP
-Validate the my_data.biom file.
-.IP
-biom_validator \fB\-i\fR my_data.biom
-.SH OPTIONS
-.TP
-\fB\-\-version\fR
-show program's version number and exit
-.TP
-\fB\-h\fR, \fB\-\-help\fR
-show this help message and exit
-.TP
-\fB\-v\fR, \fB\-\-verbose\fR
-Print information during execution \fB\-\-\fR useful for
-debugging [default: False]
-.TP
-\fB\-f\fR FORMAT_VERSION, \fB\-\-format\-version\fR=\fIFORMAT_VERSION\fR
-The specific format string, defaults to [default:
-Biological Observation Matrix 1.0.0]
-.IP
-REQUIRED options:
-.IP
-The following options must be provided under all circumstances.
-.TP
-\fB\-i\fR BIOM_FP, \fB\-\-biom_fp\fR=\fIBIOM_FP\fR
-the BIological Observation Matrix filepath to validate
-[REQUIRED]

Deleted: trunk/packages/python-biom-format/trunk/debian/convert_biom.1
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/convert_biom.1	2013-08-15 20:06:03 UTC (rev 14459)
+++ trunk/packages/python-biom-format/trunk/debian/convert_biom.1	2013-08-16 23:32:01 UTC (rev 14460)
@@ -1,68 +0,0 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.10.
-.TH CONVERT_BIOM "1" "August 2012" "convert_biom 1.0.0c" "User Commands"
-.SH NAME
-convert_biom \- Script to convert biom formatted files
-.SH SYNOPSIS
-.B Detailed
-\fIusage examples can be found here: http://biom-format.org/documentation/biom_conversion.html\fR
-.SH DESCRIPTION
-Script to convert biom formatted files.
-.SH OPTIONS
-.TP
-\fB\-\-version\fR
-show program's version number and exit
-.TP
-\fB\-h\fR, \fB\-\-help\fR
-show this help message and exit
-.IP
-Required Options:
-.TP
-\fB\-i\fR INPUT_FP, \fB\-\-input_fp\fR=\fIINPUT_FP\fR
-the input filepath
-.TP
-\fB\-o\fR OUTPUT_FP, \fB\-\-output_fp\fR=\fIOUTPUT_FP\fR
-the output filepath
-.IP
-Optional Options:
-.TP
-\fB\-t\fR BIOM_TYPE, \fB\-\-biom_type\fR=\fIBIOM_TYPE\fR
-Type of biom file to write (dense or sparse)
-whenpassed a classic table [default: sparse]
-.TP
-\fB\-b\fR, \fB\-\-biom_to_classic_table\fR
-Convert biom file to classictable file [default:
-convert classic table file to biom file]
-.TP
-\fB\-\-sparse_biom_to_dense_biom\fR
-Convert sparse biom file to a dense biom file
-[default: convert classic table file to biom file]
-.TP
-\fB\-\-dense_biom_to_sparse_biom\fR
-Convert dense biom file to a sparse biom file
-[default: convert classic table file to biom file]
-.TP
-\fB\-m\fR SAMPLE_MAPPING_FP, \fB\-\-sample_mapping_fp\fR=\fISAMPLE_MAPPING_FP\fR
-The mapping filepath (will add sample metadata to biom
-file, if provided) [default: none]
-.TP
-\fB\-\-observation_mapping_fp\fR=\fIOBSERVATION_MAPPING_FP\fR
-The mapping filepath (will add observation metadata to
-biom file, if provided) [default: none]
-.TP
-\fB\-\-header_key\fR=\fIHEADER_KEY\fR
-Pull this key from observation metadata within a biom
-file when writing a classic table [default: no
-observation metadata will be written]
-.TP
-\fB\-\-output_metadata_id\fR=\fIOUTPUT_METADATA_ID\fR
-Name for the observation metadata column when writing
-a biom file as a classic table [default: same name as
-in biom\-formatted table]
-.TP
-\fB\-\-process_obs_metadata\fR=\fIPROCESS_OBS_METADATA\fR
-Process metadata associated with observations
-(taxonomy,naive,sc_separated) when converting from a
-classic table [default: naive]
-.TP
-\fB\-\-biom_table_type\fR=\fIBIOM_TABLE_TYPE\fR
-The biom table type to get converted into

Modified: trunk/packages/python-biom-format/trunk/debian/rules
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/rules	2013-08-15 20:06:03 UTC (rev 14459)
+++ trunk/packages/python-biom-format/trunk/debian/rules	2013-08-16 23:32:01 UTC (rev 14460)
@@ -34,7 +34,12 @@
 	export PYTHONPATH=$(CURDIR)/python-code ; \
 	    help2man --no-info --version-string="$(version)" \
 		 --name="Script to add sample and/or observation metadata to BIOM-formatted files." \
-		$(bindir)/add_metadata > $(mandir)/add_metadata.1
+		$(bindir)/add_metadata > $(mandir)/add_metadata.1 ; \
+	    help2man --no-info --version-string="$(version)" \
+		--name='Test a biom file for adherence to the format specification' \
+		$(bindir)/biom_validator > $(mandir)/biom_validator.1 ; \
+	    help2man --no-info --name='Script to convert biom formatted files' \
+		$(bindir)/convert_biom > $(mandir)/convert_biom.1
 
 get-orig-source:
 	. debian/get-orig-source