Mercurial > repos > devteam > bam_to_sam
diff bam_to_sam.xml @ 4:af7c50162f0b draft
Uploaded
author | devteam |
---|---|
date | Tue, 21 Apr 2015 14:36:15 -0400 |
parents | c1419fa820c6 |
children | f57df915aa10 |
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--- a/bam_to_sam.xml Wed Mar 18 15:44:51 2015 -0400 +++ b/bam_to_sam.xml Tue Apr 21 14:36:15 2015 -0400 @@ -1,20 +1,23 @@ -<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.6"> +<tool id="bam_to_sam" name="BAM-to-SAM" version="2.0"> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"></expand> <expand macro="version_command"></expand> <expand macro="stdio"></expand> - <description>converts BAM format to SAM format</description> + <description>convert BAM to SAM</description> <command> <![CDATA[ - samtools sort -O bam -@ \${GALAXY_SLOTS:-1} "$input1" -o sorted_input.bam -T temp && - samtools view sorted_input.bam $header -o $output1 -@ \${GALAXY_SLOTS:-1} + samtools view -o "${output1}" ${header} "${input1}" ]]> </command> <inputs> <param format="bam" label="BAM File to Convert" name="input1" type="data" /> - <param checked="False" falsevalue="" label="Include header in output" name="header" truevalue="-h" type="boolean" /> + <param name="header" label="Header options" type="select" help="Allows to choose between seeing the entire dataset with the header, header only, or data only."> + <option value="-h">Include header in SAM output (-h)</option> + <option value="-H">Print header only (-H)</option> + <option value="">Exclude header</option> + </param> </inputs> <outputs> <data format="sam" label="${tool.name} on ${on_string}: converted SAM" name="output1" /> @@ -22,17 +25,17 @@ <tests> <test> <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" /> - <param name="header" value="" /> + <param name="header" value="-h" /> <output file="bam_to_sam_out1.sam" name="output1" sorted="True" /> </test> <test> - <param ftype="bam" name="input1" value="bam_to_sam_in2.bam" /> - <param name="header" value="" /> + <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" /> + <param name="header" value="-H" /> <output file="bam_to_sam_out2.sam" name="output1" sorted="True" /> </test> <test> <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" /> - <param name="header" value="True" /> + <param name="header" value="" /> <output file="bam_to_sam_out3.sam" name="output1" sorted="True" /> </test> </tests> @@ -41,9 +44,10 @@ **What it does** -This tool uses the SAMTools_ toolkit to produce a SAM file from a BAM file. +Converts BAM dataset to SAM using ``samtools view`` command:: -.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml + samtools view -o [OUTPUT SAM] [-h|-H] [INPUT BAM] + ]]> </help> <expand macro="citations"></expand>