Mercurial > repos > devteam > bam_to_sam
view bam_to_sam.xml @ 3:c1419fa820c6 draft
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author | devteam |
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date | Wed, 18 Mar 2015 15:44:51 -0400 |
parents | c09a20532957 |
children | af7c50162f0b |
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<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.6"> <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> <command> <![CDATA[ samtools sort -O bam -@ \${GALAXY_SLOTS:-1} "$input1" -o sorted_input.bam -T temp && samtools view sorted_input.bam $header -o $output1 -@ \${GALAXY_SLOTS:-1} ]]> </command> <inputs> <param format="bam" label="BAM File to Convert" name="input1" type="data" /> <param checked="False" falsevalue="" label="Include header in output" name="header" truevalue="-h" type="boolean" /> </inputs> <outputs> <data format="sam" label="${tool.name} on ${on_string}: converted SAM" name="output1" /> </outputs> <tests> <test> <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" /> <param name="header" value="" /> <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="" /> <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" /> <output file="bam_to_sam_out3.sam" name="output1" sorted="True" /> </test> </tests> <help> <![CDATA[ **What it does** This tool uses the SAMTools_ toolkit to produce a SAM file from a BAM file. .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml ]]> </help> <expand macro="citations"></expand> </tool>