Mercurial > repos > devteam > bam_to_sam
diff bam_to_sam.xml @ 3:c1419fa820c6 draft
Uploaded
author | devteam |
---|---|
date | Wed, 18 Mar 2015 15:44:51 -0400 |
parents | c09a20532957 |
children | af7c50162f0b |
line wrap: on
line diff
--- a/bam_to_sam.xml Thu Mar 05 21:22:11 2015 -0500 +++ b/bam_to_sam.xml Wed Mar 18 15:44:51 2015 -0400 @@ -1,63 +1,50 @@ -<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.4"> - <requirements> - <requirement type="package" version="0.1.19">samtools</requirement> - </requirements> - <description>converts BAM format to SAM format</description> - <command interpreter="python"> - bam_to_sam.py - --input1=$input1 - --output1=$output1 - $header - </command> - <inputs> - <param name="input1" type="data" format="bam" label="BAM File to Convert" /> - <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" label="Include header in output" /> - </inputs> - <outputs> - <data format="sam" name="output1" label="${tool.name} on ${on_string}: converted SAM" /> - </outputs> - <tests> - <test> - <!-- - Bam-to-Sam command: - samtools view -o bam_to_sam_out1.sam test-data/bam_to_sam_in1.bam - bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam - --> - <param name="input1" value="bam_to_sam_in1.bam" ftype="bam" /> - <param name="header" value="" /> - <output name="output1" file="bam_to_sam_out1.sam" sorted="True" /> - </test> - <test> - <!-- - Bam-to-Sam command: - samtools view -o bam_to_sam_out2.sam test-data/bam_to_sam_in2.bam - bam_to_sam_in2.bam can be created from bam_to_sam_in2.sam - --> - <param name="input1" value="bam_to_sam_in2.bam" ftype="bam" /> - <param name="header" value="" /> - <output name="output1" file="bam_to_sam_out2.sam" sorted="True" /> - </test> - <test> - <!-- - Bam-to-Sam command: - samtools view -h -o bam_to_sam_out3.sam test-data/bam_to_sam_in1.bam - bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam - --> - <param name="input1" value="bam_to_sam_in1.bam" ftype="bam" /> - <param name="header" value="--header" /> - <output name="output1" file="bam_to_sam_out3.sam" sorted="True" lines_diff="6" /><!-- header param not working in func tests so won't produce correct 6-line header (fine in browser) --> - </test> - </tests> - <help> +<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.6"> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"></expand> + <expand macro="version_command"></expand> + <expand macro="stdio"></expand> + <description>converts BAM format to SAM format</description> + <command> +<![CDATA[ + samtools sort -O bam -@ \${GALAXY_SLOTS:-1} "$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> - <citations> - <citation type="doi">10.1093/bioinformatics/btp352</citation> - </citations> + <expand macro="citations"></expand> </tool>