Mercurial > repos > devteam > bam_to_sam
diff bam_to_sam.xml @ 4:3bade5114f21 draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author | devteam |
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date | Tue, 13 Oct 2015 12:53:40 -0400 |
parents | 6eebf8420e31 |
children | eac9d3319326 |
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--- a/bam_to_sam.xml Wed Mar 04 22:28:17 2015 -0500 +++ b/bam_to_sam.xml Tue Oct 13 12:53:40 2015 -0400 @@ -1,63 +1,54 @@ -<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 ${on_string}: converted SAM" /> - </outputs> - <tests> - <test> - <!-- - Bam-to-Sam command: - samtools view -o bam_to_sam_out1.sam test-data/bam_to_sam_in1.bam - bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam - --> - <param name="input1" value="bam_to_sam_in1.bam" ftype="bam" /> - <param name="header" value="" /> - <output name="output1" file="bam_to_sam_out1.sam" sorted="True" /> - </test> - <test> - <!-- - Bam-to-Sam command: - samtools view -o bam_to_sam_out2.sam test-data/bam_to_sam_in2.bam - bam_to_sam_in2.bam can be created from bam_to_sam_in2.sam - --> - <param name="input1" value="bam_to_sam_in2.bam" ftype="bam" /> - <param name="header" value="" /> - <output name="output1" file="bam_to_sam_out2.sam" sorted="True" /> - </test> - <test> - <!-- - Bam-to-Sam command: - samtools view -h -o bam_to_sam_out3.sam test-data/bam_to_sam_in1.bam - bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam - --> - <param name="input1" value="bam_to_sam_in1.bam" ftype="bam" /> - <param name="header" value="--header" /> - <output name="output1" file="bam_to_sam_out3.sam" sorted="True" lines_diff="6" /><!-- header param not working in func tests so won't produce correct 6-line header (fine in browser) --> - </test> - </tests> - <help> +<tool id="bam_to_sam" name="BAM-to-SAM" version="2.0"> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"></expand> + <expand macro="version_command"></expand> + <expand macro="stdio"></expand> + <description>convert BAM to SAM</description> + <command> +<![CDATA[ + samtools view -o "${output1}" ${header} "${input1}" +]]> + </command> + <inputs> + <param format="bam" label="BAM File to Convert" name="input1" type="data" /> + <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" /> + </outputs> + <tests> + <test> + <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" /> + <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_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="" /> + <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. +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> - <citations> - <citation type="doi">10.1093/bioinformatics/btp352</citation> - </citations> + <expand macro="citations"></expand> </tool>