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view bam_to_sam.xml @ 9:3c661e57a88f draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author | iuc |
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date | Sun, 08 Sep 2024 03:24:55 +0000 |
parents | a53efedba9e7 |
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<tool id="bam_to_sam" name="BAM-to-SAM" version="2.0.4" profile="@PROFILE@"> <description>convert BAM to SAM</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ samtools view -o '${output1}' ${header} '${input1}' ]]></command> <inputs> <param format="bam" name="input1" type="data" label="BAM File to Convert" /> <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">Return 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" lines_diff="2" /> </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" lines_diff="2" /> </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" /> </test> </tests> <help><![CDATA[ **What it does** Converts BAM dataset to SAM using the ``samtools view`` command. ]]></help> <expand macro="citations"/> </tool>