Mercurial > repos > greg > bam_to_psl
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author | greg |
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date | Mon, 12 Dec 2022 14:42:58 +0000 |
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<tool id="bam_to_psl" name="Convert BAM to PSL format" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description></description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ #if $input.ext == 'bam': samtools view -o 'input.sam' -h '$input' && #else: ln -s '$input' 'input.sam' && #end if python '${__tool_directory__}/bam_to_psl.py' --input_file 'input.sam' --output_file '$output' ]]></command> <inputs> <param name="input" type="data" format="bam,sam" label="BAM or SAM file"/> </inputs> <outputs> <data name="output" format="psl"/> </outputs> <tests> <test> <param name="input" value="input_1.sam" ftype="sam"/> <output name="output" value="output_1.psl" ftype="psl" compare="contains"/> </test> <test> <param name="input" value="input_2.bam" ftype="bam"/> <output name="output" value="output_2.psl" ftype="psl" compare="contains"/> </test> </tests> <help> **What it does** Converts a BAM or SAM dataset to PSL format - https://genome.ucsc.edu/FAQ/FAQformat.html#format2. </help> <expand macro="citations"/> </tool>