Mercurial > repos > greg > bam_to_psl
diff bam_to_psl.xml @ 0:b6794f4cb1c6 draft default tip
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author | greg |
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date | Mon, 12 Dec 2022 14:42:58 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bam_to_psl.xml Mon Dec 12 14:42:58 2022 +0000 @@ -0,0 +1,40 @@ +<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> +