Mercurial > repos > biomonika > linkyx

annotate LINKYX_mpileup_wrapper.xml @ 1:4c5de3a2c54e

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author biomonika <biomonika@psu.edu>
date Sun, 07 Sep 2014 23:12:26 -0400
parents 05c27700e5ca
children 0d8315be76b7
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1 <tool id="LINKYX_mpileup" name="LINKYX_mpileup">
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2 <description>Run mpileup with LINKYX-specific parameters</description>
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3 <requirements>
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4 <requirement type="set_environment">LINKYX_PATH</requirement>
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5 <requirement type="set_environment">SAMTOOLS</requirement>
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6 <requirement type="package" version="0.1.19">samtools</requirement>
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7 </requirements>
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8 <command interpreter="bash">LINKYX_mpileup_wrapper.sh $output $input1 $input2</command>
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9 <inputs>
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10 <param format="bam" name="input1" type="data" label="Alignment file"/>
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11 <param format="fasta" name="input2" type="data" label="Reference file"/>
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12 </inputs>
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13 <outputs>
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14 <data format="vcf" name="output" />
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15 </outputs>
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17 <tests>
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18 <test>
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19 <output name="out_file1" file="alignent_mpileup.txt"/>
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20 </test>
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21 </tests>
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23 <help>
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24 This tool tests if primers are present in gorilla female or on human Y or chimp Y chromosome.
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25 </help>
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26
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27 </tool>