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annotate LINKYX_identify_Y_linked_SNPs.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_Y" name="LINKYX_Y">
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2 <description>Identify Y linked contigs from cross</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 <requirement type="package" version="1.0.4">fastq_groomer</requirement>
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8 <requirement type="package" version="0.0.1">trinityrnaseq</requirement>
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9 <requirement type="package" version="1.2.3">bwa_wrappers</requirement>
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10 <requirement type="package" version="1.1.4">sam_to_bam</requirement>
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11 <requirement type="package" version="1.0.2">samtools_sort</requirement>
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12 <requirement type="package" version="1.56.0">picard</requirement>
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13 </requirements>
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14 <command interpreter="bash">LINKYX_identify_Y_linked_SNPs.sh $output $input1 $input2 $input3 $input4 $input5 $output1 $output2 $output3 $output4 $output5</command>
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15 <inputs>
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16 <param format="fasta" name="input1" type="data" label="Reference"/>
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17 <param format="bam" name="input2" type="data" label="Mother - Binary alignment format"/>
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18 <param format="bam" name="input3" type="data" label="Father - Binary alignment format"/>
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19 <param format="bam" name="input4" type="data" label="Daughter - Binary alignment format"/>
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20 <param format="bam" name="input5" type="data" label="Son - Binary alignment format"/>
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21 </inputs>
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22 <outputs>
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23 <data format="txt" name="output" />
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24 <data format="fasta" name="output1" label="Y_results_sequences.fasta" />
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25 <data format="bam" name="output2" label="Mother male bam file - Y linked " />
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26 <data format="bam" name="output3" label="Father male bam file - Y linked " />
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27 <data format="bam" name="output4" label="Daughter male bam file - Y linked " />
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28 <data format="bam" name="output5" label="Son bam male file - Y linked " />
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29 </outputs>
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30
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31 <tests>
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32 <test>
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33 </test>
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34 </tests>
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35
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36 <help>
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37 This tool identifies Y linked contigs from cross (represented as 4 bam files mapped on male reference).
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38 </help>
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39
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40 </tool>