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1 <tool id="LINKYX_Y" name="LINKYX_Y" version="1.1">
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0
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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-fpic</requirement>
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7 <requirement type="package" version="1.6.922">bioperl</requirement>
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0
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8 </requirements>
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9 <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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10 <inputs>
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11 <param format="fasta" name="input1" type="data" label="Reference"/>
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12 <param format="bam" name="input2" type="data" label="Mother - Binary alignment format"/>
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13 <param format="bam" name="input3" type="data" label="Father - Binary alignment format"/>
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14 <param format="bam" name="input4" type="data" label="Daughter - Binary alignment format"/>
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15 <param format="bam" name="input5" type="data" label="Son - Binary alignment format"/>
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16 </inputs>
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17 <outputs>
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18 <data format="txt" name="output" />
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19 <data format="fasta" name="output1" label="Y_results_sequences.fasta" />
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20 <data format="bam" name="output2" label="Mother male bam file - Y linked " />
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21 <data format="bam" name="output3" label="Father male bam file - Y linked " />
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22 <data format="bam" name="output4" label="Daughter male bam file - Y linked " />
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23 <data format="bam" name="output5" label="Son bam male file - Y linked " />
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24 </outputs>
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25
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26 <tests>
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27 <test>
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28 </test>
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29 </tests>
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30
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31 <help>
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32 This tool identifies Y linked contigs from cross (represented as 4 bam files mapped on male reference).
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33 </help>
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34
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35 </tool>
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