diff LINKYX_identify_Y_linked_SNPs.xml @ 0:05c27700e5ca

initial commit

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LINKYX_identify_Y_linked_SNPs.xml	Thu Sep 04 18:24:19 2014 -0400
@@ -0,0 +1,34 @@
+<tool id="LINKYX_Y" name="LINKYX_Y">
+      <description>Identify Y linked contigs from cross</description>
+      <requirements>
+        <requirement type="set_environment">LINKYX_PATH</requirement>
+        <requirement type="set_environment">SAMTOOLS</requirement>
+        <requirement type="package" version="0.1.19">samtools</requirement>
+      </requirements>
+      <command interpreter="bash">LINKYX_identify_Y_linked_SNPs.sh $output $input1 $input2 $input3 $input4 $input5 $output1 $output2 $output3 $output4 $output5</command>
+      <inputs>
+        <param format="fasta" name="input1" type="data" label="Reference"/>
+        <param format="bam" name="input2" type="data" label="Mother - Binary alignment format"/>
+        <param format="bam" name="input3" type="data" label="Father - Binary alignment format"/>
+        <param format="bam" name="input4" type="data" label="Daughter - Binary alignment format"/>
+        <param format="bam" name="input5" type="data" label="Son - Binary alignment format"/>
+      </inputs>
+      <outputs>
+        <data format="txt" name="output" />
+        <data format="fasta" name="output1" label="Y_results_sequences.fasta" />
+        <data format="bam" name="output2" label="Mother male bam file - Y linked " />
+        <data format="bam" name="output3" label="Father male bam file - Y linked " />
+        <data format="bam" name="output4" label="Daughter male bam file - Y linked " />
+        <data format="bam" name="output5" label="Son bam male file - Y linked " />
+      </outputs>
+  
+     <tests>
+       <test>
+       </test>
+     </tests>
+   
+     <help>
+   This tool identifies Y linked contigs from cross (represented as 4 bam files mapped on male reference).
+     </help>
+   
+   </tool>
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