# HG changeset patch
# User biomonika <biomonika@psu.edu>
# Date 1410145946 14400
# Node ID 4c5de3a2c54e3981dd83173b66db782f0a033d65
# Parent  05c27700e5caaff920f42407c4495b49afeebeb9
toolshed2

diff -r 05c27700e5ca -r 4c5de3a2c54e LINKYX_identify_X_linked_SNPs.xml
--- a/LINKYX_identify_X_linked_SNPs.xml	Thu Sep 04 18:24:19 2014 -0400
+++ b/LINKYX_identify_X_linked_SNPs.xml	Sun Sep 07 23:12:26 2014 -0400
@@ -4,6 +4,12 @@
         <requirement type="set_environment">LINKYX_PATH</requirement>
         <requirement type="set_environment">SAMTOOLS</requirement>
         <requirement type="package" version="0.1.19">samtools</requirement>
+        <requirement type="package" version="1.0.4">fastq_groomer</requirement>
+        <requirement type="package" version="0.0.1">trinityrnaseq</requirement>
+        <requirement type="package" version="1.2.3">bwa_wrappers</requirement>
+        <requirement type="package" version="1.1.4">sam_to_bam</requirement>
+        <requirement type="package" version="1.0.2">samtools_sort</requirement>
+        <requirement type="package" version="1.56.0">picard</requirement>
       </requirements>
       <command interpreter="bash">LINKYX_identify_X_linked_SNPs.sh $output $input1 $input2 $input3 $input4 $input5 $input6 $input7 $input8 $input9 $output1 $output2 $output3 $output4 $output5</command>
       <inputs>
diff -r 05c27700e5ca -r 4c5de3a2c54e LINKYX_identify_Y_linked_SNPs.xml
--- a/LINKYX_identify_Y_linked_SNPs.xml	Thu Sep 04 18:24:19 2014 -0400
+++ b/LINKYX_identify_Y_linked_SNPs.xml	Sun Sep 07 23:12:26 2014 -0400
@@ -4,6 +4,12 @@
         <requirement type="set_environment">LINKYX_PATH</requirement>
         <requirement type="set_environment">SAMTOOLS</requirement>
         <requirement type="package" version="0.1.19">samtools</requirement>
+        <requirement type="package" version="1.0.4">fastq_groomer</requirement>
+        <requirement type="package" version="0.0.1">trinityrnaseq</requirement>
+        <requirement type="package" version="1.2.3">bwa_wrappers</requirement>
+        <requirement type="package" version="1.1.4">sam_to_bam</requirement>
+        <requirement type="package" version="1.0.2">samtools_sort</requirement>
+        <requirement type="package" version="1.56.0">picard</requirement>
       </requirements>
       <command interpreter="bash">LINKYX_identify_Y_linked_SNPs.sh $output $input1 $input2 $input3 $input4 $input5 $output1 $output2 $output3 $output4 $output5</command>
       <inputs>
diff -r 05c27700e5ca -r 4c5de3a2c54e LINKYX_mpileup_wrapper.xml
--- a/LINKYX_mpileup_wrapper.xml	Thu Sep 04 18:24:19 2014 -0400
+++ b/LINKYX_mpileup_wrapper.xml	Sun Sep 07 23:12:26 2014 -0400
@@ -1,5 +1,10 @@
 <tool id="LINKYX_mpileup" name="LINKYX_mpileup">
       <description>Run mpileup with LINKYX-specific parameters</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_mpileup_wrapper.sh $output $input1 $input2</command>
       <inputs>
         <param format="bam" name="input1" type="data" label="Alignment file"/>
diff -r 05c27700e5ca -r 4c5de3a2c54e reformat_trinity_header.xml
--- a/reformat_trinity_header.xml	Thu Sep 04 18:24:19 2014 -0400
+++ b/reformat_trinity_header.xml	Sun Sep 07 23:12:26 2014 -0400
@@ -1,5 +1,10 @@
 <tool id="reformat_trinity_header" name="reformat_trinity_header">
       <description>Reformat Trinity header</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">reformat_trinity_header.sh $output $input1</command>
       <inputs>
         <param format="fasta" name="input1" type="data" label="Trinity.fasta"/>