# HG changeset patch
# User biomonika <biomonika@psu.edu>
# Date 1410285514 14400
# Node ID 92bc88be0e9d4987aa585efe753766c0d7187cf0
# Parent  8474773590004b714cc12cdbb9de2a4d2cf5d114
toolshed5

diff -r 847477359000 -r 92bc88be0e9d LINKYX_mpileup_wrapper.xml
--- a/LINKYX_mpileup_wrapper.xml	Tue Sep 09 00:09:35 2014 -0400
+++ b/LINKYX_mpileup_wrapper.xml	Tue Sep 09 13:58:34 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 847477359000 -r 92bc88be0e9d README.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.txt	Tue Sep 09 13:58:34 2014 -0400
@@ -0,0 +1,14 @@
+LinkYX
+
+Fully automated pipeline for detection of sex linked genes using RNA-Seq data
+bitbucket.org/biomonika/linkyx
+
+Please install following dependencies from toolshed:
+toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4
+testtoolshed.g2.bx.psu.edu/view/jjohnson/trinityrnaseq/0.0.2
+toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3
+toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4
+toolshed.g2.bx.psu.edu/repos/iuc/samtools_sort/samtools_sort/1.0.2
+toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0
+
+If you have any questions, please use following email address: biomonika@psu.edu
\ No newline at end of file
diff -r 847477359000 -r 92bc88be0e9d demo_files/.DS_Store
Binary file demo_files/.DS_Store has changed
diff -r 847477359000 -r 92bc88be0e9d reformat_trinity_header.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reformat_trinity_header.sh	Tue Sep 09 13:58:34 2014 -0400
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+results=$1 #reformatted fasta sequence written here
+trinity_fasta=${2}
+
+perl -pe 's/(>[\S]+).+/$1/' $trinity_fasta >$results
+samtools faidx $results
+
+
diff -r 847477359000 -r 92bc88be0e9d reformat_trinity_header.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reformat_trinity_header.xml	Tue Sep 09 13:58:34 2014 -0400
@@ -0,0 +1,26 @@
+<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"/>
+      </inputs>
+      <outputs>
+        <data format="fasta" name="output" />
+      </outputs>
+  
+     <tests>
+       <test>
+        <output name="out_file1" file="Trinity.fasta"/>
+       </test>
+     </tests>
+   
+     <help>
+   Reformat Trinity header, keep only part until first space.
+     </help>
+   
+   </tool>
\ No newline at end of file