changeset 10:3200a0299230 draft

planemo upload for repository https://github.com/portiahollyoak/Tools commit debe4684eaa00ffcae3c79e7581fdbe41da91d5d
author portiahollyoak
date Wed, 27 Apr 2016 11:44:13 -0400
parents 20a6e46295d6
children e19d9742c99b
files temp.xml tool_dependencies.xml
diffstat 2 files changed, 28 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/temp.xml	Tue Apr 26 06:36:46 2016 -0400
+++ b/temp.xml	Wed Apr 27 11:44:13 2016 -0400
@@ -1,11 +1,17 @@
-<tool id ="run_TEMP" name="Run TEMP" version=" 0.1.1">
+<tool id ="run_TEMP" name="Run TEMP" version=" 0.1.2">
     <description></description>
     <requirements>
-        <requirement type="package" version="0.1.19">samtools</requirement>
+        <!-- The following are classical toolshed packages and should be removed
+        once conda is deemed stable-->
+        <requirement type="package" version="1.6.922">bioperl</requirement>
+        <requirement type="package" version="0.7.12">bwa</requirement>
+        <requirement type="package" version="2.24">bedtools</requirement>
+        <!-- end of toolshed package definitions -->
         <requirement type="package" version="1.6.924">perl-bioperl</requirement>
         <requirement type="package" version="0.7.13">bwa</requirement>
         <requirement type="package" version="2.25.0">bedtools</requirement>
         <requirement type="package" version="324">ucsc-twobittofa</requirement>
+        <requirement type="package" version="0.1.19">samtools</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
@@ -14,7 +20,7 @@
 
         ln -f -s "$alignment.metadata.bam_index" alignment.sorted.bam.bai &&
         ln -f -s "$alignment" alignment.sorted.bam &&
-        bash $__tool_directory__/scripts/TEMP_Insertion.sh -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$consensus_te_seqs" -t "$bed_te_locations" -m 3 -f "$median_insertsize" -c \${GALAXY_SLOTS:-2} && ls -l &&
+        bash $__tool_directory__/scripts/TEMP_Insertion.sh -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$consensus_te_seqs" -t "$bed_te_locations" -m 3 -f "$median_insertsize" -c \${GALAXY_SLOTS:-2} &&
         bash $__tool_directory__/scripts/TEMP_Absence.sh -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$bed_te_locations" -t "$reference2bit" -f 500 -c \${GALAXY_SLOTS:-2} &&
         mv alignment.insertion.bp.bed $insertion_bed &&
         mv alignment.insertion.refined.bp $insertion_bed_refined &&
@@ -67,4 +73,4 @@
 
 
     ]]> </help>
-</tool>
\ No newline at end of file
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Apr 27 11:44:13 2016 -0400
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="bioperl" version="1.6.922">
+        <repository changeset_revision="52a377d1c8de" name="package_bioperl_1_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="perl" version="5.18.1">
+        <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bedtools" version="2.24">
+        <repository changeset_revision="39b86c1e267d" name="package_bedtools_2_24" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bwa" version="0.7.12">
+        <repository changeset_revision="6af9b24ddeee" name="package_bwa_0_7_12" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="samtools" version="0.1.19">
+        <repository changeset_revision="96aab723499f" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>