# HG changeset patch
# User iracooke
# Date 1445388453 14400
# Node ID fc1decb780ba72810e9e61211d0cf1f4ef881b27
# Parent  529ea20c1e6c63bc4688404eaf06effb1df3d2dd
planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty

diff -r 529ea20c1e6c -r fc1decb780ba repository_dependencies.xml
--- a/repository_dependencies.xml	Sun May 24 01:12:42 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-<?xml version="1.0"?>
-<repositories description="Proteomics datatypes">
-    <repository changeset_revision="6ab4a0bf67df" name="proteomics_datatypes" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" />
- </repositories>
diff -r 529ea20c1e6c -r fc1decb780ba tandem.xml
--- a/tandem.xml	Sun May 24 01:12:42 2015 -0400
+++ b/tandem.xml	Tue Oct 20 20:47:33 2015 -0400
@@ -1,8 +1,8 @@
-<tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.1.0">
+<tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.1.1">
     <description>Run an X!Tandem Search</description>
    <requirements>
-         <container type="docker">iracooke/protk-1.4.1</container>
-        <requirement type="package" version="1.4.2">protk</requirement>
+         <container type="docker">iracooke/protk-1.4.3</container>
+        <requirement type="package" version="1.4.3">protk</requirement>
     </requirements>
     <command>
         #if $database.source_select=="built_in":
@@ -44,7 +44,7 @@
         $acetyl_protein_nterm
         $cleavage_semi
         $keep_spectra
-        --threads "\${GALAXY_SLOTS:-1}"
+        --threads "\${GALAXY_SLOTS:-12}"
 
     </command>
     <inputs>
@@ -127,7 +127,7 @@
             <label>Enzyme</label>
             <option value="[R]__pc__{P}">argc - [R]|{P}</option>
             <option value="[X]__pc__[D]">aspn - [X]|[D]</option>
-            <option value="[FLMWY]__pc__{P}">chymotrypsin - [FLMWY]|{P}</option>
+            <option value="[FLWY]__pc__{P}">chymotrypsin - [FLWY]|{P}</option>
             <option value="[R]__pc__[X]">clostripain - [R]|[X]</option>
             <option value="[M]__pc__{X}">cnbr - [M]|{X}</option>
             <option value="[AGILV]__pc__{P}">elastase - [AGILV]|{P}</option>
diff -r 529ea20c1e6c -r fc1decb780ba tandem_to_pepxml.xml
--- a/tandem_to_pepxml.xml	Sun May 24 01:12:42 2015 -0400
+++ b/tandem_to_pepxml.xml	Tue Oct 20 20:47:33 2015 -0400
@@ -1,8 +1,8 @@
-<tool id="tandem_to_pepxml_1" name="Tandem to pepXML" version="1.1.0">
+<tool id="tandem_to_pepxml_1" name="Tandem to pepXML" version="1.1.1">
     <description>Converts a tandem result file to pepXML</description>
     <requirements>
-        <container type="docker">iracooke/protk-1.4.1</container>
-        <requirement type="package" version="1.4.2">protk</requirement>
+        <container type="docker">iracooke/protk-1.4.3</container>
+        <requirement type="package" version="1.4.3">protk</requirement>
         <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
     </requirements>
     <command>
diff -r 529ea20c1e6c -r fc1decb780ba tool_dependencies.xml
--- a/tool_dependencies.xml	Sun May 24 01:12:42 2015 -0400
+++ b/tool_dependencies.xml	Tue Oct 20 20:47:33 2015 -0400
@@ -1,6 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="protk" version="1.4.2">
-        <repository changeset_revision="3e1aa28972a3" name="package_protk_1_4_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="protk" version="1.4.3">
+        <repository changeset_revision="2b240f1be1ce" name="package_protk_1_4_3" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="trans_proteomic_pipeline" version="4.8.0">
+        <repository changeset_revision="3d56da50b195" name="package_tpp_4_8_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>