# HG changeset patch
# User iracooke
# Date 1445388103 14400
# Node ID f6fd2798879af070f7ab82614aa942ad84a79a8f
# Parent  cf953fb3f0c0adbe793318c7abc1b5f05984bc5d
planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty

diff -r cf953fb3f0c0 -r f6fd2798879a repository_dependencies.xml
--- a/repository_dependencies.xml	Wed May 20 01:59:41 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 cf953fb3f0c0 -r f6fd2798879a spectrast_create.xml
--- a/spectrast_create.xml	Wed May 20 01:59:41 2015 -0400
+++ b/spectrast_create.xml	Tue Oct 20 20:41:43 2015 -0400
@@ -1,58 +1,60 @@
 <tool id="spectrast_create_1" name="SpectraST Create" version="1.0.0">
+    <description>Create Spectral Libraries</description>
     <requirements>
-        <container type="docker">iracooke/protk-1.4.2</container>
-        <requirement type="package" version="1.4">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>
-   
-	<description>Create Spectral Libraries</description>
-
     <stdio>
         <exit_code range="1:" level="fatal" description="Job Failed" />
     </stdio>
-
-	<command>
-        spectrast_create.rb --galaxy 
+    <command>
+<![CDATA[
+        spectrast_create.rb --galaxy
 
         #for $pepxml_file in $pepxml_files:
-        ${pepxml_file}
+            ${pepxml_file}
         #end for
 
         --spectrum-files='$spectrum_files'
-
         --predicate 'Protein!~$decoy_prefix_string'
-
         --p-thresh $p_thresh
-
         --instrument-acquisition $instrument_acquisition
+        -o library
 
-        -o library;
+        &&
+
+        mkdir -p $output.files_path
 
-        mkdir -p $output.extra_files_path;
+        &&
 
-        cp library.splib library.spidx library.pepidx  $output.extra_files_path/;
+        cp library.splib library.spidx library.pepidx  $output.files_path/
+
+        &&
 
         echo "Spectral Library Primary File" > $output
-
-	</command>
-
-	<inputs>
+]]>
+    </command>
+    <inputs>
 
         <param name="pepxml_files" multiple="true" type="data" format="pepxml,peptideprophet_pepxml,interprophet_pepxml" label="PepXML Files to use in library generation" help=""/>
-	
         <param name="spectrum_files" multiple="true" type="data" format="mzml" label="Data files containing spectra referred to in pepxml files" help=""/>
-
         <param name="decoy_prefix_string" help="String to identify decoys. All decoys wil be excluded" type="text" value="decoy" label="Decoy String" size="20"/> 
-
-        <param name="instrument_acquisition" help="Set the instrument and acquisition settings of the spectra (in case not specified in data files).
-                                 Examples: CID, ETD, CID-QTOF, HCD. The latter two are treated as high-mass accuracy spectra." type="text" value="CID-QTOF" label="Decoy String" size="20"/>
+        <param name="instrument_acquisition" type="text" value="CID-QTOF" label="Decoy String" size="20" 
+            help="Set the instrument and acquisition settings of the spectra (in case not specified in data files).
+            Examples: CID, ETD, CID-QTOF, HCD. The latter two are treated as high-mass accuracy spectra."/>
+        <param name="p_thresh" type="float" value="0.99" min="0" max="1" label="Probability Threshold"
+            help="Matches scoring less than this value are discarded" />
+    </inputs>
+    <outputs>
+        <data format="splib" name="output"/>
+    </outputs>
+    <help>
+<![CDATA[
+**What it does**
 
-        <param name="p_thresh" help="Matches scoring less than this value are discarded" type="float" value="0.99" min="0" max="1" label="Probability Threshold"/>
-	
-    </inputs>
+Create Spectral Libraries.
 
-      <outputs>
-        <data format="splib" name="output"/>
-      </outputs>
-
+]]>
+    </help>
 </tool>
diff -r cf953fb3f0c0 -r f6fd2798879a spectrast_filter.xml
--- a/spectrast_filter.xml	Wed May 20 01:59:41 2015 -0400
+++ b/spectrast_filter.xml	Tue Oct 20 20:41:43 2015 -0400
@@ -1,42 +1,39 @@
 <tool id="spectrast_filter_1" name="SpectraST Filter" version="1.0.0">
+    <description>Filter and Manipulate Spectral Libraries</description>
     <requirements>
-        <container type="docker">iracooke/protk-1.4.2</container>
-        <requirement type="package" version="1.4">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>
-   
-	<description>Filter and Manipulate Spectral Libraries</description>
-
+    </requirements>
     <stdio>
         <exit_code range="1:" level="fatal" description="Job Failed" />
     </stdio>
-
-	<command>
+    <command>
+<![CDATA[
         spectrast_filter.rb  --merge $merge
 
-
         #for $splib_file in $splib_files:
-        ${splib_file.extra_files_path}/library.splib
+            ${splib_file.extra_files_path}/library.splib
         #end for
 
-
         --replicates $replicates
+        -o library
 
-        -o library;
+        &&
+
+        mkdir -p ${output.files_path}
 
-        mkdir -p ${output.extra_files_path};
+        &&
 
-        cp library.splib library.spidx library.pepidx  ${output.extra_files_path}/;
+        cp library.splib library.spidx library.pepidx  ${output.files_path}/
 
+        &&
 
         echo "Spectral Library Primary File" > $output
-
-	</command>
-
-	<inputs>
-
+]]>
+    </command>
+    <inputs>
         <param name="splib_files" multiple="true" type="data" format="splib" label="Spectral Libraries to operate on" help=""/>
-	
         <param name="merge" type="select" format="text">
             <label>Merge Method</label>
             <option value="U">Union</option>
@@ -51,12 +48,16 @@
             <option value="C">Consensus</option>
             <option value="B">Best replicate</option>
         </param>
-
-	
     </inputs>
+    <outputs>
+        <data format="splib" name="output"/>
+    </outputs>
+    <help>
+<![CDATA[
+**What it does**
 
-      <outputs>
-        <data format="splib" name="output"/>
-      </outputs>
+Filter and Manipulate Spectral Libraries
 
+]]>
+    </help>
 </tool>
diff -r cf953fb3f0c0 -r f6fd2798879a tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Oct 20 20:41:43 2015 -0400
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <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>