diff spectrast_create.xml @ 12:f6fd2798879a draft default tip

planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty

--- 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>