diff spectrast_filter.xml @ 12:f6fd2798879a draft default tip

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

--- 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>