diff spectrast_filter.xml @ 8:276ff5e1732c draft

Add spectrast_filter tool

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spectrast_filter.xml	Wed May 20 01:35:51 2015 -0400
@@ -0,0 +1,62 @@
+<tool id="spectrast_filter_1" name="SpectraST Filter" version="1.0.0">
+    <requirements>
+        <container type="docker">iracooke/protk-1.4.2</container>
+        <requirement type="package" version="1.4">protk</requirement>
+        <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
+   </requirements>
+   
+	<description>Filter and Manipulate Spectral Libraries</description>
+
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Job Failed" />
+    </stdio>
+
+	<command>
+        spectrast_filter.rb
+
+        #for $splib_file in $splib_files:
+        ${splib_file.extra_files_path/library.splib}
+        #end for
+
+        --merge $merge
+
+        --replicates $replicates
+
+        -o library;
+
+        mkdir -p $output.extra_files_path;
+
+        cp library.splib library.spidx library.pepidx  $output.extra_files_path/;
+
+
+        echo "Spectral Library Primary File" > $output
+
+	</command>
+
+	<inputs>
+
+        <param name="splib_files" multiple="true" type="data" format="pepxml,peptideprophet_pepxml,interprophet_pepxml" label="PepXML Files to use in library generation" help=""/>
+	
+        <param name="merge" type="select" format="text">
+            <label>Merge Method</label>
+            <option value="U">Union</option>
+            <option value="S">Subtraction</option>
+            <option value="H">Subtraction of homologs</option>
+            <option value="A">Appending</option>
+        </param>
+
+        <param name="replicates" type="select" format="text">
+            <label>How to deal with replicate spectra</label>
+            <option value="None">Keep All</option>
+            <option value="C">Consensus</option>
+            <option value="B">Best replicate</option>
+        </param>
+
+	
+    </inputs>
+
+      <outputs>
+        <data format="splib" name="output"/>
+      </outputs>
+
+</tool>