changeset 8:276ff5e1732c draft

Add spectrast_filter tool

--- a/repository_dependencies.xml	Tue May 19 22:36:35 2015 -0400
+++ b/repository_dependencies.xml	Wed May 20 01:35:51 2015 -0400
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="Proteomics datatypes">
-    <repository changeset_revision="9cfabf0b942d" name="proteomics_datatypes" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="6ab4a0bf67df" name="proteomics_datatypes" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" />
  </repositories>

--- a/spectrast_create.xml	Tue May 19 22:36:35 2015 -0400
+++ b/spectrast_create.xml	Wed May 20 01:35:51 2015 -0400
@@ -26,7 +26,13 @@
 
         --instrument-acquisition $instrument_acquisition
 
-        -o output
+        -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>
 
@@ -41,13 +47,12 @@
         <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="p_thresh" help="Matches scoring less than this value are discarded" type="float" value="0.95" min="0" max="1" label="Probability Threshold"/>
-
+        <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>
 
       <outputs>
-        <data format="splib" name="output" from_work_dir="output.splib"/>
+        <data format="splib" name="output"/>
       </outputs>
 
 </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>