diff spectrast_create.xml @ 0:c8895a92b74d draft default tip

planemo upload for repository https://github.com/galaxyproteomics/protk-galaxytools/tree/master/spectrast commit 34735d62618a252173e3c90436f240659484727a

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spectrast_create.xml	Thu Mar 29 09:51:50 2018 -0400
@@ -0,0 +1,62 @@
+<tool id="spectrast_create_1" name="SpectraST Create" version="5.0.0">
+    <description>Create Spectral Libraries</description>
+    <requirements>
+        <!--
+        <container type="docker">iracooke/protk-1.4.3</container>
+        -->
+        <requirement type="package" version="1.4.4a">protk</requirement>
+        <requirement type="package" version="5.0.0">tpp</requirement>
+   </requirements>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Job Failed" />
+    </stdio>
+    <command>
+<![CDATA[
+        spectrast_create.rb --galaxy
+
+        #for $pepxml_file in $pepxml_files:
+            ${pepxml_file}
+        #end for
+
+        --spectrum-files='$spectrum_files'
+        --predicate 'Protein!~$decoy_prefix_string'
+        --p-thresh $p_thresh
+        --instrument-acquisition $instrument_acquisition
+        -o library
+
+        &&
+
+        mkdir -p $output.files_path
+
+        &&
+
+        cp library.splib library.spidx library.pepidx  $output.files_path/
+
+        &&
+
+        echo "Spectral Library Primary File" > $output
+]]>
+    </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" 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**
+
+Create Spectral Libraries.
+
+]]>
+    </help>
+</tool>