Mercurial > repos > galaxyp > hardklor

diff hardklor.xml @ 6:73fc27617b2e draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit 44c3e37a12f60b01521d3e3f18b7f16664f954cc"
author galaxyp
date Tue, 07 Apr 2020 03:27:32 -0400
parents 539f157784e7
children
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--- a/hardklor.xml	Sat Aug 19 08:00:25 2017 -0400
+++ b/hardklor.xml	Tue Apr 07 03:27:32 2020 -0400
@@ -1,16 +1,29 @@
-<tool id="hardklor" name="Hardklor" version="2.30.1">
+<tool id="hardklor" name="Hardklor" version="2.30.1+galaxy1">
     <description>identification of features from mass spectra</description>
     <requirements>
         <requirement type="package" version="2.3.0">hardklor</requirement>
+        <requirement type="package" version="3.7">python</requirement>
     </requirements>
-    <stdio>
-        <exit_code range="1:" level="fatal"/>
-    </stdio>
-    <command>python $__tool_directory__/hardklor.py "$ms1_in.extension" "$ms1_in"
-    "$output" -charge_algo=$cdm -resolution=$res -centroided=$centroided -instrument=$instrument -algorithm=$algorithm -mincharge=$chMin 
-    -maxcharge=$chMax -mslvl=$mslvl -correlation=$corr -depth=$depth -sensitivity=$sens -maxfeat=$maxfeat</command>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/hardklor.py'
+    '$ms1_in.extension'
+    '$ms1_in'
+    '$output'
+    -charge_algo=$cdm 
+    -resolution=$res 
+    -centroided=$centroided 
+    -instrument=$instrument 
+    -algorithm=$algorithm 
+    -mincharge=$chMin 
+    -maxcharge=$chMax 
+    -mslvl=$mslvl 
+    -correlation=$corr 
+    -depth=$depth 
+    -sensitivity=$sens 
+    -maxfeat=$maxfeat
+    ]]></command>
     <inputs>
-	<param name="ms1_in" type="data" format="mzml" label="MS1 files with precursor spectra " />
+        <param name="ms1_in" type="data" format="mzml" label="MS1 files with precursor spectra" />
         <param name="res" type="integer" value="60000" label="Spectral resolution at 400m/z" />
         <param name="centroided" type="select" display="radio" label="Centroided data?">
           <option value="0" selected="true">No</option>