# HG changeset patch
# User galaxyp
# Date 1586244452 14400
# Node ID 73fc27617b2ecd1b3a4cb825aafe878f4af36442
# Parent  c5b3b7eafd4603c2396fb1d2d5114141fe04a0d0
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit 44c3e37a12f60b01521d3e3f18b7f16664f954cc"

diff -r c5b3b7eafd46 -r 73fc27617b2e hardklor.py
--- a/hardklor.py	Sat Aug 19 08:00:25 2017 -0400
+++ b/hardklor.py	Tue Apr 07 03:27:32 2020 -0400
@@ -10,10 +10,10 @@
 
 CONFIG_FILE = 'hk.conf'
 extension_lookup = {
-    'mzml'  :   'mzML',
-    'mzxml' :   'mzXML',
-    'ms1'   :   'MS1',
-    }
+    'mzml': 'mzML',
+    'mzxml': 'mzXML',
+    'ms1': 'MS1',
+}
 
 # input:
 ms1_ext = sys.argv[1]
@@ -33,7 +33,7 @@
     ms1_ext = extension_lookup[ms1_ext]
     linkname = 'ms1_dsetlink.{0}'.format(ms1_ext)
     os.symlink(ms1_file, linkname)
-    ms1_file = linkname 
+    ms1_file = linkname
 
 # load template and dump to config file
 with open(config_load) as fp:
@@ -53,7 +53,7 @@
     maxfeat=options['maxfeat'],
     inputfile=ms1_file,
     outputfile=output_file,
-    )
+)
 with open(CONFIG_FILE, 'w') as fp:
     fp.write(config_to_dump)
 
diff -r c5b3b7eafd46 -r 73fc27617b2e hardklor.xml
--- 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>
diff -r c5b3b7eafd46 -r 73fc27617b2e kronik.xml
--- a/kronik.xml	Sat Aug 19 08:00:25 2017 -0400
+++ b/kronik.xml	Tue Apr 07 03:27:32 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="kronik" name="Kronik" version="2.20">
+<tool id="kronik" name="Kronik" version="2.20+galaxy1">
     <description>processes Hardklor features to find peptides by chromatographic profiling</description>
     <requirements>
         <requirement type="package" version="2.20">kronik</requirement>
@@ -6,7 +6,7 @@
     <stdio>
         <exit_code range="1:" level="fatal" description="Error occurred while running Kronik"/>
     </stdio>
-    <command>kronik -c $c -d $d -g $g -m $m -n $n -p $p "$inputfile" "$output"</command>
+    <command>kronik -c $c -d $d -g $g -m $m -n $n -p $p '$inputfile' '$output'</command>
     <inputs>
         <param name="inputfile" type="data" format="hardklor" label="Hardklör isotope distributions" />
         <param name="c" type="integer" value="5" label="Contaminant threshold in minutes" help="Peptides persisting for longer than this value are excluded" />