diff hardklor.xml @ 0:d796e6613d19 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hardklor.xml	Mon May 23 11:12:40 2016 -0400
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+<tool id="hardklor" name="Hardklor" version="2.30">
+    <description>identification of features from mass spectra</description>
+    <requirements>
+        <requirement type="package" version="2.30">hardklor</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>
+    <inputs>
+	<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>
+          <option value="1">Yes</option>
+        </param>
+        <param name="instrument" type="select" label="Instrument" >
+            <option value="Orbitrap" selected="true">Orbitrap</option>
+            <option value="FTICR" >FTICR</option>
+            <option value="TOF" >TOF</option>
+            <option value="QIT" >Quadrupole ion trap</option>
+        </param>
+        <param name="mslvl" type="select" display="radio" label="MS level">
+          <option value="0" >All</option>
+          <option value="1" selected="true">MS1</option>
+          <option value="2">MS2</option>
+          <option value="3">MS3</option>
+        </param>
+        <param name="algorithm" type="select" label="Algorithm">
+            <option value="Basic">Basic</option>
+            <option value="Version1">Version 1</option>
+            <option value="Version2" selected="true">Version 2</option>
+        </param>
+        <param name="cdm" type="select" label="Charge determination method">
+            <option value="None">None</option>
+            <option value="FFT">Fast Fourier Transform</option>
+            <option value="Patterson">Patterson Algorithm</option>
+            <option value="Quick" selected="true">Quick</option>
+            <option value="Senko">Senko</option>
+        </param>
+        
+        <param name="chMin" type="integer" value="1" label="Min charge state" />
+        <param name="chMax" type="integer" value="5" label="Max charge state" />
+
+        <param name="corr" type="float" value="0.95" label="Correlation threshold" />
+        <param name="sens" type="integer" value="2" label="Sensitivity level" help="Ranges from 0 (min, fast) to 3 (max, slow)" />
+        <param name="depth" type="integer" value="2" label="Depth of combinatorial analysis" 
+help="Max number of overlapping features in any mz window. Keep as low as necessary for speed" />
+        <param name="maxfeat" type="integer" value="12" label="Max nr. of features for mz-window to solve" />
+
+<!--        <param name="sn" type="float" value="1" label="Signal to noise threshold" help="Must be >=0"  />
+        <param name="snWin" type="float" optional="true" label="Dynamic signal to noise window length (m/z)" 
+                help="For spectra with varying noise levels (not for Thermo data)"/>
+        <param name="win" type="float" value="5.25" label="Max width of any set of peaks in a spectrum" /> -->
+    </inputs>
+    
+    <outputs>
+        <data format="hk" name="output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="ms1_in" value="ms1_spectra.mzml"/>
+            <output name="output" file="hardklor_result.hk"/>
+        </test>
+    </tests>
+    <help>
+        Hardklör identifies peptide or protein-like features in mass spectra. It deconvolves overlapping ion signals and can be used on a variety of input formats. The output of Hardklör can be used by the Krönik tool which summarizes the peptide features over time in an LC-MS experiment.
+    </help>
+    <citations>
+        <citation type="doi">10.1021/ac0700833</citation>
+        <citation type="doi">10.1002/0471250953.bi1318s37</citation>
+    </citations>
+</tool>