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annotate hardklor.xml @ 3:a979b9ff3272 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit b4871f9659a924a68430aed3a93f4f9bad733fd6
author galaxyp
date Wed, 07 Dec 2016 16:36:36 -0500
parents d796e6613d19
children 539f157784e7
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a979b9ff3272 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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1 <tool id="hardklor" name="Hardklor" version="2.30.1">
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2 <description>identification of features from mass spectra</description>
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3 <requirements>
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4 <requirement type="package" version="2.3.0">hardklor</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" level="fatal"/>
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8 </stdio>
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9 <command>python $__tool_directory__/hardklor.py "$ms1_in.extension" "$ms1_in"
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10 "$output" -charge_algo=$cdm -resolution=$res -centroided=$centroided -instrument=$instrument -algorithm=$algorithm -mincharge=$chMin
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11 -maxcharge=$chMax -mslvl=$mslvl -correlation=$corr -depth=$depth -sensitivity=$sens -maxfeat=$maxfeat</command>
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12 <inputs>
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13 <param name="ms1_in" type="data" format="mzml" label="MS1 files with precursor spectra " />
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14 <param name="res" type="integer" value="60000" label="Spectral resolution at 400m/z" />
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15 <param name="centroided" type="select" display="radio" label="Centroided data?">
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16 <option value="0" selected="true">No</option>
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17 <option value="1">Yes</option>
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18 </param>
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19 <param name="instrument" type="select" label="Instrument" >
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20 <option value="Orbitrap" selected="true">Orbitrap</option>
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21 <option value="FTICR" >FTICR</option>
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22 <option value="TOF" >TOF</option>
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23 <option value="QIT" >Quadrupole ion trap</option>
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24 </param>
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25 <param name="mslvl" type="select" display="radio" label="MS level">
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26 <option value="0" >All</option>
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27 <option value="1" selected="true">MS1</option>
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28 <option value="2">MS2</option>
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29 <option value="3">MS3</option>
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30 </param>
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31 <param name="algorithm" type="select" label="Algorithm">
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32 <option value="Basic">Basic</option>
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33 <option value="Version1">Version 1</option>
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34 <option value="Version2" selected="true">Version 2</option>
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35 </param>
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36 <param name="cdm" type="select" label="Charge determination method">
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37 <option value="None">None</option>
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38 <option value="FFT">Fast Fourier Transform</option>
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39 <option value="Patterson">Patterson Algorithm</option>
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40 <option value="Quick" selected="true">Quick</option>
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41 <option value="Senko">Senko</option>
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42 </param>
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43
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44 <param name="chMin" type="integer" value="1" label="Min charge state" />
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45 <param name="chMax" type="integer" value="5" label="Max charge state" />
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46
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47 <param name="corr" type="float" value="0.95" label="Correlation threshold" />
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48 <param name="sens" type="integer" value="2" label="Sensitivity level" help="Ranges from 0 (min, fast) to 3 (max, slow)" />
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49 <param name="depth" type="integer" value="2" label="Depth of combinatorial analysis"
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50 help="Max number of overlapping features in any mz window. Keep as low as necessary for speed" />
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51 <param name="maxfeat" type="integer" value="12" label="Max nr. of features for mz-window to solve" />
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52
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53 <!-- <param name="sn" type="float" value="1" label="Signal to noise threshold" help="Must be >=0" />
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54 <param name="snWin" type="float" optional="true" label="Dynamic signal to noise window length (m/z)"
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55 help="For spectra with varying noise levels (not for Thermo data)"/>
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56 <param name="win" type="float" value="5.25" label="Max width of any set of peaks in a spectrum" /> -->
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57 </inputs>
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58
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59 <outputs>
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60 <data format="hk" name="output" />
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61 </outputs>
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62 <tests>
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63 <test>
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64 <param name="ms1_in" value="ms1_spectra.mzml"/>
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65 <output name="output" file="hardklor_result.hk"/>
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66 </test>
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67 </tests>
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68 <help>
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69 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.
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70 </help>
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71 <citations>
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72 <citation type="doi">10.1021/ac0700833</citation>
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73 <citation type="doi">10.1002/0471250953.bi1318s37</citation>
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74 </citations>
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75 </tool>