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annotate 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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6
73fc27617b2e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit 44c3e37a12f60b01521d3e3f18b7f16664f954cc"
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1 <tool id="hardklor" name="Hardklor" version="2.30.1+galaxy1">
0
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2 <description>identification of features from mass spectra</description>
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3 <requirements>
3
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4 <requirement type="package" version="2.3.0">hardklor</requirement>
6
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5 <requirement type="package" version="3.7">python</requirement>
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6 </requirements>
6
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7 <command detect_errors="exit_code"><![CDATA[
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8 python '$__tool_directory__/hardklor.py'
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9 '$ms1_in.extension'
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10 '$ms1_in'
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11 '$output'
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12 -charge_algo=$cdm
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13 -resolution=$res
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14 -centroided=$centroided
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15 -instrument=$instrument
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16 -algorithm=$algorithm
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17 -mincharge=$chMin
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18 -maxcharge=$chMax
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19 -mslvl=$mslvl
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20 -correlation=$corr
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21 -depth=$depth
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22 -sensitivity=$sens
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23 -maxfeat=$maxfeat
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24 ]]></command>
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25 <inputs>
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26 <param name="ms1_in" type="data" format="mzml" label="MS1 files with precursor spectra" />
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27 <param name="res" type="integer" value="60000" label="Spectral resolution at 400m/z" />
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28 <param name="centroided" type="select" display="radio" label="Centroided data?">
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29 <option value="0" selected="true">No</option>
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30 <option value="1">Yes</option>
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31 </param>
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32 <param name="instrument" type="select" label="Instrument" >
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33 <option value="Orbitrap" selected="true">Orbitrap</option>
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34 <option value="FTICR" >FTICR</option>
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35 <option value="TOF" >TOF</option>
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36 <option value="QIT" >Quadrupole ion trap</option>
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37 </param>
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38 <param name="mslvl" type="select" display="radio" label="MS level">
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39 <option value="0" >All</option>
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40 <option value="1" selected="true">MS1</option>
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41 <option value="2">MS2</option>
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42 <option value="3">MS3</option>
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43 </param>
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44 <param name="algorithm" type="select" label="Algorithm">
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45 <option value="Basic">Basic</option>
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46 <option value="Version1">Version 1</option>
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47 <option value="Version2" selected="true">Version 2</option>
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48 </param>
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49 <param name="cdm" type="select" label="Charge determination method">
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50 <option value="None">None</option>
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51 <option value="FFT">Fast Fourier Transform</option>
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52 <option value="Patterson">Patterson Algorithm</option>
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53 <option value="Quick" selected="true">Quick</option>
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54 <option value="Senko">Senko</option>
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55 </param>
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56
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57 <param name="chMin" type="integer" value="1" label="Min charge state" />
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58 <param name="chMax" type="integer" value="5" label="Max charge state" />
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59
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60 <param name="corr" type="float" value="0.95" label="Correlation threshold" />
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61 <param name="sens" type="integer" value="2" label="Sensitivity level" help="Ranges from 0 (min, fast) to 3 (max, slow)" />
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62 <param name="depth" type="integer" value="2" label="Depth of combinatorial analysis"
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63 help="Max number of overlapping features in any mz window. Keep as low as necessary for speed" />
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64 <param name="maxfeat" type="integer" value="12" label="Max nr. of features for mz-window to solve" />
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65
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66 <!-- <param name="sn" type="float" value="1" label="Signal to noise threshold" help="Must be >=0" />
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67 <param name="snWin" type="float" optional="true" label="Dynamic signal to noise window length (m/z)"
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68 help="For spectra with varying noise levels (not for Thermo data)"/>
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69 <param name="win" type="float" value="5.25" label="Max width of any set of peaks in a spectrum" /> -->
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70 </inputs>
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71
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72 <outputs>
4
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73 <data format="hardklor" name="output" />
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74 </outputs>
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75 <tests>
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76 <test>
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77 <param name="ms1_in" value="ms1_spectra.mzml"/>
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78 <output name="output" file="hardklor_result.hk"/>
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79 </test>
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80 </tests>
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81 <help>
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82 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.
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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83 </help>
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84 <citations>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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85 <citation type="doi">10.1021/ac0700833</citation>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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86 <citation type="doi">10.1002/0471250953.bi1318s37</citation>
d796e6613d19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit f37e6d0357de4d9b1cd743ca291a7d4df2cc7a5f-dirty
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87 </citations>
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88 </tool>