Mercurial > repos > galaxyp > openms_novoradapter

annotate NovorAdapter.xml @ 6:fa544e12732f draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:45:52 +0000
parents 34dda034b019
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562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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1 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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2 <!--Proposed Tool Section: [Identification of Proteins/Peptides (SearchEngines)]-->
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3 <tool id="NovorAdapter" name="NovorAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Performs de novo sequencing of peptides from MS/MS data with Novor</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">NovorAdapter</token>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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12 @EXT_FOO@
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13 #import re
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562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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15 ## Preprocessing
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16 mkdir in &&
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17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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18 mkdir out &&
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19 #if $novorFile:
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20 mkdir novorFile &&
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21 cp '$novorFile' 'novorFile/${re.sub("[^\w\-_]", "_", $novorFile.element_identifier)}.$gxy2omsext($novorFile.ext)' &&
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22 #end if
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24 ## Main program call
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562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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26 set -o pipefail &&
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27 @EXECUTABLE@ -write_ctd ./ &&
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28 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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29 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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30 -in
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31 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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32 -out
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33 'out/output.${gxy2omsext("idxml")}'
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34 #if $novorFile:
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35 -novorFile
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36 'novorFile/${re.sub("[^\w\-_]", "_", $novorFile.element_identifier)}.$gxy2omsext($novorFile.ext)'
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37 #end if
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38
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39 ## Postprocessing
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40 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
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41 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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42 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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43 #end if]]></command>
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44 <configfiles>
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45 <inputs name="args_json" data_style="paths"/>
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46 <configfile name="hardcoded_json"><![CDATA[{"executable": "/home/berntm/Downloads/novor/lib/novor.jar", "java_executable": "java", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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47 </configfiles>
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48 <inputs>
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49 <param argument="-in" type="data" format="mzml" label="MzML Input file" help=" select mzml data sets(s)"/>
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50 <param argument="-enzyme" type="select" label="Digestion enzyme - currently only Trypsin is supported" help="">
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51 <option value="Trypsin" selected="true">Trypsin</option>
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52 <expand macro="list_string_san" name="enzyme"/>
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53 </param>
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54 <param argument="-fragmentation" type="select" label="Fragmentation method" help="">
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55 <option value="CID" selected="true">CID</option>
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56 <option value="HCD">HCD</option>
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57 <expand macro="list_string_san" name="fragmentation"/>
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58 </param>
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59 <param argument="-massAnalyzer" type="select" label="MassAnalyze" help="e.g. (Oritrap CID-Trap, CID-FT, HCD-FT; QTof CID-TOF)">
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60 <option value="Trap" selected="true">Trap</option>
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61 <option value="TOF">TOF</option>
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62 <option value="FT">FT</option>
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63 <expand macro="list_string_san" name="massAnalyzer"/>
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64 </param>
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65 <param argument="-fragment_mass_tolerance" type="float" value="0.5" label="Fragmentation error tolerance (Da)" help=""/>
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66 <param argument="-precursor_mass_tolerance" type="float" value="15.0" label="Precursor error tolerance (ppm or Da)" help=""/>
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67 <param argument="-precursor_error_units" type="select" label="Unit of precursor mass tolerance" help="">
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68 <option value="ppm" selected="true">ppm</option>
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69 <option value="Da">Da</option>
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70 <expand macro="list_string_san" name="precursor_error_units"/>
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71 </param>
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72 <param argument="-variable_modifications" type="select" multiple="true" optional="true" label="Variable modifications" help="">
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73 <option value="Acetyl (K)">Acetyl (K)</option>
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74 <option value="Acetyl (N-term)">Acetyl (N-term)</option>
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75 <option value="Amidated (C-term)">Amidated (C-term)</option>
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76 <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option>
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77 <option value="Biotin (K)">Biotin (K)</option>
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78 <option value="Biotin (N-term)">Biotin (N-term)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
79 <option value="Carbamidomethyl (C)">Carbamidomethyl (C)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
80 <option value="Carbamyl (K)">Carbamyl (K)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
81 <option value="Carbamyl (N-term)">Carbamyl (N-term)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
82 <option value="Carboxymethyl (C)">Carboxymethyl (C)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
83 <option value="Deamidated (NQ)">Deamidated (NQ)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
84 <option value="Dehydrated (N-term C)">Dehydrated (N-term C)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
85 <option value="Dioxidation (M)">Dioxidation (M)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
86 <option value="Methyl (C-term)">Methyl (C-term)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
87 <option value="Methyl (DE)">Methyl (DE)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
88 <option value="Oxidation (M)">Oxidation (M)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
89 <option value="Oxidation (HW)">Oxidation (HW)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
90 <option value="Phospho (ST)">Phospho (ST)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
91 <option value="Phospho (Y)">Phospho (Y)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
92 <option value="Pyro-carbamidomethyl (N-term C)">Pyro-carbamidomethyl (N-term C)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
93 <option value="Pyro-Glu (E)">Pyro-Glu (E)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
94 <option value="Pyro-Glu (Q)">Pyro-Glu (Q)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
95 <option value="Sodium (C-term)">Sodium (C-term)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
96 <option value="Sodium (DE)">Sodium (DE)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
97 <option value="Sulfo (STY)">Sulfo (STY)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
98 <option value="Trimethyl (RK)">Trimethyl (RK)</option>
5
34dda034b019 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
99 <expand macro="list_string_san" name="variable_modifications"/>
0
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
100 </param>
6
fa544e12732f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 5
diff changeset
101 <param argument="-fixed_modifications" type="select" multiple="true" optional="true" label="Fixed modifications" help="">
0
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
102 <option value="Acetyl (K)">Acetyl (K)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
103 <option value="Acetyl (N-term)">Acetyl (N-term)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
104 <option value="Amidated (C-term)">Amidated (C-term)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
105 <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
106 <option value="Biotin (K)">Biotin (K)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
107 <option value="Biotin (N-term)">Biotin (N-term)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
108 <option value="Carbamidomethyl (C)">Carbamidomethyl (C)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
109 <option value="Carbamyl (K)">Carbamyl (K)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
110 <option value="Carbamyl (N-term)">Carbamyl (N-term)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
111 <option value="Carboxymethyl (C)">Carboxymethyl (C)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
112 <option value="Deamidated (NQ)">Deamidated (NQ)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
113 <option value="Dehydrated (N-term C)">Dehydrated (N-term C)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
114 <option value="Dioxidation (M)">Dioxidation (M)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
115 <option value="Methyl (C-term)">Methyl (C-term)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
116 <option value="Methyl (DE)">Methyl (DE)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
117 <option value="Oxidation (M)">Oxidation (M)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
118 <option value="Oxidation (HW)">Oxidation (HW)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
119 <option value="Phospho (ST)">Phospho (ST)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
120 <option value="Phospho (Y)">Phospho (Y)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
121 <option value="Pyro-carbamidomethyl (N-term C)">Pyro-carbamidomethyl (N-term C)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
122 <option value="Pyro-Glu (E)">Pyro-Glu (E)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
123 <option value="Pyro-Glu (Q)">Pyro-Glu (Q)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
124 <option value="Sodium (C-term)">Sodium (C-term)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
125 <option value="Sodium (DE)">Sodium (DE)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
126 <option value="Sulfo (STY)">Sulfo (STY)</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
127 <option value="Trimethyl (RK)">Trimethyl (RK)</option>
5
34dda034b019 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
128 <expand macro="list_string_san" name="fixed_modifications"/>
0
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
129 </param>
6
fa544e12732f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 5
diff changeset
130 <param argument="-forbiddenResidues" type="select" multiple="true" optional="true" label="Forbidden Resiudes" help="">
0
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
131 <option value="I">I</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
132 <option value="U">U</option>
5
34dda034b019 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
133 <expand macro="list_string_san" name="forbiddenResidues"/>
0
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
134 </param>
5
34dda034b019 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
135 <param argument="-novorFile" type="data" format="txt" optional="true" label="File to introduce customized algorithm parameters for advanced users (otional .novor file)" help=" select txt data sets(s)"/>
0
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
136 <expand macro="adv_opts_macro">
5
34dda034b019 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
137 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
6
fa544e12732f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 5
diff changeset
138 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
5
34dda034b019 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
139 <expand macro="list_string_san" name="test"/>
0
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
140 </param>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
141 </expand>
2
16fcd0ea9937 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
parents: 0
diff changeset
142 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
0
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
143 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
144 </param>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
145 </inputs>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
146 <outputs>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
147 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
148 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
149 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
150 </data>
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
151 </outputs>
6
fa544e12732f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 5
diff changeset
152 <tests>
fa544e12732f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 5
diff changeset
153 <!-- TOPP_NovorAdapter_1 -->
0
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
diff changeset
154 </tests>
5
34dda034b019 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
155 <help><![CDATA[Performs de novo sequencing of peptides from MS/MS data with Novor.
0
562d46a2f8b6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
galaxyp
parents:
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156
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158 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_NovorAdapter.html]]></help>
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159 <expand macro="references"/>
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160 </tool>