Mercurial > repos > galaxyp > openms_mascotadapter

annotate MascotAdapter.xml @ 14:087b9d721a08 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 21:43:35 +0000
parents 27e308170367
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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="MascotAdapter" name="MascotAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Annotates MS/MS spectra using Mascot</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">MascotAdapter</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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15 ## Preprocessing
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16 mkdir in &&
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17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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18 mkdir out &&
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19
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20 ## Main program call
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22 set -o pipefail &&
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23 @EXECUTABLE@ -write_ctd ./ &&
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24 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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25 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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26 -in
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27 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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28 -out
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29 'out/output.${out_type}'
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31 ## Postprocessing
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32 && mv 'out/output.${out_type}' '$out'
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33 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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34 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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35 #end if]]></command>
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36 <configfiles>
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37 <inputs name="args_json" data_style="paths"/>
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38 <configfile name="hardcoded_json"><![CDATA[{"mascot_directory": "TODO", "temp_data_directory": "\$TMP_DIR", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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39 </configfiles>
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40 <inputs>
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41 <param argument="-in" type="data" format="mascotxml,mzdata" label="input file in mzData format" help="Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read select mascotxml,mzdata data sets(s)"/>
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42 <param argument="-out_type" type="select" label="output file type (for TOPPAS)" help="">
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43 <option value="idXML">idxml</option>
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44 <option value="mgf">mgf</option>
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45 <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
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46 <expand macro="list_string_san" name="out_type"/>
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47 </param>
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48 <param argument="-instrument" type="text" value="Default" label="the instrument that was used to measure the spectra" help="">
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49 <expand macro="list_string_san" name="instrument"/>
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50 </param>
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51 <param argument="-precursor_mass_tolerance" type="float" value="2.0" label="the precursor mass tolerance" help=""/>
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52 <param argument="-peak_mass_tolerance" type="float" value="1.0" label="the peak mass tolerance" help=""/>
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53 <param argument="-taxonomy" type="select" label="the taxonomy" help="">
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54 <option value="All entries" selected="true">All entries</option>
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55 <option value=". . Archaea (Archaeobacteria)">. . Archaea (Archaeobacteria)</option>
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56 <option value=". . Eukaryota (eucaryotes)">. . Eukaryota (eucaryotes)</option>
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57 <option value=". . . . Alveolata (alveolates)">. . . . Alveolata (alveolates)</option>
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58 <option value=". . . . . . Plasmodium falciparum (malaria parasite)">. . . . . . Plasmodium falciparum (malaria parasite)</option>
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59 <option value=". . . . . . Other Alveolata">. . . . . . Other Alveolata</option>
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60 <option value=". . . . Metazoa (Animals)">. . . . Metazoa (Animals)</option>
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61 <option value=". . . . . . Caenorhabditis elegans">. . . . . . Caenorhabditis elegans</option>
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62 <option value=". . . . . . Drosophila (fruit flies)">. . . . . . Drosophila (fruit flies)</option>
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63 <option value=". . . . . . Chordata (vertebrates and relatives)">. . . . . . Chordata (vertebrates and relatives)</option>
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64 <option value=". . . . . . . . bony vertebrates">. . . . . . . . bony vertebrates</option>
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65 <option value=". . . . . . . . . . lobe-finned fish and tetrapod clade">. . . . . . . . . . lobe-finned fish and tetrapod clade</option>
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66 <option value=". . . . . . . . . . . . Mammalia (mammals)">. . . . . . . . . . . . Mammalia (mammals)</option>
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67 <option value=". . . . . . . . . . . . . . Primates">. . . . . . . . . . . . . . Primates</option>
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68 <option value=". . . . . . . . . . . . . . . . Homo sapiens (human)">. . . . . . . . . . . . . . . . Homo sapiens (human)</option>
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69 <option value=". . . . . . . . . . . . . . . . Other primates">. . . . . . . . . . . . . . . . Other primates</option>
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70 <option value=". . . . . . . . . . . . . . Rodentia (Rodents)">. . . . . . . . . . . . . . Rodentia (Rodents)</option>
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71 <option value=". . . . . . . . . . . . . . . . Mus.">. . . . . . . . . . . . . . . . Mus.</option>
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72 <option value=". . . . . . . . . . . . . . . . . . Mus musculus (house mouse)">. . . . . . . . . . . . . . . . . . Mus musculus (house mouse)</option>
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73 <option value=". . . . . . . . . . . . . . . . Rattus">. . . . . . . . . . . . . . . . Rattus</option>
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74 <option value=". . . . . . . . . . . . . . . . Other rodentia">. . . . . . . . . . . . . . . . Other rodentia</option>
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75 <option value=". . . . . . . . . . . . . . Other mammalia">. . . . . . . . . . . . . . Other mammalia</option>
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76 <option value=". . . . . . . . . . . . Xenopus laevis (African clawed frog)">. . . . . . . . . . . . Xenopus laevis (African clawed frog)</option>
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galaxyp
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77 <option value=". . . . . . . . . . . . Other lobe-finned fish and tetrapod clade">. . . . . . . . . . . . Other lobe-finned fish and tetrapod clade</option>
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galaxyp
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78 <option value=". . . . . . . . . . Actinopterygii (ray-finned fishes)">. . . . . . . . . . Actinopterygii (ray-finned fishes)</option>
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galaxyp
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79 <option value=". . . . . . . . . . . . Takifugu rubripes (Japanese Pufferfish)">. . . . . . . . . . . . Takifugu rubripes (Japanese Pufferfish)</option>
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galaxyp
parents:
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80 <option value=". . . . . . . . . . . . Danio rerio (zebra fish)">. . . . . . . . . . . . Danio rerio (zebra fish)</option>
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galaxyp
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81 <option value=". . . . . . . . . . . . Other Actinopterygii">. . . . . . . . . . . . Other Actinopterygii</option>
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galaxyp
parents:
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82 <option value=". . . . . . . . Other Chordata">. . . . . . . . Other Chordata</option>
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galaxyp
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83 <option value=". . . . . . Other Metazoa">. . . . . . Other Metazoa</option>
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galaxyp
parents:
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84 <option value=". . . . Dictyostelium discoideum">. . . . Dictyostelium discoideum</option>
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galaxyp
parents:
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85 <option value=". . . . Fungi">. . . . Fungi</option>
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galaxyp
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86 <option value=". . . . . . Saccharomyces Cerevisiae (baker's yeast)">. . . . . . Saccharomyces Cerevisiae (baker's yeast)</option>
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galaxyp
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87 <option value=". . . . . . Schizosaccharomyces pombe (fission yeast)">. . . . . . Schizosaccharomyces pombe (fission yeast)</option>
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galaxyp
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88 <option value=". . . . . . Pneumocystis carinii">. . . . . . Pneumocystis carinii</option>
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galaxyp
parents:
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89 <option value=". . . . . . Other Fungi">. . . . . . Other Fungi</option>
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galaxyp
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90 <option value=". . . . Viridiplantae (Green Plants)">. . . . Viridiplantae (Green Plants)</option>
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galaxyp
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91 <option value=". . . . . . Arabidopsis thaliana (thale cress)">. . . . . . Arabidopsis thaliana (thale cress)</option>
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galaxyp
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92 <option value=". . . . . . Oryza sativa (rice)">. . . . . . Oryza sativa (rice)</option>
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galaxyp
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93 <option value=". . . . . . Other green plants">. . . . . . Other green plants</option>
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galaxyp
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94 <option value=". . . . Other Eukaryota">. . . . Other Eukaryota</option>
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galaxyp
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95 <option value=". . Bacteria (Eubacteria)">. . Bacteria (Eubacteria)</option>
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galaxyp
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96 <option value=". . . . Actinobacteria (class)">. . . . Actinobacteria (class)</option>
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galaxyp
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97 <option value=". . . . . . Mycobacterium tuberculosis complex">. . . . . . Mycobacterium tuberculosis complex</option>
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galaxyp
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98 <option value=". . . . . . Other Actinobacteria (class)">. . . . . . Other Actinobacteria (class)</option>
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galaxyp
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99 <option value=". . . . Firmicutes (gram-positive bacteria)">. . . . Firmicutes (gram-positive bacteria)</option>
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galaxyp
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100 <option value=". . . . . . Bacillus subtilis">. . . . . . Bacillus subtilis</option>
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101 <option value=". . . . . . Mycoplasma">. . . . . . Mycoplasma</option>
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galaxyp
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102 <option value=". . . . . . Streptococcus Pneumoniae">. . . . . . Streptococcus Pneumoniae</option>
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galaxyp
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103 <option value=". . . . . . Streptomyces coelicolor">. . . . . . Streptomyces coelicolor</option>
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galaxyp
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104 <option value=". . . . . . Other Firmicutes">. . . . . . Other Firmicutes</option>
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galaxyp
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105 <option value=". . . . Proteobacteria (purple bacteria)">. . . . Proteobacteria (purple bacteria)</option>
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galaxyp
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106 <option value=". . . . . . Agrobacterium tumefaciens">. . . . . . Agrobacterium tumefaciens</option>
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galaxyp
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107 <option value=". . . . . . Campylobacter jejuni">. . . . . . Campylobacter jejuni</option>
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galaxyp
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108 <option value=". . . . . . Escherichia coli">. . . . . . Escherichia coli</option>
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galaxyp
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109 <option value=". . . . . . Neisseria meningitidis">. . . . . . Neisseria meningitidis</option>
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110 <option value=". . . . . . Salmonella">. . . . . . Salmonella</option>
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galaxyp
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111 <option value=". . . . . . Other Proteobacteria">. . . . . . Other Proteobacteria</option>
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112 <option value=". . . . Other Bacteria">. . . . Other Bacteria</option>
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galaxyp
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113 <option value=". . Viruses">. . Viruses</option>
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galaxyp
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114 <option value=". . . . Hepatitis C virus">. . . . Hepatitis C virus</option>
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galaxyp
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115 <option value=". . . . Other viruses">. . . . Other viruses</option>
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galaxyp
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116 <option value=". . Other (includes plasmids and artificial sequences)">. . Other (includes plasmids and artificial sequences)</option>
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galaxyp
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117 <option value=". . unclassified">. . unclassified</option>
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galaxyp
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118 <option value=". . Species information unavailable">. . Species information unavailable</option>
13
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119 <expand macro="list_string_san" name="taxonomy"/>
0
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120 </param>
13
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121 <param argument="-modifications" type="text" optional="true" value="" label="the modifications i.e. Carboxymethyl (C)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
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122 <expand macro="list_string_val" name="modifications"/>
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123 <expand macro="list_string_san" name="modifications"/>
9
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124 </param>
13
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125 <param argument="-variable_modifications" type="text" optional="true" value="" label="the variable modifications i.e. Carboxymethyl (C)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
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126 <expand macro="list_string_val" name="variable_modifications"/>
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127 <expand macro="list_string_san" name="variable_modifications"/>
0
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128 </param>
14
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129 <param argument="-charges" type="text" value="1+ 2+ 3+" label="the different charge states" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
13
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130 <expand macro="list_string_val" name="charges"/>
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diff changeset
131 <expand macro="list_string_san" name="charges"/>
0
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132 </param>
14
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133 <param argument="-db" type="text" value="MSDB" label="the database to search in" help="">
13
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134 <expand macro="list_string_san" name="db"/>
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135 </param>
14
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136 <param argument="-hits" type="text" value="AUTO" label="the number of hits to report" help="">
13
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diff changeset
137 <expand macro="list_string_san" name="hits"/>
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138 </param>
14
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139 <param argument="-cleavage" type="select" label="The enzyme descriptor to the enzyme used for digestion" help="(Trypsin is default, None would be best for peptide input or unspecific digestion, for more please refer to your mascot server)">
0
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140 <option value="Trypsin" selected="true">Trypsin</option>
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galaxyp
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141 <option value="Arg-C">Arg-C</option>
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galaxyp
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142 <option value="Asp-N">Asp-N</option>
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galaxyp
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143 <option value="Asp-N_ambic">Asp-N_ambic</option>
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144 <option value="Chymotrypsin">Chymotrypsin</option>
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145 <option value="CNBr">CNBr</option>
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146 <option value="CNBr+Trypsin">CNBr+Trypsin</option>
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galaxyp
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147 <option value="Formic_acid">Formic_acid</option>
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148 <option value="Lys-C">Lys-C</option>
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149 <option value="Lys-C/P">Lys-C/P</option>
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150 <option value="PepsinA">PepsinA</option>
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151 <option value="Tryp-CNBr">Tryp-CNBr</option>
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152 <option value="TrypChymo">TrypChymo</option>
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153 <option value="Trypsin/P">Trypsin/P</option>
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154 <option value="V8-DE">V8-DE</option>
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155 <option value="V8-E">V8-E</option>
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156 <option value="semiTrypsin">semiTrypsin</option>
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157 <option value="LysC+AspN">LysC+AspN</option>
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158 <option value="None">None</option>
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159 <expand macro="list_string_san" name="cleavage"/>
0
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160 </param>
14
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161 <param argument="-missed_cleavages" type="integer" min="0" value="0" label="number of allowed missed cleavages" help=""/>
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162 <param argument="-sig_threshold" type="float" value="0.05" label="significance threshold" help=""/>
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163 <param argument="-pep_homol" type="float" value="1.0" label="peptide homology threshold" help=""/>
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164 <param argument="-pep_ident" type="float" value="1.0" label="peptide ident threshold" help=""/>
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165 <param argument="-pep_rank" type="integer" value="1" label="peptide rank" help=""/>
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166 <param argument="-prot_score" type="float" value="1.0" label="protein score" help=""/>
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167 <param argument="-pep_score" type="float" value="1.0" label="peptide score" help=""/>
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168 <param argument="-pep_exp_z" type="integer" value="1" label="peptide expected charge" help=""/>
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169 <param argument="-show_unassigned" type="integer" value="1" label="show_unassigned" help=""/>
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170 <param argument="-first_dim_rt" type="float" value="0.0" label="additional information which is added to every peptide identification as metavalue if set &gt; 0" help=""/>
13
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171 <param argument="-boundary" type="text" optional="true" value="" label="MIME boundary for mascot output format" help="">
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172 <expand macro="list_string_san" name="boundary"/>
0
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173 </param>
14
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174 <param argument="-mass_type" type="select" label="mass type" help="">
0
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175 <option value="Monoisotopic" selected="true">Monoisotopic</option>
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176 <option value="Average">Average</option>
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177 <expand macro="list_string_san" name="mass_type"/>
0
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178 </param>
9
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179 <expand macro="adv_opts_macro">
13
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180 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
14
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181 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
13
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182 <expand macro="list_string_san" name="test"/>
9
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183 </param>
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184 </expand>
11
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185 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
9
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186 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
0
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187 </param>
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188 </inputs>
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189 <outputs>
13
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190 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml">
11
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191 <change_format>
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192 <when input="out_type" value="mgf" format="mgf"/>
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193 </change_format>
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194 </data>
9
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195 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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196 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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197 </data>
0
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198 </outputs>
14
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199 <tests>
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200 <!-- TOPP_MascotAdapter_1 -->
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201 <test expect_num_outputs="2">
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202 <section name="adv_opts">
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203 <param name="force" value="false"/>
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204 <param name="test" value="true"/>
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205 </section>
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206 <param name="in" value="MascotAdapter_1_input.mzData"/>
14
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207 <output name="out" value="MascotAdapter_1_output.mascot_in" compare="sim_size" delta_frac="0.7"/>
13
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208 <param name="out_type" value="mgf"/>
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209 <param name="instrument" value="ESI-TRAP"/>
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210 <param name="precursor_mass_tolerance" value="1.3"/>
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211 <param name="peak_mass_tolerance" value="0.3"/>
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212 <param name="taxonomy" value=". . . . . . Chordata (vertebrates and relatives)"/>
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213 <param name="modifications" value="&quot;Carboxymethyl (C)&quot;"/>
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214 <param name="variable_modifications" value="&quot;Variable_Modifications_TEST_1&quot;"/>
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215 <param name="charges" value="&quot;1+&quot; &quot;2+&quot; &quot;3+&quot;"/>
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216 <param name="db" value="MSDB"/>
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217 <param name="hits" value="AUTO"/>
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218 <param name="cleavage" value="Trypsin"/>
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219 <param name="missed_cleavages" value="1"/>
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220 <param name="sig_threshold" value="0.05"/>
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221 <param name="pep_homol" value="1.0"/>
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222 <param name="pep_ident" value="1.0"/>
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223 <param name="pep_rank" value="1"/>
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224 <param name="prot_score" value="1.0"/>
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225 <param name="pep_score" value="1.0"/>
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226 <param name="pep_exp_z" value="1"/>
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227 <param name="show_unassigned" value="1"/>
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228 <param name="first_dim_rt" value="0.0"/>
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229 <param name="boundary" value="ABCDEFGHIJKMNOPQRSTUVWXYZ"/>
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230 <param name="mass_type" value="Monoisotopic"/>
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231 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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232 <output name="ctd_out" ftype="xml">
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233 <assert_contents>
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234 <is_valid_xml/>
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235 </assert_contents>
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236 </output>
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237 <assert_stdout>
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238 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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239 </assert_stdout>
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240 </test>
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241 <!-- TOPP_MascotAdapter_2 -->
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242 <test expect_num_outputs="2">
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243 <section name="adv_opts">
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244 <param name="force" value="false"/>
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245 <param name="test" value="true"/>
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246 </section>
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247 <param name="in" value="MascotAdapter_2_input.mascotXML"/>
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248 <output name="out" value="MascotAdapter_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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249 <param name="out_type" value="idXML"/>
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250 <param name="instrument" value="Default"/>
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251 <param name="precursor_mass_tolerance" value="2.0"/>
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252 <param name="peak_mass_tolerance" value="1.0"/>
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253 <param name="taxonomy" value="All entries"/>
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254 <param name="charges" value="&quot;1+&quot; &quot;2+&quot; &quot;3+&quot;"/>
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255 <param name="db" value="MSDB"/>
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256 <param name="hits" value="AUTO"/>
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257 <param name="cleavage" value="Trypsin"/>
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258 <param name="missed_cleavages" value="0"/>
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259 <param name="sig_threshold" value="0.05"/>
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260 <param name="pep_homol" value="1.0"/>
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261 <param name="pep_ident" value="1.0"/>
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262 <param name="pep_rank" value="1"/>
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263 <param name="prot_score" value="1.0"/>
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264 <param name="pep_score" value="1.0"/>
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265 <param name="pep_exp_z" value="1"/>
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266 <param name="show_unassigned" value="1"/>
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267 <param name="first_dim_rt" value="0.0"/>
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268 <param name="boundary" value=""/>
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269 <param name="mass_type" value="Monoisotopic"/>
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270 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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271 <output name="ctd_out" ftype="xml">
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272 <assert_contents>
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273 <is_valid_xml/>
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274 </assert_contents>
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275 </output>
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276 <assert_stdout>
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277 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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278 </assert_stdout>
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279 </test>
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280 </tests>
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281 <help><![CDATA[Annotates MS/MS spectra using Mascot.
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282
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283
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284 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MascotAdapter.html]]></help>
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285 <expand macro="references"/>
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286 </tool>