Mercurial > repos > galaxyp > openms_digestormotif

annotate DigestorMotif.xml @ 13:3138bbc00588 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 21:43:43 +0000
parents 01f5e95b5961
children
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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 Processing]-->
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3 <tool id="DigestorMotif" name="DigestorMotif" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>digests a protein database in-silico</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">DigestorMotif</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($in.ext)' &&
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18 mkdir out &&
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20 ## Main program call
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22 set -o pipefail &&
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23 @EXECUTABLE@ -write_ctd ./ &&
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24 python3 '$__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($in.ext)'
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28 -out
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29 'out/output.${gxy2omsext("idxml")}'
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30
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31 ## Postprocessing
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32 && mv 'out/output.${gxy2omsext("idxml")}' '$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[{"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="fasta" label="FASTA input file" help=" select fasta data sets(s)"/>
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42 <param argument="-missed_cleavages" type="integer" min="0" value="1" label="the number of allowed missed cleavages" help=""/>
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43 <param argument="-mass_accuracy" type="integer" value="1000" label="give your mass accuracy in pp" help=""/>
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44 <param argument="-min_length" type="integer" value="6" label="minimum length of peptide" help=""/>
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45 <param argument="-out_option" type="integer" value="1" label="indicate 1 (peptide table only), 2 (statistics only) or (both peptide table + statistics)" help=""/>
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46 <param argument="-enzyme" type="select" label="The enzyme used for peptide digestion" help="">
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47 <option value="Trypsin/P">Trypsin/P</option>
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48 <option value="V8-DE">V8-DE</option>
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49 <option value="V8-E">V8-E</option>
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50 <option value="leukocyte elastase">leukocyte elastase</option>
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51 <option value="proline endopeptidase">proline endopeptidase</option>
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52 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
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53 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
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54 <option value="2-iodobenzoate">2-iodobenzoate</option>
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55 <option value="iodosobenzoate">iodosobenzoate</option>
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56 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
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57 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
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58 <option value="Glu-C+P">Glu-C+P</option>
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59 <option value="PepsinA + P">PepsinA + P</option>
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60 <option value="cyanogen-bromide">cyanogen-bromide</option>
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61 <option value="Clostripain/P">Clostripain/P</option>
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62 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
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63 <option value="no cleavage">no cleavage</option>
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64 <option value="unspecific cleavage">unspecific cleavage</option>
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65 <option value="Asp-N_ambic">Asp-N_ambic</option>
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66 <option value="Chymotrypsin">Chymotrypsin</option>
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67 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
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68 <option value="CNBr">CNBr</option>
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69 <option value="Formic_acid">Formic_acid</option>
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70 <option value="Lys-C">Lys-C</option>
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71 <option value="Trypsin" selected="true">Trypsin</option>
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72 <option value="Arg-C">Arg-C</option>
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73 <option value="Arg-C/P">Arg-C/P</option>
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74 <option value="Asp-N">Asp-N</option>
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75 <option value="Asp-N/B">Asp-N/B</option>
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76 <option value="Lys-N">Lys-N</option>
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77 <option value="Lys-C/P">Lys-C/P</option>
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78 <option value="PepsinA">PepsinA</option>
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79 <option value="TrypChymo">TrypChymo</option>
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80 <expand macro="list_string_san" name="enzyme"/>
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81 </param>
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82 <param argument="-motif" type="text" value="M" label="the motif for the restricted peptidome" help="">
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83 <expand macro="list_string_san" name="motif"/>
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84 </param>
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85 <expand macro="adv_opts_macro">
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86 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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87 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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88 <expand macro="list_string_san" name="test"/>
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89 </param>
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90 </expand>
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91 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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92 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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93 </param>
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94 </inputs>
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95 <outputs>
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96 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
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97 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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98 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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99 </data>
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100 </outputs>
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101 <tests/>
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102 <help><![CDATA[digests a protein database in-silico
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103
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104
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105 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_DigestorMotif.html]]></help>
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106 <expand macro="references"/>
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107 </tool>