Mercurial > repos > galaxyp > openms_digestor

annotate Digestor.xml @ 6:94dce068fb3e draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
author galaxyp
date Thu, 11 Jan 2018 17:54:22 -0500
parents 3e8b14ad38c2
children 4a795d35e396
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Utilities]-->
3
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4 <tool id="Digestor" name="Digestor" version="2.2.0">
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5 <description>Digests a protein database in-silico.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">Digestor</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>Digestor
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 #if $param_out_type:
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22 -out_type
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23 #if " " in str($param_out_type):
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24 "$param_out_type"
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25 #else
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26 $param_out_type
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27 #end if
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28 #end if
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29 #if $param_missed_cleavages:
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30 -missed_cleavages $param_missed_cleavages
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31 #end if
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32 #if $param_min_length:
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33 -min_length $param_min_length
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34 #end if
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35 #if $param_max_length:
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36 -max_length $param_max_length
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37 #end if
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38 #if $param_enzyme:
1
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39 -enzyme
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40 #if " " in str($param_enzyme):
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41 "$param_enzyme"
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42 #else
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43 $param_enzyme
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44 #end if
0
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45 #end if
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46 #if $adv_opts.adv_opts_selector=='advanced':
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47 #if $adv_opts.param_force:
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48 -force
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49 #end if
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50 #end if
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51 </command>
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52 <inputs>
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53 <param name="param_in" type="data" format="fasta" optional="False" label="input file" help="(-in) "/>
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54 <param name="param_out_type" display="radio" type="select" optional="True" label="Set this if you cannot control the filename of 'out'," help="(-out_type) e.g., in TOPPAS">
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55 <option value="idXML">idXML</option>
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56 <option value="fasta">fasta</option>
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57 </param>
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58 <param name="param_missed_cleavages" type="integer" min="0" optional="True" value="1" label="The number of allowed missed cleavages" help="(-missed_cleavages) "/>
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59 <param name="param_min_length" type="integer" value="6" label="Minimum length of peptide" help="(-min_length) "/>
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60 <param name="param_max_length" type="integer" value="40" label="Maximum length of peptide" help="(-max_length) "/>
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61 <param name="param_enzyme" type="select" optional="False" value="Trypsin" label="The type of digestion enzyme" help="(-enzyme) ">
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62 <option value="V8-E">V8-E</option>
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63 <option value="Trypsin/P">Trypsin/P</option>
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64 <option value="PepsinA">PepsinA</option>
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65 <option value="CNBr">CNBr</option>
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66 <option value="Lys-C/P">Lys-C/P</option>
3
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67 <option value="Asp-N_ambic">Asp-N_ambic</option>
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68 <option value="Arg-C">Arg-C</option>
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69 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
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70 <option value="2-iodobenzoate">2-iodobenzoate</option>
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71 <option value="Trypsin" selected="true">Trypsin</option>
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72 <option value="TrypChymo">TrypChymo</option>
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73 <option value="Chymotrypsin">Chymotrypsin</option>
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74 <option value="Asp-N">Asp-N</option>
3
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75 <option value="Formic_acid">Formic_acid</option>
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76 <option value="V8-DE">V8-DE</option>
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77 <option value="Lys-C">Lys-C</option>
3
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78 <option value="no cleavage">no cleavage</option>
0
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79 <option value="leukocyte elastase">leukocyte elastase</option>
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80 <option value="proline endopeptidase">proline endopeptidase</option>
3
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81 <option value="unspecific cleavage">unspecific cleavage</option>
0
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82 </param>
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83 <expand macro="advanced_options">
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84 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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85 </expand>
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86 </inputs>
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87 <outputs>
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88 <data name="param_out" format="fasta"/>
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89 </outputs>
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90 <help>Digests a protein database in-silico.
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91
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92
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93 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_Digestor.html</help>
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94 </tool>