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annotate DigestorMotif.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
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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]-->
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4 <tool id="DigestorMotif" name="DigestorMotif" version="2.0.0">
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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@">DigestorMotif</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>DigestorMotif
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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_missed_cleavages:
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22 -missed_cleavages $param_missed_cleavages
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23 #end if
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24 #if $param_mass_accuracy:
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25 -mass_accuracy $param_mass_accuracy
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26 #end if
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27 #if $param_min_length:
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28 -min_length $param_min_length
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29 #end if
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30 #if $param_out_option:
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31 -out_option $param_out_option
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32 #end if
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33 #if $param_enzyme:
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34 -enzyme
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35 #if &quot; &quot; in str($param_enzyme):
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36 &quot;$param_enzyme&quot;
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37 #else
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38 $param_enzyme
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39 #end if
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40 #end if
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41 #if $param_motif:
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42 -motif &quot;$param_motif&quot;
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43 #end if
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44 -threads \${GALAXY_SLOTS:-24}
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45 #if $adv_opts.adv_opts_selector=='advanced':
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46 #if $adv_opts.param_force:
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47 -force
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48 #end if
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49 #end if
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50 </command>
4
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51 <inputs>
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52 <param format="fasta" help="(-in) " label="FASTA input file" name="param_in" optional="False" type="data"/>
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53 <param help="(-missed_cleavages) " label="the number of allowed missed cleavages" min="0" name="param_missed_cleavages" optional="True" type="integer" value="1"/>
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54 <param help="(-mass_accuracy) " label="give your mass accuracy in pp" name="param_mass_accuracy" type="integer" value="1000"/>
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55 <param help="(-min_length) " label="minimum length of peptide" name="param_min_length" type="integer" value="6"/>
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56 <param help="(-out_option) " label="indicate 1 (peptide table only), 2 (statistics only) or (both peptide table + statistics)" name="param_out_option" type="integer" value="1"/>
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57 <param help="(-enzyme) " label="The enzyme used for peptide digestion" name="param_enzyme" optional="True" type="select" value="Trypsin">
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58 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
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59 <option value="Asp-N">Asp-N</option>
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60 <option value="Trypsin">Trypsin</option>
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61 <option value="leukocyte elastase">leukocyte elastase</option>
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62 <option value="no cleavage">no cleavage</option>
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63 <option value="unspecific cleavage">unspecific cleavage</option>
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64 <option value="TrypChymo">TrypChymo</option>
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65 <option value="V8-E">V8-E</option>
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66 <option value="Formic_acid">Formic_acid</option>
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67 <option value="Lys-C/P">Lys-C/P</option>
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68 <option value="Chymotrypsin">Chymotrypsin</option>
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69 <option value="2-iodobenzoate">2-iodobenzoate</option>
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70 <option value="CNBr">CNBr</option>
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71 <option value="Lys-C">Lys-C</option>
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72 <option value="Trypsin/P">Trypsin/P</option>
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73 <option value="Asp-N_ambic">Asp-N_ambic</option>
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74 <option value="PepsinA">PepsinA</option>
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75 <option value="proline endopeptidase">proline endopeptidase</option>
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76 <option value="V8-DE">V8-DE</option>
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77 <option value="Arg-C">Arg-C</option>
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78 </param>
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79 <param help="(-motif) " label="the motif for the restricted peptidome" name="param_motif" size="30" type="text" value="M">
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80 <sanitizer>
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81 <valid initial="string.printable">
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82 <remove value="'"/>
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83 <remove value="&quot;"/>
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84 </valid>
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85 </sanitizer>
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86 </param>
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87 <expand macro="advanced_options">
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88 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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89 </expand>
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90 </inputs>
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91 <outputs>
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92 <data format="xml" name="param_out"/>
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93 </outputs>
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94 <help>digests a protein database in-silico
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95
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96
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97 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DigestorMotif.html</help>
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98 </tool>