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annotate Digestor.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
parents 3d84209d3178
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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="Digestor" name="Digestor" 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@">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
0
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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 $param_out_type:
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22 -out_type
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23 #if &quot; &quot; in str($param_out_type):
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24 &quot;$param_out_type&quot;
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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 $param_enzyme:
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39 -enzyme
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40 #if &quot; &quot; in str($param_enzyme):
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41 &quot;$param_enzyme&quot;
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42 #else
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43 $param_enzyme
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44 #end if
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45 #end if
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46 -threads \${GALAXY_SLOTS:-24}
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47 #if $adv_opts.adv_opts_selector=='advanced':
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48 #if $adv_opts.param_force:
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49 -force
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50 #end if
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51 #end if
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52 </command>
4
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53 <inputs>
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54 <param format="fasta" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
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55 <param help="(-out_type) e.g., in TOPPAS" label="Set this if you cannot control the filename of 'out'," name="param_out_type" optional="True" type="select">
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56 <option value="idXML">idXML</option>
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57 <option value="fasta">fasta</option>
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58 </param>
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59 <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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60 <param help="(-min_length) " label="Minimum length of peptide" name="param_min_length" type="integer" value="6"/>
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61 <param help="(-max_length) " label="Maximum length of peptide" name="param_max_length" type="integer" value="40"/>
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62 <param help="(-enzyme) " label="The type of digestion enzyme" name="param_enzyme" optional="True" type="select" value="Trypsin">
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63 <option value="no cleavage">no cleavage</option>
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64 <option value="Arg-C">Arg-C</option>
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65 <option value="Lys-C">Lys-C</option>
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66 <option value="PepsinA">PepsinA</option>
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67 <option value="leukocyte elastase">leukocyte elastase</option>
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68 <option value="unspecific cleavage">unspecific cleavage</option>
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69 <option value="V8-DE">V8-DE</option>
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70 <option value="CNBr">CNBr</option>
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71 <option value="Chymotrypsin">Chymotrypsin</option>
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72 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
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73 <option value="Asp-N_ambic">Asp-N_ambic</option>
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74 <option value="2-iodobenzoate">2-iodobenzoate</option>
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75 <option value="proline endopeptidase">proline endopeptidase</option>
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76 <option value="Formic_acid">Formic_acid</option>
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77 <option value="TrypChymo">TrypChymo</option>
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78 <option value="Asp-N">Asp-N</option>
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79 <option value="Trypsin/P">Trypsin/P</option>
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80 <option value="Lys-C/P">Lys-C/P</option>
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81 <option value="V8-E">V8-E</option>
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82 <option value="Trypsin">Trypsin</option>
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83 </param>
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84 <expand macro="advanced_options">
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85 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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86 </expand>
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87 </inputs>
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88 <outputs>
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89 <data format="xml" name="param_out"/>
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90 </outputs>
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91 <help>Digests a protein database in-silico.
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94 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_Digestor.html</help>
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95 </tool>