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annotate ProteinResolver.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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4
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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: [Quantitation]-->
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4 <tool id="ProteinResolver" name="ProteinResolver" version="2.0.0">
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5 <description>protein inference</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">ProteinResolver</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>ProteinResolver
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14
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15 #if $param_fasta:
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16 -fasta $param_fasta
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17 #end if
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18 -in
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19 #for token in $param_in:
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20 $token
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21 #end for
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22 #if $param_in_path:
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23 -in_path &quot;$param_in_path&quot;
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24 #end if
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25 #if $param_design:
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26 -design $param_design
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27 #end if
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28 #if $param_protein_groups:
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29 -protein_groups $param_protein_groups
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30 #end if
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31 #if $param_peptide_table:
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32 -peptide_table $param_peptide_table
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33 #end if
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34 #if $param_protein_table:
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35 -protein_table $param_protein_table
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36 #end if
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37 #if $param_additional_info:
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38 -additional_info $param_additional_info
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39 #end if
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40 -threads \${GALAXY_SLOTS:-24}
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41 #if $param_resolver_missed_cleavages:
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42 -resolver:missed_cleavages $param_resolver_missed_cleavages
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43 #end if
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44 #if $param_resolver_min_length:
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45 -resolver:min_length $param_resolver_min_length
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46 #end if
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47 #if $param_resolver_enzyme:
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48 -resolver:enzyme &quot;$param_resolver_enzyme&quot;
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49 #end if
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50 #if $param_designer_experiment:
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51 -designer:experiment &quot;$param_designer_experiment&quot;
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52 #end if
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53 #if $param_designer_file:
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54 -designer:file &quot;$param_designer_file&quot;
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55 #end if
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56 #if $param_designer_separator:
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57 -designer:separator
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58 #if &quot; &quot; in str($param_designer_separator):
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59 &quot;$param_designer_separator&quot;
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60 #else
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61 $param_designer_separator
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62 #end if
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63 #end if
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64 #if $adv_opts.adv_opts_selector=='advanced':
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65 #if $adv_opts.param_force:
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66 -force
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67 #end if
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68 #end if
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69 </command>
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70 <inputs>
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71 <param format="fasta" help="(-fasta) " label="Input database file" name="param_fasta" optional="False" type="data"/>
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72 <param format="xml,consensusxml" help="(-in) " label="Input file(s) holding experimental data" multiple="true" name="param_in" optional="True" size="30" type="data">
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73 <sanitizer>
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74 <valid initial="string.printable">
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75 <remove value="'"/>
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76 <remove value="&quot;"/>
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77 </valid>
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78 </sanitizer>
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79 </param>
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80 <param help="(-in_path) Ignored if 'in' is given" label="Path to idXMLs or consensusXMLs files" name="param_in_path" size="30" type="text">
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81 <sanitizer>
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82 <valid initial="string.printable">
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83 <remove value="'"/>
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84 <remove value="&quot;"/>
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85 </valid>
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86 </sanitizer>
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87 </param>
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88 <param format="txt" help="(-design) See documentation for specific format requirements" label="Text file containing the experimental design" name="param_design" optional="True" type="data"/>
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89 <param help="(-missed_cleavages) " label="Number of allowed missed cleavages" min="0" name="param_resolver_missed_cleavages" optional="True" type="integer" value="2"/>
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90 <param help="(-min_length) " label="Minimum length of peptide" min="1" name="param_resolver_min_length" optional="True" type="integer" value="6"/>
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91 <param help="(-enzyme) " label="Digestion enzyme" name="param_resolver_enzyme" size="30" type="text" value="Trypsin">
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92 <sanitizer>
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93 <valid initial="string.printable">
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94 <remove value="'"/>
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95 <remove value="&quot;"/>
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96 </valid>
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97 </sanitizer>
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98 </param>
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99 <param help="(-experiment) " label="Identifier for the experimental design" name="param_designer_experiment" size="30" type="text" value="ExperimentalSetting">
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100 <sanitizer>
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101 <valid initial="string.printable">
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102 <remove value="'"/>
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103 <remove value="&quot;"/>
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104 </valid>
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105 </sanitizer>
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106 </param>
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107 <param help="(-file) " label="Identifier for the file name" name="param_designer_file" size="30" type="text" value="File">
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108 <sanitizer>
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109 <valid initial="string.printable">
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110 <remove value="'"/>
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111 <remove value="&quot;"/>
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112 </valid>
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113 </sanitizer>
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114 </param>
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115 <param help="(-separator) " label="Separator, which should be used to split a row into columns" name="param_designer_separator" optional="True" type="select" value="tab">
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116 <option value="tab">tab</option>
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117 <option value="semi-colon">semi-colon</option>
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118 <option value="comma">comma</option>
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119 <option value="whitespace">whitespace</option>
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120 </param>
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121 <expand macro="advanced_options">
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122 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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123 </expand>
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124 </inputs>
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125 <outputs>
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126 <data format="tabular" name="param_protein_groups"/>
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127 <data format="tabular" name="param_peptide_table"/>
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128 <data format="tabular" name="param_protein_table"/>
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129 <data format="tabular" name="param_additional_info"/>
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130 </outputs>
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131 <help>protein inference
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132
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133
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134 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinResolver.html</help>
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135 </tool>