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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="ProteinResolver" name="ProteinResolver" version="2.0.0">
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3 <description>protein inference</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">ProteinResolver</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>ProteinResolver
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11
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12 #if $param_fasta:
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13 -fasta $param_fasta
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14 #end if
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15 -in
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16 #for token in $param_in:
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17 $token
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18 #end for
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19 #if $param_in_path:
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20 -in_path "$param_in_path"
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21 #end if
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22 #if $param_design:
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23 -design $param_design
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24 #end if
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25 #if $param_protein_groups:
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26 -protein_groups $param_protein_groups
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27 #end if
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28 #if $param_peptide_table:
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29 -peptide_table $param_peptide_table
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30 #end if
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31 #if $param_protein_table:
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32 -protein_table $param_protein_table
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33 #end if
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34 #if $param_additional_info:
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35 -additional_info $param_additional_info
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36 #end if
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37 -threads \${GALAXY_SLOTS:-24}
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38 #if $param_resolver_missed_cleavages:
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39 -resolver:missed_cleavages $param_resolver_missed_cleavages
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40 #end if
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41 #if $param_resolver_min_length:
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42 -resolver:min_length $param_resolver_min_length
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43 #end if
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44 #if $param_resolver_enzyme:
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45 -resolver:enzyme
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46 #if " " in str($param_resolver_enzyme):
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47 "$param_resolver_enzyme"
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48 #else
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49 $param_resolver_enzyme
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50 #end if
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51 #end if
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52 #if $param_designer_experiment:
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53 -designer:experiment "$param_designer_experiment"
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54 #end if
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55 #if $param_designer_file:
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56 -designer:file "$param_designer_file"
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57 #end if
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58 #if $param_designer_separator:
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59 -designer:separator
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60 #if " " in str($param_designer_separator):
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61 "$param_designer_separator"
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62 #else
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63 $param_designer_separator
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64 #end if
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65 #end if
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66 #if $adv_opts.adv_opts_selector=='advanced':
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67 #if $adv_opts.param_force:
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68 -force
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69 #end if
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70 #end if
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71 </command>
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72 <inputs>
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73 <param name="param_fasta" type="data" format="fasta" optional="False" label="Input database file" help="(-fasta) "/>
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74 <param name="param_in" type="data" format="consensusxml,idxml" multiple="true" optional="True" size="30" label="Input file(s) holding experimental data" help="(-in) ">
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75 <sanitizer>
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76 <valid initial="string.printable">
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77 <remove value="'"/>
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78 <remove value="""/>
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79 </valid>
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80 </sanitizer>
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81 </param>
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82 <param name="param_in_path" type="text" size="30" label="Path to idXMLs or consensusXMLs files" help="(-in_path) Ignored if 'in' is given">
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83 <sanitizer>
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84 <valid initial="string.printable">
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85 <remove value="'"/>
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86 <remove value="""/>
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87 </valid>
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88 </sanitizer>
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89 </param>
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90 <param name="param_design" type="data" format="txt" optional="True" label="Text file containing the experimental design" help="(-design) See documentation for specific format requirements"/>
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91 <param name="param_resolver_missed_cleavages" type="integer" min="0" optional="True" value="2" label="Number of allowed missed cleavages" help="(-missed_cleavages) "/>
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92 <param name="param_resolver_min_length" type="integer" min="1" optional="True" value="6" label="Minimum length of peptide" help="(-min_length) "/>
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93 <param name="param_resolver_enzyme" type="select" optional="True" value="Trypsin" label="Digestion enzyme" help="(-enzyme) ">
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94 <option value="Trypsin">Trypsin</option>
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95 <option value="none">none</option>
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96 </param>
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97 <param name="param_designer_experiment" type="text" size="30" value="ExperimentalSetting" label="Identifier for the experimental design" help="(-experiment) ">
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98 <sanitizer>
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99 <valid initial="string.printable">
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100 <remove value="'"/>
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101 <remove value="""/>
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102 </valid>
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103 </sanitizer>
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104 </param>
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105 <param name="param_designer_file" type="text" size="30" value="File" label="Identifier for the file name" help="(-file) ">
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106 <sanitizer>
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107 <valid initial="string.printable">
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108 <remove value="'"/>
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109 <remove value="""/>
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110 </valid>
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111 </sanitizer>
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112 </param>
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113 <param name="param_designer_separator" type="select" optional="True" value="tab" label="Separator, which should be used to split a row into columns" help="(-separator) ">
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114 <option value="tab">tab</option>
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115 <option value="semi-colon">semi-colon</option>
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116 <option value="comma">comma</option>
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117 <option value="whitespace">whitespace</option>
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118 </param>
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119 <expand macro="advanced_options">
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120 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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121 </expand>
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122 </inputs>
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123 <outputs>
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124 <data name="param_protein_groups" format="tabular"/>
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125 <data name="param_peptide_table" format="tabular"/>
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126 <data name="param_protein_table" format="tabular"/>
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127 <data name="param_additional_info" format="tabular"/>
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128 </outputs>
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129 <help>**What it does**
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130
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131 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 <expand macro="references"/>
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136 </tool>
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