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1 <tool id="scaffold" name="Scaffold" version="0.1.0">
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2 <description>
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3 Visualize and Validate Complex MS/MS Proteomics Experiments
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4 </description>
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5 <configfiles>
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6 <configfile name="sample_config"># Simple format group:group_name followed by pairs of name:name and path:path lines
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7 #if $sample_mode.mode == "full"
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8 #set $samples = $sample_mode.samples
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9 #for $sample in $samples:
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10 #if $sample.category.specify
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11 #set $category = $sample.category.name
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12 #else
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13 #set $category = $sample.sample_name
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14 #end if
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15 sample:$sample.sample_name
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16 mudpit:$sample.mudpit
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17 category:$category
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18 #for $sample_input in $sample.sample_inputs:
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19 name:${sample_input.display_name}
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20 path:${sample_input}
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21 ext:${sample_input.ext}
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22 #end for
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23 #end for
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24 #elif $sample_mode.mode == "sample_per_file":
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25 #for $sample_input in $sample_mode.sample_inputs:
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26 sample:${sample_input.display_name}
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27 mudpit:false
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28 category:${sample_input.display_name}
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29 name:${sample_input.display_name}
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30 path:${sample_input}
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31 ext:${sample_input.ext}
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32 #end for
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33 #end if
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34 </configfile>
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35 </configfiles>
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36 <command interpreter="python">
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37 scaffold_wrapper.py run \
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38 --samples $sample_config \
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39 --database $database \
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40 --database_name '$database.display_name'\
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41 --output $output \
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42 --database_type $database_type \
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43 --database_decoy_regex '$database_decoy_regex' \
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44 #if $thresholds.specify
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45 --protein_probability '$thresholds.protein_probability' \
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46 --peptide_probability '$thresholds.peptide_probability' \
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47 #end if
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48 #if $advanced.specify
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49 #if $advanced.output_driver
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50 --output_driver $output_drirver \
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51 #end if
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52 #end if
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53 </command>
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54 <inputs>
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55 <param format="fasta" name="database" type="data" label="Search Database" />
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56 <param type="select" name="database_type" label="Database Type">
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57 <option value="GENERIC">Generic</option>
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58 <option value="ESTNR">EST/NR (NCBI)</option>
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59 <option value="IPI">IPI (EBI)</option>
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60 <option value="SWISSPROT">Swiss-Prot (SIB/EBI)</option>
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61 <option value="UNIPROT">UniProt/Swiss-Prot (UniProtKB)</option>
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62 <option value="UNIREF">UniRef/NREF (UniProt)</option>
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63 <option value="ENSEMBL">Ensembl (EMBL/EBI)</option>
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64 <option value="MSDB">MSDB (Proteomics Group)</option>
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65 </param>
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66 <param name="database_decoy_regex" type="text" label="Database Decoy Prefix" help="Regular expression describing decoys in specified FASTA databse." value="REV|RRR">
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67 <sanitizer>
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68 <valid initial="string.printable">
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69 <add value="|"/>
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70 </valid>
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71 </sanitizer>
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72 </param>
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73 <conditional name="sample_mode">
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74 <param name="mode" type="select" label="How should samples be created">
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75 <option value="full">Create Samples Manually</option>
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76 <option value="sample_per_file">Create Sample per File</option>
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77 </param>
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78 <when value="full">
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79 <repeat name="samples" title="Biological Sample">
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80 <param name="sample_name" type="text" label="Sample Name" help="Name for the scample (use only letters and numbers)." />
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81 <param format="t.xml,omx" name="sample_inputs" type="data" multiple="true" label="Sample Input Files" />
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82 <param name="mudpit" type="boolean" label="Mudpit" help="" truevalue="true" falsevalue="false" />
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83 <conditional name="category">
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84 <param name="specify" type="boolean" label="Specify Custom Category" help="" truevalue="true" falsevalue="false" />
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85 <when value="false" />
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86 <when value="true">
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87 <param name="name" type="text" label="Category Name" help="" />
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88 </when>
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89 </conditional>
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90 </repeat>
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91 </when>
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92 <when value="sample_per_file">
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93 <param format="t.xml,omx" name="sample_inputs" type="data" multiple="true" label="Input Files" />
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94 </when>
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95 </conditional>
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96 <conditional name="thresholds">
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97 <param name="specify" type="boolean" label="Specify Reporting Thresholds" help="" truevalue="true" falsevalue="false" />
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98 <when value="false" />
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99 <when value="true">
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100 <param name="protein_probability" type="float" label="Minimum Protein Probility" help="Optional value between 0.0 and 1.0." optional="true" />
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101 <param name="peptide_probability" type="float" label="Minimum Peptide Probility" help="Optional value between 0.0 and 1.0." optional="true" />
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102 </when>
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103 </conditional>
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104 <conditional name="advanced">
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105 <param name="specify" type="boolean" label="Specify Advanced Options" help="" truevalue="true" falsevalue="false" />
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106 <when value="false" />
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107 <when value="true">
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108 <param name="output_driver" type="boolean" label="Include Scaffold Driver File in Output" truevalue="true" falsevalue="false" />
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109 <!--
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110 <param name="ncbi_annotate" type="boolean" label="" truevalue="true" falsevalue="false" />
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111 <param name="go_annotate" type="boolean" label="" truevalue="true" falsevalue="false" />
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112 -->
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113 </when>
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114 </conditional>
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115 </inputs>
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116 <outputs>
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117 <data format="xml" name="output_drirver" label="Scaffold Driver for ${on_string}">
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118 <filter>(advanced['specify'] and advanced["output_driver"])</filter>
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119 </data>
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120 <data format="sf3" name="output" />
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121 </outputs>
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122 <requirements>
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123 <requirement type="package">scaffold</requirement>
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124 </requirements>
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125 <help>
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126 **What it does**
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127
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128 Merges multiple protein identification search results together into a single SF3 file for viewing. A free viewer for Scaffold SF3 files can be obtained from Proteome software at http://www.proteomesoftware.com/Scaffold/Scaffold_viewer.htm.
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129
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130 ------
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131
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132
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133 **Citation**
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134
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135 For the underlying tool, please cite `TODO`
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136
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137 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-scaffold
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138 </help>
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139 </tool> |
