annotate interproscan5/ipsfaux.xml @ 7:1a4c5ab108fc draft

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author mkh
date Fri, 05 Feb 2016 13:08:08 -0500
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1 <tool id="ipsfaux" name="Faux Interproscan" version="1.0.2a">
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2 <description>Interproscan functional predictions of ORFs (faux). Input file and computation options are
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3 ignored (other than the types of outputs). The same precomputed results are produced every time.</description>
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4 <requirements>
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5 <!--
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6 <requirement type="package">signalp</requirement>
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7 <requirement type="package">phobius</requirement>
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8 <requirement type="package">tmhmm</requirement>
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9 -->
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10 <requirement type="set_environment">INTERPROSCAN_SCRIPT_PATH</requirement>
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11 </requirements>
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12
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13 <command>
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14 #import os
3
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15 echo "Start timestamp: \$(date)";
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16 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/fake_ips.py
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17 ## disables the precalculated lookup service, all calculation will be run locally
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18 -dp
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19 --input $infile
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20 --seqtype $seqtype
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21 -f tsv,$output_types
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22 --applications $appl
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23
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24 $pathways
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25 $goterms
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26 $iprlookup
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27 $mode
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28 --output-file-base __base__
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29 2>&#38;1;
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30
3
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31 mv __base__.tsv $tsv_file;
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32
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33 #if 'gff3' in str($output_types):
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34 mv __base__.gff3 $gff3_file;
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35 #end if
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36
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37 #if 'xml' in str($output_types):
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38 mv __base__.xml $xml_file;
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39 #end if
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40
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41 #if 'html' in str($output_types):
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42 mkdir -p $html_file.files_path;
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43 #set temp_archive_file = '__base__.html.tar.gz'
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44 tar -C $html_file.files_path -xvmzf $temp_archive_file;
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45 #if str($seqtype) == 'p' and not str($getorfed):
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46 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 0 $tsv_file $html_file $html_file.files_path;
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47 #else
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48 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 1 $tsv_file $html_file $html_file.files_path;
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49 #end if
0
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50 rm $temp_archive_file;
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51 #end if
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52
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53 #if 'svg' in str($output_types):
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54 mkdir -p $svg_file.files_path;
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55 #set temp_archive_file = '__base__.svg.tar.gz'
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56 tar -C $svg_file.files_path -xvmzf $temp_archive_file;
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57 #if str($seqtype) == 'p' and not str($getorfed):
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58 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 0 $tsv_file $svg_file $svg_file.files_path;
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59 #else
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60 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 1 $tsv_file $svg_file $svg_file.files_path;
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61 #end if
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62 rm $temp_archive_file;
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63 #end if
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64
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65 echo "End timestamp: \$(date)"
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66 </command>
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67
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68 <inputs>
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69 <param name="infile" type="data" format="fasta" label="Sequence Fasta File (ignored -- faux mode)"/>
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70
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71 <param name="seqtype" type="select" label="Type of the input sequences" help="">
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72 <option value="p" selected="true">Protein</option>
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73 <option value="n">DNA / RNA</option>
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74 </param>
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75
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76 <param name="getorfed" type="boolean" label="DNA/RNA was externally processed by getorf?" help="Ignored for DNA inputs."
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77 truevalue="getorfed"
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78 falsevalue=""/>
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79
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80 <param name="mode" type="boolean" label="Run on cluster?" help="Check to submit job to cluster."
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81 truevalue="--mode=cluster --clusterrunid=gtdi-ips-analysis"
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82 falsevalue=""/>
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83
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84 <param name="appl" type="select" multiple="True" display="checkboxes" label="Applications to run"
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85 help="Select your programm.">
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86 <option value="TIGRFAM"
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87 selected="true">TIGRFAM: protein families based on Hidden Markov Models or HMMs</option>
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88 <option value="PIRSF" selected="true">PIRSF: non-overlapping clustering of UniProtKB sequences into a hierarchical order (evolutionary relationships)</option>
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89 <option value="ProDom"
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90 selected="true">ProDom: set of protein domain families generated from the UniProtKB</option>
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91 <option value="Panther"
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92 selected="true">Panther: Protein ANalysis THrough Evolutionary Relationships</option>
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93 <option value="SMART" selected="true">SMART: identification and analysis of domain architectures based on Hidden Markov Models or HMMs</option>
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94 <option value="PrositeProfiles" selected="true">PROSITE Profiles: protein domains, families and functional sites as well as associated profiles to identify them</option>
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95 <option value="PrositePatterns" selected="true">PROSITE Pattern: protein domains, families and functional sites as well as associated patterns to identify them</option>
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96 <option value="HAMAP"
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97 selected="true">HAMAP: High-quality Automated Annotation of Microbial Proteomes</option>
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98 <option value="PfamA" selected="true">PfamA: protein families, each represented by multiple sequence alignments and hidden Markov models</option>
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99 <option value="PRINTS" selected="true">PRINTS: group of conserved motifs (fingerprints) used to characterise a protein family</option>
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100 <option value="SuperFamily"
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101 selected="true">SUPERFAMILY: database of structural and functional annotation</option>
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102 <option value="Coils" selected="true">Coils: Prediction of Coiled Coil Regions in Proteins</option>
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103 <option value="Gene3d" selected="true">Gene3d: Structural assignment for whole genes and genomes using the CATH domain structure database</option>
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104 <option value="SignalP-GRAM_POSITIVE" selected="false">SignalP Gram Positive Bacteria</option>
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105 <option value="SignalP-GRAM_NEGATIVE" selected="false">SignalP Gram Negative Bacteria</option>
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106 <option value="SignalP-EUK" selected="false">SignalP Eukaryotic Bacteria</option>
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107 <option value="Phobius" selected="false">Phobius: combined transmembrane topology and signal peptide predictor</option>
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108 <option value="TMHMM" selected="false">TMHMM: Prediction of transmembrane helices in proteins</option>
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109 </param>
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110
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111 <param name="pathways" truevalue="--pathways" falsevalue="" checked="True" type="boolean"
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112 label="Include pathway information"
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113 help="Option that provides mappings from matches to pathway information, which is based on the matched manually curated InterPro entries. (--pathways)"/>
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114 <param name="goterms" truevalue="--goterms" falsevalue="" checked="True" type="boolean"
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115 label="Include Gene Ontology (GO) mappings"
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116 help="Look up of corresponding Gene Ontology annotation. Implies -iprlookup option. (--goterms)"/>
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117
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118 <param name="iprlookup" truevalue="--iprlookup" falsevalue="" checked="False" type="boolean"
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119 label="Provide additional mappings"
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120 help="Provide mappings from matched member database signatures to the InterPro entries that they are integrated into (--iprlookup)"/>
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121
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122 <param name="output_types" type="select" display="checkboxes" multiple="true" label="Output formats (in addition to TSV)"
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123 help="Select the output formats to generate (at least one)">
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124 <option value="html" selected="true">HTML (Graphical)</option>
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125 <option value="svg" selected="false">SVG (Scalable Vector Graphics)</option>
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126 <option value="gff3" selected="true">GFF3</option>
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127 <option value="xml" selected="false">XML</option>
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128 </param>
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129 </inputs>
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130
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131 <outputs>
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132 <data format="tabular" name="tsv_file" label="Interproscan TSV on ${on_string}"/>
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133 <data format="html" name="html_file" label="Interproscan HTML on ${on_string}">
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134 <filter>'html' in output_types</filter>
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135 </data>
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136 <data format="html" name="svg_file" label="Interproscan SVG on ${on_string}">
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137 <filter>'svg' in output_types</filter>
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138 </data>
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139 <data format="gff3" name="gff3_file" label="Interproscan GFF3 on ${on_string}">
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140 <filter>'gff3' in output_types</filter>
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141 </data>
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142 <data format="xml" name="xml_file" label="Interproscan XML on ${on_string}">
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143 <filter>'xml' in output_types</filter>
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144 </data>
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145 </outputs>
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146
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147 <requirements>
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148 </requirements>
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149
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150 <help>
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151
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152 **What it does**
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153
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154 Interproscan is a batch tool to query the Interpro database. It provides annotations based on multiple searches of profile and other functional databases.
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155
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156
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157 #####
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158 Input
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159 #####
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160
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161 Required is a FASTA file containing protein or nucleotide sequences.
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162
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163
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164 ######
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165 Output
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166 ######
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167
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168 In this version of InterProScan_, you can retrieve output in any of the following five formats:
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169
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170 * TSV: a simple tab-delimited file format
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171 * XML: the new "IMPACT" XML format (XSD available here_).
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172 * GFF: The `GFF 3.0`_ format
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173 * HTML: An HTML representation of the protein matches
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174 * SVG: An Scalable Vector Graphics representation of the protein matches
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175
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176
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177 .. _`GFF 3.0`: http://gmod.org/wiki/GFF#GFF3_Format
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178 .. _here: http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5
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179
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180
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181
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182 Tab-separated values format (TSV)
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183 =================================
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184
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185 Basic tab delimited format.
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186
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187
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188 Example Output
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189 --------------
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190
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191 ::
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192
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193 P51587 14086411a2cdf1c4cba63020e1622579 3418 Pfam PF09103 BRCA2, oligonucleotide/oligosaccharide-binding, domain 1 2670 2799 7.9E-43 T 15-03-2013
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194 P51587 14086411a2cdf1c4cba63020e1622579 3418 ProSiteProfiles PS50138 BRCA2 repeat profile. 1002 1036 0.0 T 18-03-2013 IPR002093 BRCA2 repeat GO:0005515|GO:0006302
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195 P51587 14086411a2cdf1c4cba63020e1622579 3418 Gene3D G3DSA:2.40.50.140 2966 3051 3.1E-52 T 15-03-2013
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196 ...
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197
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198
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199 The TSV format presents the match data in columns as follows:
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200
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201 - Protein Accession (e.g. P51587)
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202 - Sequence MD5 digest (e.g. 14086411a2cdf1c4cba63020e1622579)
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203 - Sequence Length (e.g. 3418)
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204 - Analysis (e.g. Pfam / PRINTS / Gene3D)
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205 - Signature Accession (e.g. PF09103 / G3DSA:2.40.50.140)
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206 - Signature Description (e.g. BRCA2 repeat profile)
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207 - Start location
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208 - Stop location
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209 - Score - is the e-value of the match reported by member database method (e.g. 3.1E-52)
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210 - Status - is the status of the match (T: true)
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211 - Date - is the date of the run
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212 - (InterProScan_ annotations - accession (e.g. IPR002093) - optional column; only displayed if -iprscan option is switched on)
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213 - (InterProScan_ annotations - description (e.g. BRCA2 repeat) - optional column; only displayed if -iprscan option is switched on)
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214 - (GO annotations (e.g. GO:0005515) - optional column; only displayed if --goterms option is switched on)
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215 - (Pathways annotations (e.g. REACT_71) - optional column; only displayed if --pathways option is switched on)
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216
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217
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218 Extensible Markup Language (XML)
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219 ================================
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220
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221 XML representation of the matches - this is the richest form of the data. The XML Schema Definition (XSD) is available [http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5 here].
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222
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223 Example Output
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224 --------------
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225
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226 .. image:: $PATH_TO_IMAGES/example_xml_output.png
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227
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228
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229
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230 Generic Feature Format Version 3 (GFF3)
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231 =======================================
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232
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233 The GFF3 format is a flat tab-delimited file, which is much richer then the TSV output format. It allows you to trace back from matches to predicted proteins and to nucleic acid sequences. It also contains a FASTA format representation of the predicted protein sequences and their matches. You will find a documentation of all the columns and attributes used on [http://www.sequenceontology.org/gff3.shtml].
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234
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235 Example Output
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236 --------------
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237
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238 ::
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239
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240 ##gff-version 3
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241 ##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269
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242 ##sequence-region AACH01000027 1 1347
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243 ##seqid|source|type|start|end|score|strand|phase|attributes
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244 AACH01000027 provided_by_user nucleic_acid 1 1347 . + . Name=AACH01000027;md5=b2a7416cb92565c004becb7510f46840;ID=AACH01000027
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245 AACH01000027 getorf ORF 1 1347 . + . Name=AACH01000027.2_21;Target=pep_AACH01000027_1_1347 1 449;md5=b2a7416cb92565c004becb7510f46840;ID=orf_AACH01000027_1_1347
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246 AACH01000027 getorf polypeptide 1 449 . + . md5=fd0743a673ac69fb6e5c67a48f264dd5;ID=pep_AACH01000027_1_1347
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247 AACH01000027 Pfam protein_match 84 314 1.2E-45 + . Name=PF00696;signature_desc=Amino acid kinase family;Target=null 84 314;status=T;ID=match$8_84_314;Ontology_term="GO:0008652";date=15-04-2013;Dbxref="InterPro:IPR001048","Reactome:REACT_13"
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248 ##sequence-region 2
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249 ...
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250 >pep_AACH01000027_1_1347
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251 LVLLAAFDCIDDTKLVKQIIISEIINSLPNIVNDKYGRKVLLYLLSPRDPAHTVREIIEV
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252 LQKGDGNAHSKKDTEIRRREMKYKRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEA
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253 GHELILVSSGAIAAGFGALGFKKRPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQI
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254 LLTQDDFVDKRRYKNAHQALSVLLNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQ
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255 ADLLVFLTDVDGLYTGNPNSDPRAKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAA
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256 TIATESGVPVYICSSLKSDSMIEAAEETEDGSYFVAQEKGLRTQKQWLAFYAQSQGSIWV
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257 DKGAAEALSQYGKSLLLSGIVEAEGVFSYGDIVTVFDKESGKSLGKGRVQFGASALEDML
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258 RSQKAKGVLIYRDDWISITPEIQLLFTEF
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259 ...
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260 >match$8_84_314
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261 KRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEAGHELILVSSGAIAAGFGALGFKK
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262 RPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQILLTQDDFVDKRRYKNAHQALSVL
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263 LNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQADLLVFLTDVDGLYTGNPNSDPR
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264 AKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAATIATESGVPVYICS
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265
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266
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267 Scalable Vector Graphics (SVG) and HyperText Markup Language (HTML)
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268 ====================================================================
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269
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270 InterProScan_ 5 outputs a single HTML/SVG file for each protein sequence analysed.
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271
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272
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273 Example Output
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274 --------------
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275
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276 .. image:: $PATH_TO_IMAGES/P51587.svg.png
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277
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278 .. _InterProScan: http://www.ebi.ac.uk/interpro
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279
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280
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281 ----------
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282 References
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283 ----------
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284
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285
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286 If you use this Galaxy tool in work leading to a scientific publication please
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287 cite the following papers:
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288
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289 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
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290 Galaxy tools and workflows for sequence analysis with applications
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291 in molecular plant pathology. PeerJ 1:e167
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292 http://dx.doi.org/10.7717/peerj.167
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293
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294 Zdobnov EM, Apweiler R (2001)
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295 InterProScan an integration platform for the signature-recognition methods in InterPro.
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296 Bioinformatics 17, 847-848.
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297 http://dx.doi.org/10.1093/bioinformatics/17.9.847
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298
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299 Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005)
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300 InterProScan: protein domains identifier.
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301 Nucleic Acids Research 33 (Web Server issue), W116-W120.
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302 http://dx.doi.org/10.1093/nar/gki442
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303
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304 Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. (2009)
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305 InterPro: the integrative protein signature database.
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306 Nucleic Acids Research 37 (Database Issue), D224-228.
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307 http://dx.doi.org/10.1093/nar/gkn785
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308
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309
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310 This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at
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311 http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan5
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312
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313
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314 **Galaxy Wrapper Author**::
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315
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316 * Bjoern Gruening, University of Freiburg
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317 * Konrad Paszkiewicz, University of Exeter
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318
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319 </help>
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320 </tool>