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1 <tool id="interproscan" name="Interproscan functional predictions of ORFs" version="5.0.0">
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2 <description>Interproscan functional predictions of ORFs</description>
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3 <requirements>
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4 <requirement type="package">signalp</requirement>
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5 <requirement type="package">phobius</requirement>
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6 <requirement type="package">tmhmm</requirement>
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7 <requirement type="set_environment">INTERPROSCAN_SCRIPT_PATH</requirement>
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8 </requirements>
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9 <command>
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10
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11 #import os
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12 interproscan.sh
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13 ## disables the precalculated lookup service, all calculation will be run locally
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14 -dp
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15 --input $infile
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16 --seqtype $seqtype
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17 -f $oformat
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18 --applications $appl
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19 --tempdir \$TEMP
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20
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21 $pathways
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22 $goterms
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23 $iprlookup
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24
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25 #if str($oformat) in ['SVG', 'HTML']:
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26 --output-file-base $outfile
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27 2>&1;
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28 mkdir -p $outfile.files_path;
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29 #set temp_archive_file = str($outfile) + '.' + str($oformat).lower() + '.tar.gz'
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30 tar -C $outfile.files_path -xvmzf $temp_archive_file;
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31 python \$INTERPROSCAN_SCRIPT_PATH/create_index.py $outfile $outfile.files_path;
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32 rm $temp_archive_file
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33 #else:
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34 -o $outfile
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35 2>&1
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36 #end if
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37
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38 </command>
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39 <inputs>
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40 <param name="infile" type="data" format="fasta" label="Protein Fasta File"/>
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41
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42 <param name="seqtype" type="select" label="Type of the input sequences" help="">
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43 <option value="p" selected="true">Protein</option>
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44 <option value="n">DNA / RNA</option>
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45 </param>
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46
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47 <param name="appl" type="select" multiple="True" display="checkboxes" label="Applications to run" help="Select your programm.">
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48 <option value="TIGRFAM" selected="true">TIGRFAM: protein families based on Hidden Markov Models or HMMs</option>
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49 <option value="PIRSF" selected="true">PIRSF: non-overlapping clustering of UniProtKB sequences into a hierarchical order (evolutionary relationships)</option>
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50 <option value="ProDom" selected="true">ProDom: set of protein domain families generated from the UniProtKB</option>
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51 <option value="Panther" selected="true">Panther: Protein ANalysis THrough Evolutionary Relationships</option>
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52 <option value="SMART" selected="true">SMART: identification and analysis of domain architectures based on Hidden Markov Models or HMMs</option>
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53 <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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54 <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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55 <option value="HAMAP" selected="true">HAMAP: High-quality Automated Annotation of Microbial Proteomes</option>
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56 <option value="PfamA" selected="true">PfamA: protein families, each represented by multiple sequence alignments and hidden Markov models</option>
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57 <option value="PRINTS" selected="true">PRINTS: group of conserved motifs (fingerprints) used to characterise a protein family</option>
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58 <option value="SuperFamily" selected="true">SUPERFAMILY: database of structural and functional annotation</option>
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59 <option value="Coils" selected="true">Coils: Prediction of Coiled Coil Regions in Proteins</option>
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60 <option value="Gene3d" selected="true">Gene3d: Structural assignment for whole genes and genomes using the CATH domain structure database</option>
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61 <option value="SignalP-GRAM_POSITIVE" selected="false">SignalP Gram Positive Bacteria</option>
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62 <option value="SignalP-GRAM_NEGATIVE" selected="false">SignalP Gram Negative Bacteria</option>
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63 <option value="SignalP-EUK" selected="true">SignalP Eukaryotic Bacteria</option>
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64 <option value="Phobius" selected="true">Phobius: combined transmembrane topology and signal peptide predictor</option>
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65 <option value="TMHMM" selected="true">TMHMM: Prediction of transmembrane helices in proteins</option>
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66 </param>
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67
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68 <param name="pathways" truevalue="--pathways" falsevalue="" checked="True" type="boolean" label="Include pathway information"
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69 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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70 <param name="goterms" truevalue="--goterms" falsevalue="" checked="True" type="boolean" label="Include Gene Ontology (GO) mappings"
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71 help="Look up of corresponding Gene Ontology annotation. Implies -iprlookup option. (--goterms)"/>
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72 <param name="iprlookup" truevalue="--iprlookup" falsevalue="" checked="False" type="boolean"
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73 label="Provide additional mappings" help="Provide mappings from matched member database signatures to the InterPro entries that they are integrated into (--iprlookup)"/>
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74
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75 <param name="oformat" type="select" label="Output format" help="Please select a output format.">
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76 <option value="TSV" selected="true">Tab-separated values format (TSV)</option>
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77 <option value="GFF3">GFF3</option>
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78 <option value="SVG">SVG</option>
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79 <option value="HTML">HTML</option>
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80 <option value="XML">XML</option>
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81 </param>
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82
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83 </inputs>
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84 <outputs>
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85
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86 <data format="tabular" name="outfile" label="Interproscan calculation on ${on_string}">
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87 <change_format>
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88 <when input="oformat" value="HTML" format="html"/>
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89 <when input="oformat" value="XML" format="xml"/>
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90 <when input="oformat" value="SVG" format="html"/>
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91 <when input="oformat" value="GFF3" format="gff"/>
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92 </change_format>
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93 </data>
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94
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95 </outputs>
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96 <requirements>
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97 </requirements>
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98 <help>
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99
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100 **What it does**
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101
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102 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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103
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104
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105 #####
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106 Input
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107 #####
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108
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109 Required is a FASTA file containing protein or nucleotide sequences.
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110
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111
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112 ######
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113 Output
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114 ######
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115
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116 In this version of InterProScan_, you can retrieve output in any of the following five formats:
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117
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118 * TSV: a simple tab-delimited file format
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119 * XML: the new "IMPACT" XML format (XSD available here_).
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120 * GFF: The `GFF 3.0`_ format
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121 * HTML: An HTML representation of the protein matches
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122 * SVG: An Scalable Vector Graphics representation of the protein matches
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123
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124
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125 .. _`GFF 3.0`: http://gmod.org/wiki/GFF#GFF3_Format
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126 .. _here: http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5
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127
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128
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129
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130 Tab-separated values format (TSV)
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131 =================================
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132
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133 Basic tab delimited format.
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134
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135
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136 Example Output
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137 --------------
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138
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139 ::
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140
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141 P51587 14086411a2cdf1c4cba63020e1622579 3418 Pfam PF09103 BRCA2, oligonucleotide/oligosaccharide-binding, domain 1 2670 2799 7.9E-43 T 15-03-2013
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142 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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143 P51587 14086411a2cdf1c4cba63020e1622579 3418 Gene3D G3DSA:2.40.50.140 2966 3051 3.1E-52 T 15-03-2013
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144 ...
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145
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146
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147 The TSV format presents the match data in columns as follows:
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148
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149 - Protein Accession (e.g. P51587)
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150 - Sequence MD5 digest (e.g. 14086411a2cdf1c4cba63020e1622579)
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151 - Sequence Length (e.g. 3418)
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152 - Analysis (e.g. Pfam / PRINTS / Gene3D)
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153 - Signature Accession (e.g. PF09103 / G3DSA:2.40.50.140)
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154 - Signature Description (e.g. BRCA2 repeat profile)
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155 - Start location
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156 - Stop location
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157 - Score - is the e-value of the match reported by member database method (e.g. 3.1E-52)
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158 - Status - is the status of the match (T: true)
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159 - Date - is the date of the run
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160 - (InterProScan_ annotations - accession (e.g. IPR002093) - optional column; only displayed if -iprscan option is switched on)
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161 - (InterProScan_ annotations - description (e.g. BRCA2 repeat) - optional column; only displayed if -iprscan option is switched on)
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162 - (GO annotations (e.g. GO:0005515) - optional column; only displayed if --goterms option is switched on)
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163 - (Pathways annotations (e.g. REACT_71) - optional column; only displayed if --pathways option is switched on)
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164
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165
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166 Extensible Markup Language (XML)
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167 ================================
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168
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169 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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170
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171 Example Output
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172 --------------
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173
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174 .. image:: $PATH_TO_IMAGES/example_xml_output.png
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175
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176
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177
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178 Generic Feature Format Version 3 (GFF3)
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179 =======================================
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180
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181 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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182
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183 Example Output
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184 --------------
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185
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186 ::
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187
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188 ##gff-version 3
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189 ##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269
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190 ##sequence-region AACH01000027 1 1347
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191 ##seqid|source|type|start|end|score|strand|phase|attributes
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192 AACH01000027 provided_by_user nucleic_acid 1 1347 . + . Name=AACH01000027;md5=b2a7416cb92565c004becb7510f46840;ID=AACH01000027
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193 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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194 AACH01000027 getorf polypeptide 1 449 . + . md5=fd0743a673ac69fb6e5c67a48f264dd5;ID=pep_AACH01000027_1_1347
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195 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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196 ##sequence-region 2
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197 ...
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198 >pep_AACH01000027_1_1347
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199 LVLLAAFDCIDDTKLVKQIIISEIINSLPNIVNDKYGRKVLLYLLSPRDPAHTVREIIEV
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200 LQKGDGNAHSKKDTEIRRREMKYKRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEA
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201 GHELILVSSGAIAAGFGALGFKKRPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQI
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202 LLTQDDFVDKRRYKNAHQALSVLLNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQ
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203 ADLLVFLTDVDGLYTGNPNSDPRAKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAA
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204 TIATESGVPVYICSSLKSDSMIEAAEETEDGSYFVAQEKGLRTQKQWLAFYAQSQGSIWV
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205 DKGAAEALSQYGKSLLLSGIVEAEGVFSYGDIVTVFDKESGKSLGKGRVQFGASALEDML
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206 RSQKAKGVLIYRDDWISITPEIQLLFTEF
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207 ...
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208 >match$8_84_314
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209 KRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEAGHELILVSSGAIAAGFGALGFKK
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210 RPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQILLTQDDFVDKRRYKNAHQALSVL
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211 LNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQADLLVFLTDVDGLYTGNPNSDPR
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212 AKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAATIATESGVPVYICS
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213
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214
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215 Scalable Vector Graphics (SVG) and HyperText Markup Language (HTML)
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216 ====================================================================
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217
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218 InterProScan_ 5 outputs a single HTML/SVG file for each protein sequence analysed.
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219
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220
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221 Example Output
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222 --------------
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223
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224 .. image:: $PATH_TO_IMAGES/P51587.svg.png
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225
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226 .. _InterProScan: http://www.ebi.ac.uk/interpro
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227
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228
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229 ----------
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230 References
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231 ----------
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232
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233
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234 If you use this Galaxy tool in work leading to a scientific publication please
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235 cite the following papers:
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236
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237 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
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238 Galaxy tools and workflows for sequence analysis with applications
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239 in molecular plant pathology. PeerJ 1:e167
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240 http://dx.doi.org/10.7717/peerj.167
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241
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242 Zdobnov EM, Apweiler R (2001)
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243 InterProScan an integration platform for the signature-recognition methods in InterPro.
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244 Bioinformatics 17, 847-848.
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245 http://dx.doi.org/10.1093/bioinformatics/17.9.847
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246
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247 Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005)
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248 InterProScan: protein domains identifier.
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249 Nucleic Acids Research 33 (Web Server issue), W116-W120.
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250 http://dx.doi.org/10.1093/nar/gki442
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251
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252 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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253 InterPro: the integrative protein signature database.
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254 Nucleic Acids Research 37 (Database Issue), D224-228.
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255 http://dx.doi.org/10.1093/nar/gkn785
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256
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257
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258 This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at
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259 http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan5
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260
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261
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262 **Galaxy Wrapper Author**::
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263
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264 * Bjoern Gruening, University of Freiburg
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265 * Konrad Paszkiewicz, University of Exeter
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266
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267 </help>
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268 </tool>
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