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1 <tool id="interproscan" name="Interproscan functional predictions of ORFs" version="1.2">
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2 <description>Interproscan functional predictions of ORFs</description>
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3 <command>
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4 ## The command is a Cheetah template which allows some Python based syntax.
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5 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
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6
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7 ## create temp directory
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8 #import tempfile, os
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9 #set $tfile = tempfile.mkstemp()[1]
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10
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11 sed 's/ /_/g' $input > $tfile;
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12
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13 ## Hack, because interproscan does not seem to produce gff output even if it is configured
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14 #if str($oformat) == "gff":
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15 #set $tfile2 = tempfile.mkstemp()[1]
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16 iprscan -cli -nocrc -i $tfile -o $tfile2 -goterms -seqtype p -altjobs -format raw -appl $appl 2>&1;
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17 converter.pl -format gff3 -input $tfile2 -output $output;
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18 rm $tfile2;
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19 #else
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20 iprscan -cli -nocrc -i $tfile -o $output -goterms -seqtype p -altjobs -format $oformat -appl $appl 2>&1;
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21 #end if
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22
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23 rm $tfile
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24
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25 </command>
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26 <inputs>
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27 <param name="input" type="data" format="fasta" label="Protein Fasta File"/>
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28
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29 <param name="appl" type="select" format="text" help="Select your programm.">
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30 <label>Applications to run ...</label>
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31 <option value="blastprodom+coils+gene3d+hamap+hmmpanther+hmmpir+hmmpfam+hmmsmart+hmmtigr+fprintscan+patternscan+profilescan+superfamily+seg+signalp+tmhmm" selected="true">all</option>
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32 <option value="seg">seg</option>
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33 <option value="signalp">signalp</option>
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34 <option value="tmhmm">tmhmm</option>
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35 <option value="fprintscan">fprintscan</option>
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36 <option value="patternscan">patternscan</option>
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37 <option value="profilescan">profilescan</option>
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38 <option value="superfamily">superfamily</option>
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39 <option value="hmmpir">hmmpir</option>
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40 <option value="hmmpfam">hmmpfam</option>
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41 <option value="hmmsmart">hmmsmart</option>
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42 <option value="hmmtigr">hmmtigr</option>
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43 <option value="hmmpanther">hmmpanther</option>
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44 <option value="hamap">hamap</option>
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45 <option value="gene3d">gene3d</option>
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46 <option value="coils">coils</option>
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47 <option value="blastprodom">blastprodom</option>
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48 </param>
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49
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50 <param name="oformat" type="select" label="Output format" help="Please select a output format.">
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51 <option value="gff" selected="true">gff</option>
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52 <option value="raw">raw</option>
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53 <option value="txt">txt</option>
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54 <option value="html">html</option>
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55 <option value="xml">xml</option>
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56 <option value="ebixml">EBI header on top of xml</option>
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57 </param>
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58
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59 </inputs>
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60 <outputs>
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61
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62 <data format="txt" name="output" label="Interproscan calculation on ${on_string}">
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63 <change_format>
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64 <when input="oformat" value="html" format="html"/>
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65 <when input="oformat" value="xml" format="xml"/>
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66 <when input="oformat" value="ebixml" format="xml"/>
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67 <when input="oformat" value="gff" format="gff"/>
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68 </change_format>
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69 </data>
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70
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71 </outputs>
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72 <requirements>
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73 </requirements>
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74 <help>
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75 **What it does**
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76
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77 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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78 These include SCOP, CATH, PFAM and SUPERFAMILY.
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79
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80 **Input**
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81
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82 Required is a FASTA file containing ORF predictions. This file must NOT contain any spaces in the FASTA headers - any spaces will be convereted to underscores ``_`` by this tool before running with Interproscan.
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83
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84 **Output**
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85
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86 Example for the raw format.
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87 The output will consist of a tabular file in galaxy with 14 columns and can be easily concatenated or filtered.
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88
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89 ====== ================================================================ ======================================================================
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90 column example description
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91 ====== ================================================================ ======================================================================
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92 c1 NF00181542 the id of the input sequence
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93 c2 27A9BBAC0587AB84 the crc64 (checksum) of the protein sequence (supposed to be unique)
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94 c3 272 the length of the sequence (in AA)
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95 c4 HMMPIR the anaysis method launched.
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96 c5 PIRSF001424 the database members entry for this match
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97 c6 Prephenate dehydratase the database member description for the entry
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98 c7 1 the start of the domain match
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99 c8 270 the end of the domain match
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100 c9 6.5e-141 the evalue of the match (reported by member database method)
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101 c10 T the status of the match (T: true, ?: unknown)
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102 c11 06-Aug-2005 the date of the run.
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103 c12 IPR008237 the corresponding InterPro entry (if iprlookup requested by the user)
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104 c13 Prephenate dehydratase with ACT region the description of the InterPro entry
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105 c14 Molecular Function:prephenate dehydratase activity (GO:0004664) the GO (gene ontology) description for the InterPro entry
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106 ====== ================================================================ ======================================================================
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107
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108 **Database updates**
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109
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110 Typically these take place 2-3 times a year. Please contact your Galaxy administrator to update the databases.
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111
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112 -----
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113 Tools
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114 -----
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115
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116 **PROSITE patterns**::
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117
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118 Some biologically significant amino acid patterns can be summarised in
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119 the form of regular expressions.
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120 ScanRegExp (by Wolfgang.Fleischmann@ebi.ac.uk).
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121
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122 **PROSITE profiles**::
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123
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124 There are a number of protein families as well as functional or
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125 structural domains that cannot be detected using patterns due to their extreme
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126 sequence divergence, so the use of techniques based on weight matrices
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127 (also known as profiles) allows the detection of such proteins or domains.
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128 A profile is a table of position-specific amino acid weights and gap costs.
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129 The profile structure used in PROSITE is similar to but slightly more general
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130 (Bucher P. et al., 1996) than the one introduced by M. Gribskov and
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131 co-workers.
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132 pfscan from the Pftools package (by Philipp.Bucher@isrec.unil.ch).
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133
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134 **PRINTS**::
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135
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136 The PRINTS database houses a collection of protein family fingerprints.
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137 These are groups of motifs that together are diagnostically more
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138 powerful than single motifs by making use of the biological context inherent in a
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139 multiple-motif method. The fingerprinting method arose from the need for
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140 a reliable technique for detecting members of large, highly divergent
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141 protein super-families.
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142 FingerPRINTScan (Scordis P. et al., 1999).
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143
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144 **PFAM**::
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145
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146 Pfam is a database of protein domain families. Pfam contains curated
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147 multiple sequence alignments for each family and corresponding hidden
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148 Markov models (HMMs) (Eddy S.R., 1998).
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149 Profile hidden Markov models are statistical models of the primary
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150 structure consensus of a sequence family. The construction and use
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151 of Pfam is tightly tied to the HMMER software package.
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152 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
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153 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
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154
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155 **PRODOM**::
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156
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157 ProDom is a database of protein domain families obtained by automated
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158 analysis of the SWISS-PROT and TrEMBL protein sequences. It is useful
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159 for analysing the domain arrangements of complex protein families and the
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160 homology relationships in modular proteins. ProDom families are built by
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161 an automated process based on a recursive use of PSI-BLAST homology
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162 searches.
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163 ProDomBlast3i.pl (by Emmanuel Courcelle emmanuel.courcelle@toulouse.inra.fr
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164 and Yoann Beausse beausse@toulouse.inra.fr)
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165 a wrapper on top of the Blast package (Altschul S.F. et al., 1997).
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166
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167 **SMART**::
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168
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169 SMART (a Simple Modular Architecture Research Tool) allows the
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170 identification and annotation of genetically mobile domains and the
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171 analysis of domain architectures. These domains are extensively
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172 annotated with respect to phyletic distributions, functional class, tertiary
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173 structures and functionally important residues. SMART alignments are
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174 optimised manually and following construction of corresponding hidden Markov models (HMMs).
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175 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
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176 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
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177
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178 **TIGRFAMs**::
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179
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180 TIGRFAMs are a collection of protein families featuring curated multiple
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181 sequence alignments, Hidden Markov Models (HMMs) and associated
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182 information designed to support the automated functional identification
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183 of proteins by sequence homology. Classification by equivalog family
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184 (see below), where achievable, complements classification by orthologs,
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185 superfamily, domain or motif. It provides the information best suited
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186 for automatic assignment of specific functions to proteins from large
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187 scale genome sequencing projects.
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188 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
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189 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
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190
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191 **PIR SuperFamily**::
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192
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193 PIR SuperFamily (PIRSF) is a classification system based on evolutionary
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194 relationship of whole proteins.
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195 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
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196 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
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197
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198 **SUPERFAMILY**::
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199
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200 SUPERFAMILY is a library of profile hidden Markov models that represent
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201 all proteins of known structure, based on SCOP.
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202 hmmpfam/hmmsearch from the HMMER2.3.2 package (by Sean Eddy,
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203 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
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204 Optionally, predictions for coiled-coil, signal peptide cleavage sites
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205 (SignalP v3) and TM helices (TMHMM v2) are supported (See the FAQs file
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206 for details).
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207
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208 **GENE3D**::
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209
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210 Gene3D is supplementary to the CATH database. This protein sequence database
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211 contains proteins from complete genomes which have been clustered into protein
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212 families and annotated with CATH domains, Pfam domains and functional
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213 information from KEGG, GO, COG, Affymetrix and STRINGS.
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214 hmmpfam from the HMM2.3.2 package (by Sean Eddy,
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215 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
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216
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217 **PANTHER**::
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218
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219 The PANTHER (Protein ANalysis THrough Evolutionary Relationships)
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220 Classification System was designed to classify proteins (and their genes)
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221 in order to facilitate high-throughput analysis.
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222 hmmsearch from the HMM2.3.2 package (by Sean Eddy,
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223 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
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224 and blastall from the Blast package (Altschul S.F. et al., 1997).
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225
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226 ----------
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227 References
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228 ----------
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229
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230 Zdobnov EM, Apweiler R (2001)
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231 InterProScan an integration platform for the signature-recognition methods in InterPro.
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232 Bioinformatics 17, 847-848.
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233 http://dx.doi.org/10.1093/bioinformatics/17.9.847
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234
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235 Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005)
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236 InterProScan: protein domains identifier.
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237 Nucleic Acids Research 33 (Web Server issue), W116-W120.
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238 http://dx.doi.org/10.1093/nar/gki442
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239
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240 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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241 InterPro: the integrative protein signature database.
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242 Nucleic Acids Research 37 (Database Issue), D224-228.
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243 http://dx.doi.org/10.1093/nar/gkn785
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244
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245
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246 Galaxy Wrapper Author:
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247
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248 * Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
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249 * Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter
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250
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251 </help>
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252 </tool>
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