Mercurial > repos > bgruening > interproscan

annotate interproscan.xml @ 12:74810db257cc draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 01e8e726d711c0685f46d3146e4fe0f2a1306036
author iuc
date Wed, 07 Dec 2022 13:41:49 +0000
parents 98cafcbd2578
children
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fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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1 <tool id="interproscan" name="InterProScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">
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2 <description>functional annotation</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <xrefs>
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7 <xref type="bio.tools">interproscan_ebi</xref>
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8 </xrefs>
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9 <requirements>
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10 <requirement type="package" version="@TOOL_VERSION@">interproscan</requirement>
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11 </requirements>
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12 <version_command>interproscan.sh --version</version_command>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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13 <command><![CDATA[
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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14 ## Adapt properties file to use data from data table
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15 mkdir -p \$HOME/.interproscan-5
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16 &&
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17 sed 's|^\(data.directory=\).*$|\1${database.fields.path}/data|' \$(dirname \$(readlink -f \$(command -v interproscan.sh)))/interproscan.properties > \$HOME/.interproscan-5/interproscan.properties
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18 &&
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19 ## Java doesn't read the HOME env var
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20 export _JAVA_OPTIONS=-Duser.home=\$HOME
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21 &&
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23 ## Now run interproscan
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24 interproscan.sh
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25
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26 ## disables the precalculated lookup service, all calculation will be run locally
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27 -dp
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28 --input '$input'
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29 --seqtype $seqtype
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30 -f ${','.join($oformat)}
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32 #if $licensed.use == 'true' and $licensed.applications_licensed:
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33 --applications ${','.join($applications)},${','.join($licensed.applications_licensed)}
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34 #else:
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35 --applications ${','.join($applications)}
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36 #end if
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37 --tempdir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
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39 $pathways
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40 $goterms
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41 $iprlookup
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43 --cpu \${GALAXY_SLOTS:-4}
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45 --output-file-base 'output'
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46 ]]></command>
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47 <inputs>
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48 <param argument="--input" type="data" format="fasta" label="Protein FASTA File"/>
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49
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50 <param argument="--seqtype" type="select" label="Type of the input sequences" help="">
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51 <option value="p" selected="true">Protein</option>
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52 <option value="n">DNA / RNA</option>
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53 </param>
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55 <param name="database" label="InterProScan database" type="select">
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56 <options from_data_table="interproscan">
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57 <column name="value" index="0" />
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58 <column name="name" index="1" />
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59 <column name="path" index="3" />
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60 <filter type="sort_by" column="0" />
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61 <filter type="static_value" column="2" value="@TOOL_VERSION@" />
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62 </options>
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63 </param>
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64
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65 <param name="applications" type="select" multiple="True" label="Applications to run" help="Select your program">
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66 <option value="TIGRFAM" selected="true">TIGRFAM: protein families based on hidden Markov models (HMMs)</option>
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67 <option value="FunFam" selected="true">FunFam: Prediction of functional annotations for novel, uncharacterized sequences.</option>
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68 <option value="SFLD" selected="true">SFLD: a database of protein families based on hidden Markov models (HMMs)</option>
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69 <option value="SUPERFAMILY" selected="true">SUPERFAMILY: database of structural and functional annotation for all proteins and genomes</option>
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70 <option value="PANTHER" selected="true">PANTHER: Protein ANalysis THrough Evolutionary Relationships</option>
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71 <option value="Gene3D" selected="true">Gene3d: Structural assignment for whole genes and genomes using the CATH domain structure database</option>
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72 <option value="Hamap" selected="true">HAMAP: High-quality Automated Annotation of Microbial Proteomes</option>
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73 <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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74 <option value="Coils" selected="true">Coils: Prediction of Coiled Coil Regions in Proteins</option>
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75 <option value="SMART" selected="true">SMART: identification and analysis of domain architectures based on Hidden Markov Models or HMMs</option>
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76 <option value="CDD" selected="true">SMART: protein domains and families based on well-annotated multiple sequence alignment models</option>
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77 <option value="PRINTS" selected="true">PRINTS: group of conserved motifs (fingerprints) used to characterise a protein family</option>
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78 <option value="PIRSR" selected="true">PIRSR: protein families based on hidden Markov models (HMMs) and Site Rules</option>
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79 <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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80 <option value="AntiFam" selected="true">AntiFam: a resource of profile-HMMs designed to identify spurious protein predictions.</option>
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81 <option value="Pfam" selected="true">Pfam: protein families, each represented by multiple sequence alignments and hidden Markov models</option>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
82 <option value="MobiDBLite" selected="true">MobiDBLite: Prediction of intrinsically disordered regions in proteins</option>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
83 <option value="PIRSF" selected="true">PIRSF: non-overlapping clustering of UniProtKB sequences into a hierarchical order (evolutionary relationships)</option>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
84 </param>
0
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parents:
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85
4
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
86 <conditional name="licensed">
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
87 <param name="use" type="select" label="Use applications with restricted license, only for non-commercial use?" help="The corresponding tools must be installed manually by the administrator of this Galaxy instance" >
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
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88 <option value="false" selected="true">No</option>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
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89 <option value="true">Yes</option>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
90 </param>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
91 <when value="false" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
92 <when value="true">
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
93 <param name="applications_licensed" type="select" multiple="True" label="Applications to run" help="Select your programm.">
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
94 <option value="Phobius" selected="true">Phobius: combined transmembrane topology and signal peptide predictor</option>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
95 <option value="SignalP_GRAM_NEGATIVE" selected="false">SignalP (gram-negative): signal peptide cleavage sites in amino acid sequences for gram-negative prokaryotes</option>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
96 <option value="SignalP_EUK" selected="true">SignalP (eukaryotes): signal peptide cleavage sites in amino acid sequences for eukaryotes</option>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
97 <option value="SignalP_GRAM_POSITIVE" selected="false">SignalP (Gram Positive Bacteria): signal peptide cleavage sites in amino acid sequences for gram-positive prokaryotes</option>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
98 <option value="TMHMM" selected="true">TMHMM: Prediction of transmembrane helices in proteins</option>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
99 </param>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
100 </when>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
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101 </conditional>
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102
4
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
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103 <param argument="--pathways" truevalue="--pathways" falsevalue="" checked="True" type="boolean" label="Include pathway information"
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
104 help="Option that provides mappings from matches to pathway information, which is based on the matched manually curated InterPro entries."/>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
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105 <param argument="--goterms" truevalue="--goterms" falsevalue="" checked="True" type="boolean" label="Include Gene Ontology (GO) mappings"
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
106 help="Look up of corresponding Gene Ontology annotation. Implies -iprlookup option."/>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
107 <param argument="--iprlookup" truevalue="--iprlookup" falsevalue="" checked="False" type="boolean"
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
108 label="Provide additional mappings" help="Provide mappings from matched member database signatures to the InterPro entries that they are integrated into"/>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
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109
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
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110 <param name="oformat" type="select" multiple="true" label="Output format" help="Please select a output format (JSON output can be visualised on https://www.ebi.ac.uk/interpro/result/InterProScan/).">
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
111 <option value="TSV" selected="true">Tab-separated values format (TSV)</option>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
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112 <option value="GFF3">GFF3</option>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
113 <option value="XML">XML</option>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
114 <option value="JSON">JSON</option>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
115 </param>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
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116 </inputs>
0
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117
4
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iuc
parents: 2
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118 <outputs>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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parents: 2
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119 <data format="tabular" name="outfile_tsv" from_work_dir="output.tsv" label="InterProScan on ${on_string} (tsv)">
6
0cd163d805e3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 959550b5431b15acf3609f536efc864fd0845b3c"
iuc
parents: 5
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120 <filter>oformat and 'TSV' in oformat</filter>
4
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
121 </data>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
122 <data format="xml" name="outfile_xml" from_work_dir="output.xml" label="InterProScan on ${on_string} (xml)">
6
0cd163d805e3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 959550b5431b15acf3609f536efc864fd0845b3c"
iuc
parents: 5
diff changeset
123 <filter>oformat and 'XML' in oformat</filter>
4
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
124 </data>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
125 <data format="gff3" name="outfile_gff3" from_work_dir="output.gff3" label="InterProScan on ${on_string} (gff3)">
6
0cd163d805e3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 959550b5431b15acf3609f536efc864fd0845b3c"
iuc
parents: 5
diff changeset
126 <filter>oformat and 'GFF3' in oformat</filter>
4
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
127 </data>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
128 <data format="json" name="outfile_json" from_work_dir="output.json" label="InterProScan on ${on_string} (json)">
6
0cd163d805e3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 959550b5431b15acf3609f536efc864fd0845b3c"
iuc
parents: 5
diff changeset
129 <filter>oformat and 'JSON' in oformat</filter>
4
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
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130 </data>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
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131 </outputs>
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132
4
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iuc
parents: 2
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133 <tests>
6
0cd163d805e3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 959550b5431b15acf3609f536efc864fd0845b3c"
iuc
parents: 5
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134 <test expect_num_outputs="1">
4
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
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135 <param name="input" value="prots.fa" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
136 <param name="seqtype" value="p" />
7
1207025b9b9c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 3e5aef1ff8f33003ae2314b8df52c4f4187c37ef"
iuc
parents: 6
diff changeset
137 <param name="database" value="@TOOL_VERSION@" />
4
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
138 <param name="applications" value="MobiDBLite" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
139 <param name="oformat" value="TSV" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
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140 <output name="outfile_tsv">
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
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141 <assert_contents>
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iuc
parents: 2
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142 <has_text text="FUN_000011-T1" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
143 <has_text text="ea9924e11f7decc417e8d9ed8b9c682e" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
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144 <has_text text="FUN_000012-T1" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
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145 <has_text text="01beedc2fbf8012cba37f0c0d39aa071" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
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146 </assert_contents>
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iuc
parents: 2
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147 </output>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
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148 </test>
6
0cd163d805e3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 959550b5431b15acf3609f536efc864fd0845b3c"
iuc
parents: 5
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149 <test expect_num_outputs="4">
4
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
150 <param name="input" value="prots.fa" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
151 <param name="seqtype" value="p" />
7
1207025b9b9c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 3e5aef1ff8f33003ae2314b8df52c4f4187c37ef"
iuc
parents: 6
diff changeset
152 <param name="database" value="@TOOL_VERSION@" />
4
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
153 <param name="applications" value="MobiDBLite" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
154 <param name="oformat" value="TSV,GFF3,XML,JSON" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
155 <output name="outfile_tsv">
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
156 <assert_contents>
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iuc
parents: 2
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157 <has_text text="FUN_000011-T1" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
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158 <has_text text="ea9924e11f7decc417e8d9ed8b9c682e" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
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159 <has_text text="FUN_000012-T1" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
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160 <has_text text="01beedc2fbf8012cba37f0c0d39aa071" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
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161 </assert_contents>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
162 </output>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
163 <output name="outfile_xml">
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
164 <assert_contents>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
165 <has_text text="mobidblite-location" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
166 <has_text text="Polyampholyte" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
167 <has_text text="consensus disorder prediction" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
168 <has_text text="FUN_000011-T1 FUN_000011" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
169 </assert_contents>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
170 </output>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
171 <output name="outfile_gff3">
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
172 <assert_contents>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
173 <has_text text="protein_match" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
174 <has_text text="ID=FUN_000011-T1;md5=" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
175 <has_text text="MobiDBLite" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
176 </assert_contents>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
177 </output>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
178 <output name="outfile_json">
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
179 <assert_contents>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
180 <has_text text="signatureLibraryRelease" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
181 <has_text text="disorder_prediction" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
182 <has_text text="Polyampholyte" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
183 </assert_contents>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
184 </output>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
185 </test>
6
0cd163d805e3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 959550b5431b15acf3609f536efc864fd0845b3c"
iuc
parents: 5
diff changeset
186 <test expect_num_outputs="4">
4
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
187 <param name="input" value="transcripts.fa" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
188 <param name="seqtype" value="n" />
7
1207025b9b9c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 3e5aef1ff8f33003ae2314b8df52c4f4187c37ef"
iuc
parents: 6
diff changeset
189 <param name="database" value="@TOOL_VERSION@" />
4
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
190 <param name="applications" value="MobiDBLite" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
191 <param name="oformat" value="TSV,GFF3,XML,JSON" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
192 <output name="outfile_tsv">
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
193 <assert_contents>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
194 <has_text text="FUN_000018-T1_orf336" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
195 <has_text text="0b28fe115d4cc09260b038b19fb0b21d" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
196 <has_text text="FUN_000012-T1_orf133" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
197 <has_text text="01beedc2fbf8012cba37f0c0d39aa071" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
198 </assert_contents>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
199 </output>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
200 <output name="outfile_xml">
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
201 <assert_contents>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
202 <has_text text="mobidblite-location" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
203 <has_text text="Polyampholyte" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
204 <has_text text="consensus disorder prediction" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
205 <has_text text="orf355" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
206 </assert_contents>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
207 </output>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
208 <output name="outfile_gff3">
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
209 <assert_contents>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
210 <has_text text="protein_match" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
211 <has_text text="ID=FUN_000012-T1;" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
212 <has_text text="MobiDBLite" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
213 </assert_contents>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
214 </output>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
215 <output name="outfile_json">
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
216 <assert_contents>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
217 <has_text text="signatureLibraryRelease" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
218 <has_text text="disorder_prediction" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
219 <has_text text="Polyampholyte" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
220 </assert_contents>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
221 </output>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
222 </test>
6
0cd163d805e3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 959550b5431b15acf3609f536efc864fd0845b3c"
iuc
parents: 5
diff changeset
223 <test expect_failure="true" expect_num_outputs="1">
4
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
224 <param name="input" value="prots.fa" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
225 <param name="seqtype" value="p" />
7
1207025b9b9c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 3e5aef1ff8f33003ae2314b8df52c4f4187c37ef"
iuc
parents: 6
diff changeset
226 <param name="database" value="@TOOL_VERSION@" />
4
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
227 <param name="applications" value="MobiDBLite" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
228 <conditional name="licensed">
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
229 <param name="use" value="true" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
230 <param name="applications_licensed" value="Phobius,TMHMM" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
231 </conditional>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
232 <param name="oformat" value="TSV" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
233 <assert_stdout>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
234 <!-- expected to be "deactivated" as they are not installed by default -->
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
235 <has_text text="Analysis Phobius does not exist or is deactivated" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
236 <has_text text="Analysis TMHMM does not exist or is deactivated" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
237 </assert_stdout>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
238 </test>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
239 </tests>
0
c10e37cca7e3 Uploaded
bgruening
parents:
diff changeset
240
4
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
241 <help><![CDATA[
0
c10e37cca7e3 Uploaded
bgruening
parents:
diff changeset
242
c10e37cca7e3 Uploaded
bgruening
parents:
diff changeset
243 **What it does**
c10e37cca7e3 Uploaded
bgruening
parents:
diff changeset
244
4
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
245 Interproscan is a batch tool to query the InterPro database. It provides annotations based on multiple searches of profile and other functional databases.
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
246
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
247 Phobius (licensed software), SignalP, SMART (licensed components) and TMHMM use
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
248 licensed code and data provided by third parties. If you wish to run these
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
249 analyses it will be necessary for you to obtain a licence from the vendor and
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250 configure the Galaxy server InterProScan installation to use them.
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251
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252 **Input**
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253
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254 Required is a FASTA file containing protein or nucleotide sequences.
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255
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256 **Output**
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257
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258 In this version of InterProScan, you can retrieve output in any of the following five formats:
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259
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260 * TSV: tab-separated values format
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261 * XML: XML format
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262 * GFF: The GFF 3.0 format
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263 * JSON: A JSON representation of the protein matches that can be visualised on https://www.ebi.ac.uk/interpro/result/InterProScan/
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264
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265 **Example Output**
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266
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267
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268 ::
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269
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270 P51587 14086411a2cdf1c4cba63020e1622579 3418 Pfam PF09103 BRCA2, oligonucleotide/oligosaccharide-binding, domain 1 2670 2799 7.9E-43 T 15-03-2013
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271 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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272 P51587 14086411a2cdf1c4cba63020e1622579 3418 Gene3D G3DSA:2.40.50.140 2966 3051 3.1E-52 T 15-03-2013
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273 ...
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274
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275
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276 The TSV format presents the match data in columns as follows:
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277
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278 - Protein Accession (e.g. P51587)
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279 - Sequence MD5 digest (e.g. 14086411a2cdf1c4cba63020e1622579)
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280 - Sequence Length (e.g. 3418)
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281 - Analysis (e.g. Pfam / PRINTS / Gene3D)
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282 - Signature Accession (e.g. PF09103 / G3DSA:2.40.50.140)
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283 - Signature Description (e.g. BRCA2 repeat profile)
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284 - Start location
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285 - Stop location
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286 - Score - is the e-value of the match reported by member database method (e.g. 3.1E-52)
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287 - Status - is the status of the match (T: true)
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288 - Date - is the date of the run
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289 - (InterProScan annotations - accession (e.g. IPR002093) - optional column; only displayed if -iprscan option is switched on)
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290 - (InterProScan annotations - description (e.g. BRCA2 repeat) - optional column; only displayed if -iprscan option is switched on)
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291 - (GO annotations (e.g. GO:0005515) - optional column; only displayed if --goterms option is switched on)
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292 - (Pathways annotations (e.g. REACT_71) - optional column; only displayed if --pathways option is switched on)
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293
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294
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295 **Extensible Markup Language (XML)**
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296
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297 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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298
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299 **Generic Feature Format Version 3 (GFF3)**
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300
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301 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 [https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md].
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302
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303 **Example Output**
1
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304
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305
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306 ::
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307
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308 ##gff-version 3
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309 ##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269
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310 ##sequence-region AACH01000027 1 1347
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311 ##seqid|source|type|start|end|score|strand|phase|attributes
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312 AACH01000027 provided_by_user nucleic_acid 1 1347 . + . Name=AACH01000027;md5=b2a7416cb92565c004becb7510f46840;ID=AACH01000027
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313 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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314 AACH01000027 getorf polypeptide 1 449 . + . md5=fd0743a673ac69fb6e5c67a48f264dd5;ID=pep_AACH01000027_1_1347
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315 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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316 ##sequence-region 2
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317 ...
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318 >pep_AACH01000027_1_1347
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319 LVLLAAFDCIDDTKLVKQIIISEIINSLPNIVNDKYGRKVLLYLLSPRDPAHTVREIIEV
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320 LQKGDGNAHSKKDTEIRRREMKYKRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEA
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321 GHELILVSSGAIAAGFGALGFKKRPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQI
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322 LLTQDDFVDKRRYKNAHQALSVLLNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQ
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323 ADLLVFLTDVDGLYTGNPNSDPRAKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAA
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324 TIATESGVPVYICSSLKSDSMIEAAEETEDGSYFVAQEKGLRTQKQWLAFYAQSQGSIWV
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325 DKGAAEALSQYGKSLLLSGIVEAEGVFSYGDIVTVFDKESGKSLGKGRVQFGASALEDML
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326 RSQKAKGVLIYRDDWISITPEIQLLFTEF
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327 ...
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328 >match$8_84_314
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329 KRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEAGHELILVSSGAIAAGFGALGFKK
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330 RPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQILLTQDDFVDKRRYKNAHQALSVL
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331 LNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQADLLVFLTDVDGLYTGNPNSDPR
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332 AKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAATIATESGVPVYICS
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333
4
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334 ]]></help>
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335
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336 <expand macro="citations" />
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337 </tool>