Mercurial > repos > bgruening > interproscan

annotate interproscan.xml @ 4:fcedfe919603 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
author iuc
date Mon, 15 Nov 2021 17:53:24 +0000
parents 52f20362d488
children 2e1cf7d85dbc
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4
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">
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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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>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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6 <xrefs>
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7 <xref type="bio.tools">interproscan_4</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>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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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
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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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}|' \$(dirname \$(readlink -f \$(command -v interproscan.sh)))/interproscan.properties > \$HOME/.interproscan-5/interproscan.properties
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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18 &&
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19
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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20 ## Now run interproscan
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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21 interproscan.sh
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23 ## disables the precalculated lookup service, all calculation will be run locally
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24 -dp
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25 --input '$input'
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26 --seqtype $seqtype
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27 -f ${','.join($oformat)}
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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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29 #if $licensed.use == 'true' and $licensed.applications_licensed:
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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30 --applications ${','.join($applications)},${','.join($licensed.applications_licensed)}
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
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31 #else:
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32 --applications ${','.join($applications)}
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33 #end if
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34 --tempdir \$TEMP
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36 $pathways
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37 $goterms
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38 $iprlookup
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40 --cpu \${GALAXY_SLOTS:-4}
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42 --output-file-base 'output'
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43 ]]></command>
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44 <inputs>
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45 <param argument="--input" type="data" format="fasta" label="Protein FASTA File"/>
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46
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47 <param argument="--seqtype" type="select" label="Type of the input sequences" help="">
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48 <option value="p" selected="true">Protein</option>
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49 <option value="n">DNA / RNA</option>
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50 </param>
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52 <param name="database" label="InterProScan database" type="select">
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53 <options from_data_table="interproscan">
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54 <column name="value" index="0" />
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55 <column name="name" index="1" />
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56 <column name="path" index="3" />
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57 <filter type="sort_by" column="0" />
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58 <filter type="static_value" column="2" value="@TOOL_VERSION@" />
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59 </options>
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60 </param>
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61
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62 <param name="applications" type="select" multiple="True" label="Applications to run" help="Select your program">
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63 <option value="TIGRFAM" selected="true">TIGRFAM: protein families based on hidden Markov models (HMMs)</option>
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64 <option value="SFLD" selected="true">SFLD: a database of protein families based on hidden Markov models (HMMs)</option>
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65 <option value="SUPERFAMILY" selected="true">SUPERFAMILY: database of structural and functional annotation for all proteins and genomes</option>
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66 <option value="PANTHER" selected="true">PANTHER: Protein ANalysis THrough Evolutionary Relationships</option>
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67 <option value="Gene3D" selected="true">Gene3d: Structural assignment for whole genes and genomes using the CATH domain structure database</option>
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68 <option value="Hamap" selected="true">HAMAP: High-quality Automated Annotation of Microbial Proteomes</option>
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69 <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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70 <option value="Coils" selected="true">Coils: Prediction of Coiled Coil Regions in Proteins</option>
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71 <option value="SMART" selected="true">SMART: identification and analysis of domain architectures based on Hidden Markov Models or HMMs</option>
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72 <option value="CDD" selected="true">SMART: protein domains and families based on well-annotated multiple sequence alignment models</option>
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73 <option value="PRINTS" selected="true">PRINTS: group of conserved motifs (fingerprints) used to characterise a protein family</option>
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74 <option value="PIRSR" selected="true">PIRSR: protein families based on hidden Markov models (HMMs) and Site Rules</option>
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75 <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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76 <option value="Pfam" selected="true">Pfam: protein families, each represented by multiple sequence alignments and hidden Markov models</option>
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77 <option value="MobiDBLite" selected="true">MobiDBLite: Prediction of intrinsically disordered regions in proteins</option>
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78 <option value="PIRSF" selected="true">PIRSF: non-overlapping clustering of UniProtKB sequences into a hierarchical order (evolutionary relationships)</option>
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79 </param>
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81 <conditional name="licensed">
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82 <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
diff changeset
83 <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
diff changeset
84 <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
85 </param>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
86 <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
87 <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
88 <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
89 <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
90 <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
91 <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
92 <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
93 <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
94 </param>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
95 </when>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
96 </conditional>
0
c10e37cca7e3 Uploaded
bgruening
parents:
diff changeset
97
4
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
98 <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
99 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
diff changeset
100 <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
101 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
102 <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
103 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
diff changeset
104
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
105 <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
106 <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
diff changeset
107 <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
108 <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
109 <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
110 </param>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
111 </inputs>
0
c10e37cca7e3 Uploaded
bgruening
parents:
diff changeset
112
4
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
113 <outputs>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
114 <data format="tabular" name="outfile_tsv" from_work_dir="output.tsv" label="InterProScan on ${on_string} (tsv)">
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
115 <filter>oformat and 'TSV' in outputs</filter>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
116 </data>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
117 <data format="xml" name="outfile_xml" from_work_dir="output.xml" label="InterProScan on ${on_string} (xml)">
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
118 <filter>oformat and 'XML' in outputs</filter>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
119 </data>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
120 <data format="gff3" name="outfile_gff3" from_work_dir="output.gff3" label="InterProScan on ${on_string} (gff3)">
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
121 <filter>oformat and 'GFF3' in outputs</filter>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
122 </data>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
123 <data format="json" name="outfile_json" from_work_dir="output.json" label="InterProScan on ${on_string} (json)">
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
124 <filter>oformat and 'JSON' in outputs</filter>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
125 </data>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
126 </outputs>
0
c10e37cca7e3 Uploaded
bgruening
parents:
diff changeset
127
4
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
128 <tests>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
129 <test>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
130 <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
131 <param name="seqtype" value="p" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
132 <param name="database" value="5.52-86.0" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
133 <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
134 <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
135 <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
136 <assert_contents>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
137 <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
138 <has_text text="ea9924e11f7decc417e8d9ed8b9c682e" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
139 <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
diff changeset
140 <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
141 </assert_contents>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
142 </output>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
143 </test>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
144 <test>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
145 <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
146 <param name="seqtype" value="p" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
147 <param name="database" value="5.52-86.0" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
148 <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
149 <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
150 <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
151 <assert_contents>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
152 <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
153 <has_text text="ea9924e11f7decc417e8d9ed8b9c682e" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
154 <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
diff changeset
155 <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
156 </assert_contents>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
157 </output>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
158 <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
159 <assert_contents>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
160 <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
161 <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
162 <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
163 <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
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 </output>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
166 <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
167 <assert_contents>
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="protein_match" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
169 <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
170 <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
171 </assert_contents>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
172 </output>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
173 <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
174 <assert_contents>
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="signatureLibraryRelease" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
176 <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
177 <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
178 </assert_contents>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
179 </output>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
180 </test>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
181 <test>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
182 <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
183 <param name="seqtype" value="n" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
184 <param name="database" value="5.52-86.0" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
185 <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
186 <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
187 <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
188 <assert_contents>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
189 <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
190 <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
191 <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
192 <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
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 </output>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
195 <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
196 <assert_contents>
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="mobidblite-location" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
198 <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
199 <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
200 <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
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 </output>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
203 <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
204 <assert_contents>
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="protein_match" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
206 <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
207 <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
208 </assert_contents>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
209 </output>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
210 <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
211 <assert_contents>
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="signatureLibraryRelease" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
213 <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
214 <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
215 </assert_contents>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
216 </output>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
217 </test>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
218 <test expect_failure="true">
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
219 <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
220 <param name="seqtype" value="p" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
221 <param name="database" value="5.52-86.0" />
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
222 <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
223 <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
224 <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
225 <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
226 </conditional>
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="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
228 <assert_stdout>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
229 <!-- 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
230 <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
231 <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
232 </assert_stdout>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
233 </test>
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
234 </tests>
0
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235
4
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
236 <help><![CDATA[
0
c10e37cca7e3 Uploaded
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237
c10e37cca7e3 Uploaded
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parents:
diff changeset
238 **What it does**
c10e37cca7e3 Uploaded
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239
4
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
240 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
241
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
242 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
243 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
244 analyses it will be necessary for you to obtain a licence from the vendor and
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
245 configure the Galaxy server InterProScan installation to use them.
0
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246
c10e37cca7e3 Uploaded
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parents:
diff changeset
247 **Input**
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248
4
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
parents: 2
diff changeset
249 Required is a FASTA file containing protein or nucleotide sequences.
0
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250
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parents:
diff changeset
251 **Output**
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252
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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253 In this version of InterProScan, you can retrieve output in any of the following five formats:
0
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254
4
fcedfe919603 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
iuc
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255 * TSV: tab-separated values format
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256 * XML: XML format
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257 * GFF: The GFF 3.0 format
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258 * 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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259
4
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260 **Example Output**
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261
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262
4
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263 ::
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264
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265 P51587 14086411a2cdf1c4cba63020e1622579 3418 Pfam PF09103 BRCA2, oligonucleotide/oligosaccharide-binding, domain 1 2670 2799 7.9E-43 T 15-03-2013
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266 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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267 P51587 14086411a2cdf1c4cba63020e1622579 3418 Gene3D G3DSA:2.40.50.140 2966 3051 3.1E-52 T 15-03-2013
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268 ...
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269
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270
4
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271 The TSV format presents the match data in columns as follows:
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272
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273 - Protein Accession (e.g. P51587)
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274 - Sequence MD5 digest (e.g. 14086411a2cdf1c4cba63020e1622579)
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275 - Sequence Length (e.g. 3418)
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276 - Analysis (e.g. Pfam / PRINTS / Gene3D)
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277 - Signature Accession (e.g. PF09103 / G3DSA:2.40.50.140)
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278 - Signature Description (e.g. BRCA2 repeat profile)
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279 - Start location
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280 - Stop location
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281 - Score - is the e-value of the match reported by member database method (e.g. 3.1E-52)
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282 - Status - is the status of the match (T: true)
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283 - Date - is the date of the run
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284 - (InterProScan annotations - accession (e.g. IPR002093) - optional column; only displayed if -iprscan option is switched on)
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285 - (InterProScan annotations - description (e.g. BRCA2 repeat) - optional column; only displayed if -iprscan option is switched on)
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286 - (GO annotations (e.g. GO:0005515) - optional column; only displayed if --goterms option is switched on)
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287 - (Pathways annotations (e.g. REACT_71) - optional column; only displayed if --pathways option is switched on)
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288
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289
4
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290 **Extensible Markup Language (XML)**
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291
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292 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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293
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294 **Generic Feature Format Version 3 (GFF3)**
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295
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296 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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297
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298 **Example Output**
1
eb12db502d3c updated tool help
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299
eb12db502d3c updated tool help
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300
4
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301 ::
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302
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303 ##gff-version 3
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304 ##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269
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305 ##sequence-region AACH01000027 1 1347
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306 ##seqid|source|type|start|end|score|strand|phase|attributes
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307 AACH01000027 provided_by_user nucleic_acid 1 1347 . + . Name=AACH01000027;md5=b2a7416cb92565c004becb7510f46840;ID=AACH01000027
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308 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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309 AACH01000027 getorf polypeptide 1 449 . + . md5=fd0743a673ac69fb6e5c67a48f264dd5;ID=pep_AACH01000027_1_1347
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310 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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311 ##sequence-region 2
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312 ...
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313 >pep_AACH01000027_1_1347
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314 LVLLAAFDCIDDTKLVKQIIISEIINSLPNIVNDKYGRKVLLYLLSPRDPAHTVREIIEV
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315 LQKGDGNAHSKKDTEIRRREMKYKRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEA
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316 GHELILVSSGAIAAGFGALGFKKRPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQI
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317 LLTQDDFVDKRRYKNAHQALSVLLNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQ
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318 ADLLVFLTDVDGLYTGNPNSDPRAKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAA
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319 TIATESGVPVYICSSLKSDSMIEAAEETEDGSYFVAQEKGLRTQKQWLAFYAQSQGSIWV
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320 DKGAAEALSQYGKSLLLSGIVEAEGVFSYGDIVTVFDKESGKSLGKGRVQFGASALEDML
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321 RSQKAKGVLIYRDDWISITPEIQLLFTEF
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322 ...
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323 >match$8_84_314
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324 KRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEAGHELILVSSGAIAAGFGALGFKK
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325 RPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQILLTQDDFVDKRRYKNAHQALSVL
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326 LNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQADLLVFLTDVDGLYTGNPNSDPR
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327 AKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAATIATESGVPVYICS
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328
4
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329 ]]></help>
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330
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331 <expand macro="citations" />
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332 </tool>