Mercurial > repos > proteore > proteore_prot_features
comparison add_protein_features.xml @ 12:1a4cfa7a3a27 draft
planemo upload commit 77279e994f5751c6cd9aa165aa0604db3d241271-dirty
| author | proteore |
|---|---|
| date | Mon, 11 Mar 2019 09:16:00 -0400 |
| parents | 8df559ad14a7 |
| children | 0116d444d21f |
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| 11:8df559ad14a7 | 12:1a4cfa7a3a27 |
|---|---|
| 1 <tool id="prot_features" name="Add protein features" version="2019.01.18"> | 1 <tool id="prot_features" name="Add protein features" version="2019.03.11"> |
| 2 <description>[neXtProt] | 2 <description>[neXtProt] |
| 3 </description> | 3 </description> |
| 4 <requirements> | 4 <requirements> |
| 5 <requirement type="package" version="3.4.1">R</requirement> | 5 <requirement type="package" version="3.4.1">R</requirement> |
| 6 </requirements> | 6 </requirements> |
| 21 --type='$idtype' | 21 --type='$idtype' |
| 22 --pc_features='$Nextprot_params.pc_features' | 22 --pc_features='$Nextprot_params.pc_features' |
| 23 --localization='$Nextprot_params.localization' | 23 --localization='$Nextprot_params.localization' |
| 24 --diseases_info='$Nextprot_params.diseases_info' | 24 --diseases_info='$Nextprot_params.diseases_info' |
| 25 --output='$output' | 25 --output='$output' |
| 26 --nextprot=$__tool_directory__/tool-data/result_nextprot.txt | 26 |
| 27 #if 'nextprot_ref' in str($ref_file).split("/") | |
| 28 --nextprot="$ref_file" | |
| 29 #else | |
| 30 --nextprot="$__tool_directory__/$ref_file" | |
| 31 #end if | |
| 27 | 32 |
| 28 ]]></command> | 33 ]]></command> |
| 29 | 34 |
| 30 <inputs> | 35 <inputs> |
| 31 <conditional name="inputtype"> | 36 <conditional name="inputtype"> |
| 49 </sanitizer> | 54 </sanitizer> |
| 50 </param> | 55 </param> |
| 51 </when> | 56 </when> |
| 52 <when value="file"> | 57 <when value="file"> |
| 53 <param name="genelist" type="data" format="txt,tabular" label="Select your file" help=""/> | 58 <param name="genelist" type="data" format="txt,tabular" label="Select your file" help=""/> |
| 54 <param name="column" type="text" label="Column IDs (e.g : Enter c1 for column n°1)" value="c1"/> | 59 <param name="column" type="text" label="Column IDs (e.g : Enter c1 for column n°1)" value="c1"> |
| 60 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> | |
| 61 </param> | |
| 55 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does input file have header?" /> | 62 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does input file have header?" /> |
| 56 | |
| 57 </when> | 63 </when> |
| 58 </conditional> | 64 </conditional> |
| 59 | 65 |
| 60 <param name="idtype" type="select" label="Type of IDs" multiple="false" optional="false"> | 66 <param name="idtype" type="select" label="Type of IDs" multiple="false" optional="false"> |
| 61 <option value="Uniprot_AC" selected="true">Uniprot accession number</option> | 67 <option value="Uniprot_AC" selected="true">Uniprot accession number</option> |
| 62 <option value="NextprotID" selected="false">neXtProt IDs</option> | 68 <option value="NextprotID" selected="false">neXtProt IDs</option> |
| 63 </param> | 69 </param> |
| 64 <section name="Nextprot_params" title="Select features" expanded="True"> | 70 <section name="Nextprot_params" title="Select features" expanded="True"> |
| 65 <param name="pc_features" type="select" label="Physico-Chemical Features" multiple="true" help="" display="checkboxes" optional="true"> | 71 <param name="pc_features" type="select" label="Physico-Chemical Features" multiple="true" help="" display="checkboxes" optional="false"> |
| 66 <option value="SeqLength" selected="false">Sequence Length</option> | 72 <option value="SeqLength" selected="false">Sequence Length</option> |
| 67 <option value="MW" selected="false">Molecular Weight</option> | 73 <option value="MW" selected="false">Molecular Weight</option> |
| 68 <option value="IsoPoint" selected="false">Isoelectric point</option> | 74 <option value="IsoPoint" selected="false">Isoelectric point</option> |
| 69 <option value="TMDomains" selected="false">Number of transmembrane domains</option> | 75 <option value="TMDomains" selected="false">Number of transmembrane domains</option> |
| 70 <option value="ProteinExistence" selected="false">Protein Existence (evidence score from 1 to 5)</option> | 76 <option value="ProteinExistence" selected="false">Protein Existence (evidence score from 1 to 5)</option> |
| 76 </param> | 82 </param> |
| 77 | 83 |
| 78 <param name="diseases_info" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Disease information" /> | 84 <param name="diseases_info" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Disease information" /> |
| 79 | 85 |
| 80 </section> | 86 </section> |
| 87 <param name="ref_file" type="select" label="Release of neXtProt reference file to use"> | |
| 88 <options from_data_table="proteore_nextprot_ref"/> | |
| 89 </param> | |
| 81 | 90 |
| 82 </inputs> | 91 </inputs> |
| 83 | 92 |
| 84 | 93 |
| 85 <outputs> | 94 <outputs> |