Mercurial > repos > galaxyp > uniprotxml_downloader
view uniprotxml_downloader.xml @ 4:12692567c7f9 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
author | galaxyp |
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date | Tue, 01 Jun 2021 11:54:47 +0000 |
parents | 1a5690a5eedc |
children | 265c35540faa |
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<tool id="uniprotxml_downloader" name="UniProt" version="2.2.0" profile="21.01"> <description>download proteome as XML or fasta</description> <requirements> <requirement type="package" version="2.25.1">requests</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Error downloading proteome." /> </stdio> <command> <![CDATA[ python '$__tool_directory__/uniprotxml_downloader.py' #if $taxid.input_choice == 'common': --taxon $taxid.organism #if $taxid.reviewed: --reviewed=$taxid.reviewed #end if #elif $taxid.input_choice == 'taxids': #for $id in $taxid.taxons.split(','): -t '$id' #end for #elif $taxid.input_choice == 'history': --input='${taxid.taxon_file}' --column=#echo int(str($taxid.column)) - 1# #end if --format $format --output '${proteome}' ]]> </command> <inputs> <conditional name="taxid"> <param name="input_choice" type="select" label="Select"> <option value="common">A Common Organism</option> <option value="taxids">A manually entered list of Taxon IDs or names</option> <option value="history">A history dataset with a column containing Taxon IDs or names</option> </param> <when value="common"> <param name="organism" type="select" label="Common Organisms" help="select species for protein database"> <options from_file="uniprot_taxons.loc"> <column name="name" index="0" /> <column name="value" index="1" /> </options> </param> <param name="reviewed" type="select" label="filter by reviewed status" optional="true"> <help><![CDATA[ UniProtKB/TrEMBL (unreviewed)is a large, automatically annotated database that may contain redundant sequences, but there is a higher chance peptides will be identified. UniProtKB/Swiss-Prot (reviewed) is a smaller, manually annotated database with less of a chance peptides will be identified but less sequence redundancy ]]> </help> <option value="yes">UniProtKB/Swiss-Prot (reviewed only)</option> <option value="no">UniProtKB/TrEMBL (unreviewed only)</option> </param> </when> <when value="taxids"> <param name="taxons" type="text" label="NCBI Taxon IDs or names" help="Enter one or more Organsim IDs (separated by commas) from http://www.uniprot.org/proteomes/"> <validator type="regex" message="OrganismID[,OrganismID]">^\w+( \w+)*(,\w+( \w+)*)*$</validator> </param> </when> <when value="history"> <param name="taxon_file" type="data" format="tabular,txt" label="Dataset (tab separated) with Taxon ID/Name column"/> <param name="column" type="data_column" data_ref="taxon_file" label="Column with Taxon ID/name"/> </when> </conditional> <param name="format" type="select" label="uniprot output format"> <option value="xml">xml</option> <option value="fasta">fasta</option> </param> </inputs> <outputs> <data format="uniprotxml" name="proteome" label="UniProt.${format}"> <change_format> <when input="format" value="fasta" format="fasta" /> </change_format> </data> </outputs> <tests> <test> <param name="input_choice" value="taxids"/> <param name="taxons" value="1566990"/> <param name="format" value="xml"/> <output name="proteome"> <assert_contents> <has_text text="</uniprot>" /> </assert_contents> </output> </test> <test> <param name="input_choice" value="taxids"/> <param name="taxons" value="Shi470,PeCan4"/> <param name="format" value="fasta"/> <output name="proteome"> <assert_contents> <has_text text="Shi470" /> <has_text text="PeCan4" /> </assert_contents> </output> </test> <test> <param name="input_choice" value="history"/> <param name="taxon_file" value="Helicobacter_strains.tsv" ftype="tabular"/> <param name="column" value="1"/> <param name="format" value="fasta"/> <output name="proteome"> <assert_contents> <has_text text="Shi470" /> <has_text text="PeCan4" /> </assert_contents> </output> </test> <test> <param name="input_choice" value="history"/> <param name="taxon_file" value="Helicobacter_strains_ids.tsv" ftype="tabular"/> <param name="column" value="2"/> <param name="format" value="fasta"/> <output name="proteome"> <assert_contents> <has_text text="Shi470" /> <has_text text="PeCan4" /> </assert_contents> </output> </test> </tests> <help> <![CDATA[ **UniProt Downloader** Downloads either a UniProtXML file or a fasta file from UniProtKB The Morpheus proteomics search algorithm can use the UniProtXML format as a search database. Available proteomes: http://www.uniprot.org/proteomes/ Available taxon names: http://www.uniprot.org/taxonomy/ Example taxon: http://www.uniprot.org/taxonomy/512562 Taxon IDs or names can be entered as text or read from a column in a tabular dataset from your history. Example IDs and names releated to the Bacteria Helicobacter pylori (strain Shi470) :: - 512562 - Shi470 - Helicobacter pylori - Helicobacter - Helicobacteraceae UniProtKB help: http://www.uniprot.org/help/uniprotkb ]]> </help> <citations> <citation type="doi">10.1093/nar/gku989</citation> </citations> </tool>