Mercurial > repos > galaxyp > uniprotxml_downloader
diff uniprotxml_downloader.xml @ 5:265c35540faa draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
author | galaxyp |
---|---|
date | Fri, 04 Nov 2022 15:08:37 +0000 |
parents | 12692567c7f9 |
children | a371252a2cf6 |
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--- a/uniprotxml_downloader.xml Tue Jun 01 11:54:47 2021 +0000 +++ b/uniprotxml_downloader.xml Fri Nov 04 15:08:37 2022 +0000 @@ -1,5 +1,8 @@ -<tool id="uniprotxml_downloader" name="UniProt" version="2.2.0" profile="21.01"> +<tool id="uniprotxml_downloader" name="UniProt" version="2.3.0" profile="21.01"> <description>download proteome as XML or fasta</description> + <macros> + <import>macros.xml</import> + </macros> <requirements> <requirement type="package" version="2.25.1">requests</requirement> </requirements> @@ -11,14 +14,17 @@ python '$__tool_directory__/uniprotxml_downloader.py' #if $taxid.input_choice == 'common': --taxon $taxid.organism + --field taxonomy_id #if $taxid.reviewed: --reviewed=$taxid.reviewed #end if #elif $taxid.input_choice == 'taxids': + --field $taxid.field #for $id in $taxid.taxons.split(','): -t '$id' #end for #elif $taxid.input_choice == 'history': + --field $taxid.field --input='${taxid.taxon_file}' --column=#echo int(str($taxid.column)) - 1# #end if @@ -58,10 +64,12 @@ help="Enter one or more Organsim IDs (separated by commas) from http://www.uniprot.org/proteomes/"> <validator type="regex" message="OrganismID[,OrganismID]">^\w+( \w+)*(,\w+( \w+)*)*$</validator> </param> + <expand macro="query_field"/> </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"/> + <expand macro="query_field"/> </when> </conditional> <param name="format" type="select" label="uniprot output format"> @@ -89,7 +97,20 @@ </test> <test> <param name="input_choice" value="taxids"/> + <param name="taxons" value="765963,512562"/> + <param name="field" value="taxonomy_id"/> + <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="taxids"/> <param name="taxons" value="Shi470,PeCan4"/> + <param name="field" value="taxonomy_name"/> <param name="format" value="fasta"/> <output name="proteome"> <assert_contents> @@ -102,6 +123,7 @@ <param name="input_choice" value="history"/> <param name="taxon_file" value="Helicobacter_strains.tsv" ftype="tabular"/> <param name="column" value="1"/> + <param name="field" value="taxonomy_name"/> <param name="format" value="fasta"/> <output name="proteome"> <assert_contents> @@ -114,6 +136,7 @@ <param name="input_choice" value="history"/> <param name="taxon_file" value="Helicobacter_strains_ids.tsv" ftype="tabular"/> <param name="column" value="2"/> + <param name="field" value="taxonomy_id"/> <param name="format" value="fasta"/> <output name="proteome"> <assert_contents>