Mercurial > repos > galaxyp > uniprotxml_downloader

comparison uniprotxml_downloader.xml @ 4:12692567c7f9 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
author galaxyp
date Tue, 01 Jun 2021 11:54:47 +0000
parents 1a5690a5eedc
children 265c35540faa
comparison
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3:1a5690a5eedc 4:12692567c7f9
1 <tool id="uniprotxml_downloader" name="UniProt" version="2.1.0"> 1 <tool id="uniprotxml_downloader" name="UniProt" version="2.2.0" profile="21.01">
2 <description>download proteome as XML or fasta</description> 2 <description>download proteome as XML or fasta</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.7">python</requirement> 4 <requirement type="package" version="2.25.1">requests</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:" level="fatal" description="Error downloading proteome." /> 7 <exit_code range="1:" level="fatal" description="Error downloading proteome." />
8 </stdio> 8 </stdio>
9 <command> 9 <command>
10 <![CDATA[ 10 <![CDATA[
11 python $__tool_directory__/uniprotxml_downloader.py -v 11 python '$__tool_directory__/uniprotxml_downloader.py'
12 #if $taxid.input_choice == 'common': 12 #if $taxid.input_choice == 'common':
13 --taxon $taxid.organism 13 --taxon $taxid.organism
14 #if $taxid.reviewed: 14 #if $taxid.reviewed:
15 --reviewed=$taxid.reviewed 15 --reviewed=$taxid.reviewed
16 #end if
17 #elif $taxid.input_choice == 'taxids':
18 #for $id in $taxid.taxons.split(','):
19 -t '$id'
20 #end for
21 #elif $taxid.input_choice == 'history':
22 --input='${taxid.taxon_file}'
23 --column=#echo int(str($taxid.column)) - 1#
16 #end if 24 #end if
17 #elif $taxid.input_choice == 'taxids': 25 --format $format
18 #for $id in $taxid.taxons.split(','): 26 --output '${proteome}'
19 -t "$id"
20 #end for
21 #elif $taxid.input_choice == 'history':
22 --input="${taxid.taxon_file}"
23 --column=#echo int(str($taxid.column)) - 1#
24 #end if
25 --format=$format
26 --output="${proteome}"
27 ]]> 27 ]]>
28 </command> 28 </command>
29 <inputs> 29 <inputs>
30 <conditional name="taxid"> 30 <conditional name="taxid">
31 <param name="input_choice" type="select" label="Select"> 31 <param name="input_choice" type="select" label="Select">
32 <option value="common">A Common Organism</option> 32 <option value="common">A Common Organism</option>
33 <option value="taxids">By Organism IDs</option> 33 <option value="taxids">A manually entered list of Taxon IDs or names</option>
34 <option value="history">A history dataset with an Organism Taxonomy Name column</option> 34 <option value="history">A history dataset with a column containing Taxon IDs or names</option>
35 </param> 35 </param>
36 <when value="common"> 36 <when value="common">
37 <param name="organism" type="select" label="Common Organisms" 37 <param name="organism" type="select" label="Common Organisms"
38 help="select species for protein database"> 38 help="select species for protein database">
39 <options from_file="uniprot_taxons.loc"> 39 <options from_file="uniprot_taxons.loc">
58 help="Enter one or more Organsim IDs (separated by commas) from http://www.uniprot.org/proteomes/"> 58 help="Enter one or more Organsim IDs (separated by commas) from http://www.uniprot.org/proteomes/">
59 <validator type="regex" message="OrganismID[,OrganismID]">^\w+( \w+)*(,\w+( \w+)*)*$</validator> 59 <validator type="regex" message="OrganismID[,OrganismID]">^\w+( \w+)*(,\w+( \w+)*)*$</validator>
60 </param> 60 </param>
61 </when> 61 </when>
62 <when value="history"> 62 <when value="history">
63 <param name="taxon_file" type="data" format="tabular" label="Dataset with Taxon Name column"/> 63 <param name="taxon_file" type="data" format="tabular,txt" label="Dataset (tab separated) with Taxon ID/Name column"/>
64 <param name="column" type="data_column" data_ref="taxon_file" label="Column with Taxon name"/> 64 <param name="column" type="data_column" data_ref="taxon_file" label="Column with Taxon ID/name"/>
65 </when> 65 </when>
66 </conditional> 66 </conditional>
67 <param name="format" type="select" label="uniprot output format"> 67 <param name="format" type="select" label="uniprot output format">
68 <option value="xml">xml</option> 68 <option value="xml">xml</option>
69 <option value="fasta">fasta</option> 69 <option value="fasta">fasta</option>
108 <has_text text="Shi470" /> 108 <has_text text="Shi470" />
109 <has_text text="PeCan4" /> 109 <has_text text="PeCan4" />
110 </assert_contents> 110 </assert_contents>
111 </output> 111 </output>
112 </test> 112 </test>
113 <test>
114 <param name="input_choice" value="history"/>
115 <param name="taxon_file" value="Helicobacter_strains_ids.tsv" ftype="tabular"/>
116 <param name="column" value="2"/>
117 <param name="format" value="fasta"/>
118 <output name="proteome">
119 <assert_contents>
120 <has_text text="Shi470" />
121 <has_text text="PeCan4" />
122 </assert_contents>
123 </output>
124 </test>
113 </tests> 125 </tests>
114 <help> 126 <help>
115 <![CDATA[ 127 <![CDATA[
116 **UniProt Downloader** 128 **UniProt Downloader**
117 129