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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
author galaxyp
date Thu, 06 Jul 2023 21:15:39 +0000
parents 265c35540faa
children
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5:265c35540faa 6:a371252a2cf6
1 <tool id="uniprotxml_downloader" name="UniProt" version="2.3.0" profile="21.01"> 1 <tool id="uniprotxml_downloader" name="UniProt" version="2.4.0" profile="21.01">
2 <description>download proteome as XML or fasta</description> 2 <description>download proteome as XML or fasta</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
10 <exit_code range="1:" level="fatal" description="Error downloading proteome." /> 10 <exit_code range="1:" level="fatal" description="Error downloading proteome." />
11 </stdio> 11 </stdio>
12 <command> 12 <command>
13 <![CDATA[ 13 <![CDATA[
14 python '$__tool_directory__/uniprotxml_downloader.py' 14 python '$__tool_directory__/uniprotxml_downloader.py'
15 #if $taxid.input_choice == 'common': 15 #if $input_method.input_choice == 'common':
16 --taxon $taxid.organism 16 --search-id $input_method.organism
17 --field taxonomy_id 17 --field taxonomy_id
18 #if $taxid.reviewed: 18 #if $input_method.reviewed:
19 --reviewed=$taxid.reviewed 19 --reviewed=$input_method.reviewed
20 #end if 20 #end if
21 #elif $taxid.input_choice == 'taxids': 21 #elif $input_method.input_choice == 'enter_ids':
22 --field $taxid.field 22 --field $input_method.field
23 #for $id in $taxid.taxons.split(','): 23 #for $id in $input_method.ids.split(','):
24 -t '$id' 24 --search-id '$id'
25 #end for 25 #end for
26 #elif $taxid.input_choice == 'history': 26 #elif $input_method.input_choice == 'history':
27 --field $taxid.field 27 --field $input_method.field
28 --input='${taxid.taxon_file}' 28 --input='${input_method.id_file}'
29 --column=#echo int(str($taxid.column)) - 1# 29 --column=#echo int(str($input_method.column)) - 1#
30 #end if 30 #end if
31 --format $format 31 --format $format
32 --output '${proteome}' 32 --output '${proteome}'
33 ]]> 33 ]]>
34 </command> 34 </command>
35 <inputs> 35 <inputs>
36 <conditional name="taxid"> 36 <conditional name="input_method">
37 <param name="input_choice" type="select" label="Select"> 37 <param name="input_choice" type="select" label="Select">
38 <option value="common">A Common Organism</option> 38 <option value="common">A Common Organism</option>
39 <option value="taxids">A manually entered list of Taxon IDs or names</option> 39 <option value="enter_ids">A manually entered list of Uniprot IDs</option>
40 <option value="history">A history dataset with a column containing Taxon IDs or names</option> 40 <option value="history">A history dataset with a column containing Uniprot IDs</option>
41 </param> 41 </param>
42 <when value="common"> 42 <when value="common">
43 <param name="organism" type="select" label="Common Organisms" 43 <param name="organism" type="select" label="Common Organisms"
44 help="select species for protein database"> 44 help="select species for protein database">
45 <options from_file="uniprot_taxons.loc"> 45 <options from_file="uniprot_taxons.loc">
57 </help> 57 </help>
58 <option value="yes">UniProtKB/Swiss-Prot (reviewed only)</option> 58 <option value="yes">UniProtKB/Swiss-Prot (reviewed only)</option>
59 <option value="no">UniProtKB/TrEMBL (unreviewed only)</option> 59 <option value="no">UniProtKB/TrEMBL (unreviewed only)</option>
60 </param> 60 </param>
61 </when> 61 </when>
62 <when value="taxids"> 62 <when value="enter_ids">
63 <param name="taxons" type="text" label="NCBI Taxon IDs or names" 63 <param name="ids" type="text" label="Search ID values"
64 help="Enter one or more Organsim IDs (separated by commas) from http://www.uniprot.org/proteomes/"> 64 help="Enter one or more IDs (separated by commas) from http://www.uniprot.org/proteomes/">
65 <validator type="regex" message="OrganismID[,OrganismID]">^\w+( \w+)*(,\w+( \w+)*)*$</validator> 65 <validator type="regex" message="OrganismID[,OrganismID]">^\w+( \w+)*(,\w+( \w+)*)*$</validator>
66 </param> 66 </param>
67 <expand macro="query_field"/> 67 <expand macro="query_field"/>
68 </when> 68 </when>
69 <when value="history"> 69 <when value="history">
70 <param name="taxon_file" type="data" format="tabular,txt" label="Dataset (tab separated) with Taxon ID/Name column"/> 70 <param name="id_file" type="data" format="tabular,txt" label="Dataset (tab separated) with ID column"/>
71 <param name="column" type="data_column" data_ref="taxon_file" label="Column with Taxon ID/name"/> 71 <param name="column" type="data_column" data_ref="id_file" label="Column with ID"/>
72 <expand macro="query_field"/> 72 <expand macro="query_field"/>
73 </when> 73 </when>
74 </conditional> 74 </conditional>
75 <param name="format" type="select" label="uniprot output format"> 75 <param name="format" type="select" label="uniprot output format">
76 <option value="xml">xml</option> 76 <option value="xml">xml</option>
84 </change_format> 84 </change_format>
85 </data> 85 </data>
86 </outputs> 86 </outputs>
87 <tests> 87 <tests>
88 <test> 88 <test>
89 <param name="input_choice" value="taxids"/> 89 <param name="input_choice" value="enter_ids"/>
90 <param name="taxons" value="1566990"/> 90 <param name="ids" value="1566990"/>
91 <param name="format" value="xml"/> 91 <param name="format" value="xml"/>
92 <output name="proteome"> 92 <output name="proteome">
93 <assert_contents> 93 <assert_contents>
94 <has_text text="&lt;/uniprot&gt;" /> 94 <has_text text="&lt;/uniprot&gt;" />
95 </assert_contents> 95 </assert_contents>
96 </output> 96 </output>
97 </test> 97 </test>
98 <test> 98 <test>
99 <param name="input_choice" value="taxids"/> 99 <param name="input_choice" value="enter_ids"/>
100 <param name="taxons" value="765963,512562"/> 100 <param name="ids" value="765963,512562"/>
101 <param name="field" value="taxonomy_id"/> 101 <param name="field" value="taxonomy_id"/>
102 <param name="format" value="fasta"/> 102 <param name="format" value="fasta"/>
103 <output name="proteome"> 103 <output name="proteome">
104 <assert_contents> 104 <assert_contents>
105 <has_text text="Shi470" /> 105 <has_text text="Shi470" />
106 <has_text text="PeCan4" /> 106 <has_text text="PeCan4" />
107 </assert_contents> 107 </assert_contents>
108 </output> 108 </output>
109 </test> 109 </test>
110 <test> 110 <test>
111 <param name="input_choice" value="taxids"/> 111 <param name="input_choice" value="enter_ids"/>
112 <param name="taxons" value="Shi470,PeCan4"/> 112 <param name="ids" value="Shi470,PeCan4"/>
113 <param name="field" value="taxonomy_name"/> 113 <param name="field" value="taxonomy_name"/>
114 <param name="format" value="fasta"/> 114 <param name="format" value="fasta"/>
115 <output name="proteome"> 115 <output name="proteome">
116 <assert_contents> 116 <assert_contents>
117 <has_text text="Shi470" /> 117 <has_text text="Shi470" />
118 <has_text text="PeCan4" /> 118 <has_text text="PeCan4" />
119 </assert_contents> 119 </assert_contents>
120 </output> 120 </output>
121 </test> 121 </test>
122 <test> 122 <test>
123 <param name="input_choice" value="enter_ids"/>
124 <param name="ids" value="E1Q2I0,E1Q3C4"/>
125 <param name="field" value="accession"/>
126 <param name="format" value="fasta"/>
127 <output name="proteome">
128 <assert_contents>
129 <has_text text="E1Q2I0" />
130 <has_text text="E1Q3C4" />
131 </assert_contents>
132 </output>
133 </test>
134 <test>
123 <param name="input_choice" value="history"/> 135 <param name="input_choice" value="history"/>
124 <param name="taxon_file" value="Helicobacter_strains.tsv" ftype="tabular"/> 136 <param name="id_file" value="Helicobacter_strains.tsv" ftype="tabular"/>
125 <param name="column" value="1"/> 137 <param name="column" value="1"/>
126 <param name="field" value="taxonomy_name"/> 138 <param name="field" value="taxonomy_name"/>
127 <param name="format" value="fasta"/> 139 <param name="format" value="fasta"/>
128 <output name="proteome"> 140 <output name="proteome">
129 <assert_contents> 141 <assert_contents>
132 </assert_contents> 144 </assert_contents>
133 </output> 145 </output>
134 </test> 146 </test>
135 <test> 147 <test>
136 <param name="input_choice" value="history"/> 148 <param name="input_choice" value="history"/>
137 <param name="taxon_file" value="Helicobacter_strains_ids.tsv" ftype="tabular"/> 149 <param name="id_file" value="Helicobacter_strains_ids.tsv" ftype="tabular"/>
138 <param name="column" value="2"/> 150 <param name="column" value="2"/>
139 <param name="field" value="taxonomy_id"/> 151 <param name="field" value="taxonomy_id"/>
140 <param name="format" value="fasta"/> 152 <param name="format" value="fasta"/>
141 <output name="proteome"> 153 <output name="proteome">
142 <assert_contents> 154 <assert_contents>
143 <has_text text="Shi470" /> 155 <has_text text="Shi470" />
144 <has_text text="PeCan4" /> 156 <has_text text="PeCan4" />
157 </assert_contents>
158 </output>
159 </test>
160 <test>
161 <param name="input_choice" value="history"/>
162 <param name="id_file" value="Helicobacter_protein_accessions.tsv" ftype="tabular"/>
163 <param name="column" value="1"/>
164 <param name="field" value="accession"/>
165 <param name="format" value="fasta"/>
166 <output name="proteome">
167 <assert_contents>
168 <has_text text="E1Q2I0" />
169 <has_text text="E1Q3C4" />
145 </assert_contents> 170 </assert_contents>
146 </output> 171 </output>
147 </test> 172 </test>
148 </tests> 173 </tests>
149 <help> 174 <help>
158 183
159 Available taxon names: http://www.uniprot.org/taxonomy/ 184 Available taxon names: http://www.uniprot.org/taxonomy/
160 185
161 Example taxon: http://www.uniprot.org/taxonomy/512562 186 Example taxon: http://www.uniprot.org/taxonomy/512562
162 187
163 Taxon IDs or names can be entered as text or read from a column in a tabular dataset from your history. 188 Example protein: https://www.uniprot.org/uniprotkb/E1Q2I0/entry
189
190 Description of query fields: https://www.uniprot.org/help/query-fields
191
192 IDs can be entered as text or read from a column in a tabular dataset from your history.
164 193
165 Example IDs and names releated to the Bacteria Helicobacter pylori (strain Shi470) :: 194 Example IDs and names releated to the Bacteria Helicobacter pylori (strain Shi470) ::
166 195
167 196
168 - 512562 197 - 512562
169 - Shi470 198 - Shi470
170 - Helicobacter pylori 199 - Helicobacter pylori
171 - Helicobacter 200 - Helicobacter
172 - Helicobacteraceae 201 - Helicobacteraceae
202
203 Example protein accession numbers from Helicobacter pylori:
204
205 - E1Q2I0
206 - E1Q3C4
173 207
174 208
175 UniProtKB help: http://www.uniprot.org/help/uniprotkb 209 UniProtKB help: http://www.uniprot.org/help/uniprotkb
176 210
177 ]]> 211 ]]>