Mercurial > repos > galaxyp > uniprotxml_downloader

annotate uniprotxml_downloader.xml @ 7:4ddc8da62671 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
author galaxyp
date Wed, 11 Dec 2024 13:34:54 +0000
parents a371252a2cf6
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
1 <tool id="uniprotxml_downloader" name="UniProt" version="2.5.0" profile="23.1">
2
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
2 <description>download proteome as XML or fasta</description>
5
265c35540faa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
galaxyp
parents: 4
diff changeset
3 <macros>
7
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
4 <xml name="query_field">
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
5 <param name="field" type="select" label="Field">
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
6 <option value="taxonomy_name">Taxonomy Name</option>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
7 <option value="taxonomy_id">Taxonomy ID</option>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
8 <option value="accession">Accession</option>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
9 </param>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
10 </xml>
5
265c35540faa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
galaxyp
parents: 4
diff changeset
11 </macros>
0
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
12 <requirements>
4
12692567c7f9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
parents: 3
diff changeset
13 <requirement type="package" version="2.25.1">requests</requirement>
0
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
14 </requirements>
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
15 <stdio>
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
16 <exit_code range="1:" level="fatal" description="Error downloading proteome." />
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
17 </stdio>
1
fc8c4bd28681 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 0
diff changeset
18 <command>
0
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
19 <![CDATA[
4
12692567c7f9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
parents: 3
diff changeset
20 python '$__tool_directory__/uniprotxml_downloader.py'
6
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
21 #if $input_method.input_choice == 'common':
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
22 --search-id $input_method.organism
5
265c35540faa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
galaxyp
parents: 4
diff changeset
23 --field taxonomy_id
6
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
24 #if $input_method.reviewed:
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
25 --reviewed=$input_method.reviewed
4
12692567c7f9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
parents: 3
diff changeset
26 #end if
6
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
27 #elif $input_method.input_choice == 'enter_ids':
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
28 --field $input_method.field
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
29 #for $id in $input_method.ids.split(','):
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
30 --search-id '$id'
4
12692567c7f9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
parents: 3
diff changeset
31 #end for
6
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
32 #elif $input_method.input_choice == 'history':
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
33 --field $input_method.field
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
34 --input='${input_method.id_file}'
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
35 --column=#echo int(str($input_method.column)) - 1#
2
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
36 #end if
7
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
37 --format $format_cond.format
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
38 #if $format_cond.format == "tsv"
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
39 --output_columns #echo ','.join($format_cond.columns)
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
40 #end if
4
12692567c7f9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
parents: 3
diff changeset
41 --output '${proteome}'
0
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
42 ]]>
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
43 </command>
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
44 <inputs>
6
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
45 <conditional name="input_method">
2
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
46 <param name="input_choice" type="select" label="Select">
0
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
47 <option value="common">A Common Organism</option>
7
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
48 <option value="enter_ids">A manually entered list of accessions or taxonomy IDs/names</option>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
49 <option value="history">A history dataset with a column containing accessions or taxonomy IDs/names</option>
0
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
50 </param>
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
51 <when value="common">
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
52 <param name="organism" type="select" label="Common Organisms"
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
53 help="select species for protein database">
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
54 <options from_file="uniprot_taxons.loc">
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
55 <column name="name" index="0" />
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
56 <column name="value" index="1" />
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
57 </options>
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
58 </param>
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
59 <param name="reviewed" type="select" label="filter by reviewed status" optional="true">
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
60 <help><![CDATA[
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
61 UniProtKB/TrEMBL (unreviewed)is a large, automatically annotated database that may contain
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
62 redundant sequences, but there is a higher chance peptides will be identified.
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
63 UniProtKB/Swiss-Prot (reviewed) is a smaller, manually annotated database with
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
64 less of a chance peptides will be identified but less sequence redundancy
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
65 ]]>
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
66 </help>
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
67 <option value="yes">UniProtKB/Swiss-Prot (reviewed only)</option>
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
68 <option value="no">UniProtKB/TrEMBL (unreviewed only)</option>
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
69 </param>
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
70 </when>
6
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
71 <when value="enter_ids">
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
72 <param name="ids" type="text" label="Search ID values"
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
73 help="Enter one or more IDs (separated by commas) from http://www.uniprot.org/proteomes/">
2
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
74 <validator type="regex" message="OrganismID[,OrganismID]">^\w+( \w+)*(,\w+( \w+)*)*$</validator>
0
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
75 </param>
5
265c35540faa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
galaxyp
parents: 4
diff changeset
76 <expand macro="query_field"/>
0
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
77 </when>
2
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
78 <when value="history">
6
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
79 <param name="id_file" type="data" format="tabular,txt" label="Dataset (tab separated) with ID column"/>
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
80 <param name="column" type="data_column" data_ref="id_file" label="Column with ID"/>
5
265c35540faa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
galaxyp
parents: 4
diff changeset
81 <expand macro="query_field"/>
2
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
82 </when>
0
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
83 </conditional>
7
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
84 <conditional name="format_cond">
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
85 <param name="format" type="select" label="uniprot output format">
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
86 <option value="fasta">fasta</option>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
87 <option value="tsv">TSV</option>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
88 <option value="xml">xml</option>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
89 </param>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
90 <when value="fasta"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
91 <when value="xml"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
92 <when value="tsv">
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
93 <param name="columns" type="select" multiple="true">
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
94 <options from_url="https://rest.uniprot.org/configure/uniprotkb/result-fields">
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
95 <postprocess_expression type="ecma5.1"><![CDATA[${
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
96 var options = [];
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
97 inputs.forEach(function(group) {
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
98 var groupName = group.groupName;
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
99 group.fields.forEach(function(field) {
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
100 var D = ["accession", "id", "reviewed", "protein_name", "gene_names", "organism_name", "length"];
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
101 var selected = D.includes(field.name);
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
102 options.push([group.groupName + " - " + field.label, field.name, selected]);
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
103 });
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
104 });
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
105 return options;
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
106 }]]></postprocess_expression>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
107 </options>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
108 </param>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
109 </when>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
110 </conditional>
0
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
111 </inputs>
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
112 <outputs>
7
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
113 <data format="uniprotxml" name="proteome">
2
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
114 <change_format>
7
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
115 <when input="format_cond.format" value="fasta" format="fasta" />
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
116 <when input="format_cond.format" value="tsv" format="tsv" />
2
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
117 </change_format>
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
118 </data>
0
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
119 </outputs>
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
120 <tests>
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
121 <test>
7
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
122 <conditional name="input_method">
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
123 <param name="input_choice" value="enter_ids"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
124 <param name="ids" value="1566990"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
125 </conditional>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
126 <conditional name="format_cond">
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
127 <param name="format" value="xml"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
128 </conditional>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
129 <output name="proteome" ftype="uniprotxml">
0
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
130 <assert_contents>
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
131 <has_text text="&lt;/uniprot&gt;" />
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
132 </assert_contents>
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
133 </output>
7
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
134 <assert_stdout>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
135 <has_text_matching expression="UniProt-Release:\d{4}_\d{2}"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
136 <has_line line="Entries:0"/> <!-- searching by name using an ID -->
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
137 </assert_stdout>
0
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
138 </test>
2
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
139 <test>
7
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
140 <conditional name="input_method">
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
141 <param name="input_choice" value="enter_ids"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
142 <param name="ids" value="765963,512562"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
143 <param name="field" value="taxonomy_id"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
144 </conditional>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
145 <conditional name="format_cond">
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
146 <param name="format" value="fasta"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
147 </conditional>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
148 <output name="proteome" ftype="fasta">
5
265c35540faa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
galaxyp
parents: 4
diff changeset
149 <assert_contents>
265c35540faa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
galaxyp
parents: 4
diff changeset
150 <has_text text="Shi470" />
265c35540faa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
galaxyp
parents: 4
diff changeset
151 <has_text text="PeCan4" />
265c35540faa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
galaxyp
parents: 4
diff changeset
152 </assert_contents>
265c35540faa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
galaxyp
parents: 4
diff changeset
153 </output>
7
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
154 <assert_stdout>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
155 <has_text_matching expression="UniProt-Release:\d{4}_\d{2}"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
156 <has_text_matching expression="Entries:\d+"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
157 <has_line line="Entries:0" negate="true"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
158 </assert_stdout>
5
265c35540faa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
galaxyp
parents: 4
diff changeset
159 </test>
265c35540faa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
galaxyp
parents: 4
diff changeset
160 <test>
7
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
161 <conditional name="input_method">
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
162 <param name="input_choice" value="enter_ids"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
163 <param name="ids" value="Shi470,PeCan4"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
164 <param name="field" value="taxonomy_name"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
165 </conditional>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
166 <conditional name="format_cond">
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
167 <param name="format" value="fasta" ftype="fasta"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
168 </conditional>
2
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
169 <output name="proteome">
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
170 <assert_contents>
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
171 <has_text text="Shi470" />
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
172 <has_text text="PeCan4" />
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
173 </assert_contents>
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
174 </output>
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
175 </test>
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
176 <test>
7
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
177 <conditional name="input_method">
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
178 <param name="input_choice" value="enter_ids"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
179 <param name="ids" value="E1Q2I0,E1Q3C4"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
180 <param name="field" value="accession"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
181 </conditional>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
182 <conditional name="format_cond">
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
183 <param name="format" value="fasta"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
184 </conditional>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
185 <output name="proteome" ftype="fasta">
6
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
186 <assert_contents>
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
187 <has_text text="E1Q2I0" />
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
188 <has_text text="E1Q3C4" />
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
189 </assert_contents>
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
190 </output>
7
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
191 <assert_stdout>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
192 <has_text_matching expression="UniProt-Release:\d{4}_\d{2}"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
193 <has_text_matching expression="Entries:\d+"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
194 <has_line line="Entries:0" negate="true"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
195 </assert_stdout>
6
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
196 </test>
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
197 <test>
7
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
198 <conditional name="input_method">
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
199 <param name="input_choice" value="history"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
200 <param name="id_file" value="Helicobacter_strains.tsv" ftype="tabular"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
201 <param name="column" value="1"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
202 <param name="field" value="taxonomy_name"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
203 </conditional>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
204 <conditional name="format_cond">
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
205 <param name="format" value="fasta"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
206 </conditional>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
207 <output name="proteome" ftype="fasta">
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
208 <assert_contents>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
209 <has_text text="Shi470" />
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
210 <has_text text="PeCan4" />
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
211 </assert_contents>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
212 </output>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
213 <assert_stdout>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
214 <has_text_matching expression="UniProt-Release:\d{4}_\d{2}"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
215 <has_text_matching expression="Entries:\d+"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
216 <has_line line="Entries:0" negate="true"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
217 </assert_stdout>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
218 </test>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
219 <test>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
220 <conditional name="input_method">
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
221 <param name="input_choice" value="history"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
222 <param name="id_file" value="Helicobacter_strains_ids.tsv" ftype="tabular"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
223 <param name="column" value="2"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
224 <param name="field" value="taxonomy_id"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
225 </conditional>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
226 <conditional name="format_cond">
2
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
227 <param name="format" value="fasta"/>
7
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
228 </conditional>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
229 <output name="proteome" ftype="fasta">
2
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
230 <assert_contents>
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
231 <has_text text="Shi470" />
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
232 <has_text text="PeCan4" />
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
233 </assert_contents>
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
234 </output>
7
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
235 <assert_stdout>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
236 <has_text_matching expression="UniProt-Release:\d{4}_\d{2}"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
237 <has_text_matching expression="Entries:\d+"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
238 <has_line line="Entries:0" negate="true"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
239 </assert_stdout>
2
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
240 </test>
4
12692567c7f9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
parents: 3
diff changeset
241 <test>
7
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
242 <conditional name="input_method">
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
243 <param name="input_choice" value="history"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
244 <param name="id_file" value="Helicobacter_protein_accessions.tsv" ftype="tabular"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
245 <param name="column" value="1"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
246 <param name="field" value="accession"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
247 </conditional>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
248 <conditional name="format_cond">
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
249 <param name="format" value="fasta"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
250 </conditional>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
251 <output name="proteome" ftype="fasta">
6
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
252 <assert_contents>
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
253 <has_text text="E1Q2I0" />
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
254 <has_text text="E1Q3C4" />
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
255 </assert_contents>
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
256 </output>
7
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
257 <assert_stdout>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
258 <has_text_matching expression="UniProt-Release:\d{4}_\d{2}"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
259 <has_text_matching expression="Entries:\d+"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
260 <has_line line="Entries:0" negate="true"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
261 </assert_stdout>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
262 </test>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
263 <!-- tsv output -->
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
264 <test>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
265 <conditional name="input_method">
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
266 <param name="input_choice" value="enter_ids"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
267 <param name="ids" value="765963,512562"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
268 <param name="field" value="taxonomy_id"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
269 </conditional>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
270 <conditional name="format_cond">
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
271 <param name="format" value="tsv"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
272 </conditional>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
273 <output name="proteome" ftype="tsv">
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
274 <assert_contents>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
275 <has_n_columns n="7" />
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
276 <has_text text="Shi470" />
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
277 <has_text text="PeCan4" />
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
278 </assert_contents>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
279 </output>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
280 <assert_stdout>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
281 <has_text_matching expression="UniProt-Release:\d{4}_\d{2}"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
282 <has_text_matching expression="Entries:\d+"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
283 <has_line line="Entries:0" negate="true"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
284 </assert_stdout>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
285 </test>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
286 <!-- tsv output non default columns-->
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
287 <test>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
288 <conditional name="input_method">
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
289 <param name="input_choice" value="enter_ids"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
290 <param name="ids" value="765963,512562"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
291 <param name="field" value="taxonomy_id"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
292 </conditional>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
293 <conditional name="format_cond">
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
294 <param name="format" value="tsv"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
295 <param name="columns" value="accession,sequence"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
296 </conditional>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
297 <output name="proteome" ftype="tsv">
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
298 <assert_contents>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
299 <has_n_columns n="2" />
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
300 <has_text text="Shi470" negate="true"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
301 <has_text text="B2US14" />
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
302 </assert_contents>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
303 </output>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
304 <assert_stdout>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
305 <has_text_matching expression="UniProt-Release:\d{4}_\d{2}"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
306 <has_text_matching expression="Entries:\d+"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
307 <has_line line="Entries:0" negate="true"/>
4ddc8da62671 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 6
diff changeset
308 </assert_stdout>
6
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
309 </test>
0
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
310 </tests>
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
311 <help>
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
312 <![CDATA[
2
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
313 **UniProt Downloader**
0
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
314
2
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
315 Downloads either a UniProtXML file or a fasta file from UniProtKB
0
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
316
2
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
317 The Morpheus proteomics search algorithm can use the UniProtXML format as a search database.
0
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
318
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
319 Available proteomes: http://www.uniprot.org/proteomes/
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
320
2
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
321 Available taxon names: http://www.uniprot.org/taxonomy/
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
322
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
323 Example taxon: http://www.uniprot.org/taxonomy/512562
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
324
6
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
325 Example protein: https://www.uniprot.org/uniprotkb/E1Q2I0/entry
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
326
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
327 Description of query fields: https://www.uniprot.org/help/query-fields
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
328
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
329 IDs can be entered as text or read from a column in a tabular dataset from your history.
2
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
330
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
331 Example IDs and names releated to the Bacteria Helicobacter pylori (strain Shi470) ::
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
332
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
333
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
334 - 512562
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
335 - Shi470
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
336 - Helicobacter pylori
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
337 - Helicobacter
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
338 - Helicobacteraceae
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
339
6
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
340 Example protein accession numbers from Helicobacter pylori:
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
341
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
342 - E1Q2I0
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
343 - E1Q3C4
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
galaxyp
parents: 5
diff changeset
344
2
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 1
diff changeset
345
0
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
346 UniProtKB help: http://www.uniprot.org/help/uniprotkb
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
347
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
348 ]]>
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
349 </help>
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
350 <citations>
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
351 <citation type="doi">10.1093/nar/gku989</citation>
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
352 </citations>
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
353 </tool>
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
galaxyp
parents:
diff changeset
354