Mercurial > repos > earlhaminst > ensembl_get_genetree

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 8f8808de862973aedbf87abd4dfa9d2dc7219322
author earlhaminst
date Mon, 17 Feb 2025 14:49:15 +0000
parents 515e7181d5e9
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7:515e7181d5e9 8:935de83b470b
1 <tool id="get_genetree" name="Get gene tree by Ensembl ID" version="0.1.2"> 1 <tool id="get_genetree" name="Get gene tree by Ensembl ID" version="1.0.0">
2 <description>using REST API</description> 2 <description>using REST API</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import>
4 <xml name="sequence_conditional"> 5 <xml name="sequence_conditional">
5 <conditional name="sequence"> 6 <conditional name="sequence">
6 <param name="sequence_selector" type="select" label="Sequence type" help="The type of sequences to bring back. If 'None', no sequence is returned"> 7 <param name="sequence_selector" type="select" label="Sequence type" help="The type of sequences to bring back. If 'None', no sequence is returned">
7 <option value="protein" selected="true">Protein</option> 8 <option value="protein" selected="true">Protein</option>
8 <option value="cdna">cDNA</option> 9 <option value="cdna">cDNA</option>
19 <when value="none" /> 20 <when value="none" />
20 </conditional> 21 </conditional>
21 </xml> 22 </xml>
22 </macros> 23 </macros>
23 <requirements> 24 <requirements>
24 <requirement type="package" version="2.12.4">requests</requirement> 25 <requirement type="package" version="3.13">python</requirement>
25 <requirement type="package" version="1.10.0">six</requirement> 26 <requirement type="package" version="2.32.3">requests</requirement>
26 </requirements> 27 </requirements>
27 <command detect_errors="exit_code"> 28 <command detect_errors="exit_code">
28 <![CDATA[ 29 <![CDATA[
29 python '$__tool_directory__/get_genetree.py' 30 python3 '$__tool_directory__/get_genetree.py'
30 --id_type $input_type 31 --id_type ${input_type_conditional.input_type}
32 #if $input_type_conditional.input_type == "gene_id"
33 --species ${input_type_conditional.species}
34 #end if
31 -i '$input' 35 -i '$input'
32 --format ${output_format.output_format_selector} 36 --format ${output_format.output_format_selector}
33 #if $output_format.output_format_selector == 'json' 37 #if $output_format.output_format_selector == 'json'
34 -s ${output_format.sequence.sequence_selector} 38 -s ${output_format.sequence.sequence_selector}
35 #if $output_format.sequence.sequence_selector != 'none' 39 #if $output_format.sequence.sequence_selector != 'none'
47 > '$output' 51 > '$output'
48 ]]> 52 ]]>
49 </command> 53 </command>
50 54
51 <inputs> 55 <inputs>
52 <param name="input_type" type="select" label="Input type"> 56 <conditional name="input_type_conditional">
53 <option value="gene_id" selected="true">Ensembl gene ID</option> 57 <param name="input_type" type="select" label="Input type">
54 <option value="gene_tree_id">Ensembl genetree ID</option> 58 <option value="gene_id" selected="true">Ensembl gene ID</option>
55 </param> 59 <option value="gene_tree_id">Ensembl genetree ID</option>
60 </param>
61 <when value="gene_id">
62 <param name="species" type="text" label="Species name/alias">
63 <validator type="empty_field" />
64 </param>
65 </when>
66 <when value="gene_tree_id" />
67 </conditional>
56 <param name="input" type="text" label="Ensembl ID"> 68 <param name="input" type="text" label="Ensembl ID">
57 <validator type="empty_field" /> 69 <validator type="empty_field" />
58 </param> 70 </param>
59 <conditional name="output_format"> 71 <conditional name="output_format">
60 <param name="output_format_selector" type="select" label="Output format"> 72 <param name="output_format_selector" type="select" label="Output format">
96 </data> 108 </data>
97 </outputs> 109 </outputs>
98 110
99 <tests> 111 <tests>
100 <test> 112 <test>
101 <param name="input_type" value="gene_id" /> 113 <conditional name="input_type_conditional">
114 <param name="input_type" value="gene_id" />
115 <param name="species" value="Chicken" />
116 </conditional>
102 <param name="input" value="ENSGALP00010009242" /> 117 <param name="input" value="ENSGALP00010009242" />
103 <param name="output_format_selector" value="json" /> 118 <param name="output_format_selector" value="json" />
104 <param name="sequence_selector" value="protein" /> 119 <param name="sequence_selector" value="protein" />
105 <param name="aligned" value="0" /> 120 <param name="aligned" value="0" />
106 <param name="cigar" value="0" /> 121 <param name="cigar" value="0" />
112 <has_text text="ENSMUSG00000041147" /> 127 <has_text text="ENSMUSG00000041147" />
113 </assert_contents> 128 </assert_contents>
114 </output> 129 </output>
115 </test> 130 </test>
116 <test> 131 <test>
117 <param name="input_type" value="gene_id" /> 132 <conditional name="input_type_conditional">
133 <param name="input_type" value="gene_id" />
134 <param name="species" value="Chicken" />
135 </conditional>
118 <param name="input" value="ENSGALP00010009242" /> 136 <param name="input" value="ENSGALP00010009242" />
119 <param name="output_format_selector" value="nh" /> 137 <param name="output_format_selector" value="nh" />
120 <param name="nh_format" value="simple" /> 138 <param name="nh_format" value="simple" />
121 <output name="output" ftype="nhx"> 139 <output name="output" ftype="nhx">
122 <assert_contents> 140 <assert_contents>
124 <has_text text="ENSP00000369497" /> 142 <has_text text="ENSP00000369497" />
125 </assert_contents> 143 </assert_contents>
126 </output> 144 </output>
127 </test> 145 </test>
128 <test> 146 <test>
129 <param name="input_type" value="gene_tree_id" /> 147 <conditional name="input_type_conditional">
148 <param name="input_type" value="gene_tree_id" />
149 </conditional>
130 <param name="input" value="ENSGT00390000003602" /> 150 <param name="input" value="ENSGT00390000003602" />
131 <param name="output_format_selector" value="json" /> 151 <param name="output_format_selector" value="json" />
132 <param name="sequence_selector" value="protein" /> 152 <param name="sequence_selector" value="protein" />
133 <param name="aligned" value="0" /> 153 <param name="aligned" value="0" />
134 <param name="cigar" value="0" /> 154 <param name="cigar" value="0" />
140 <has_text text="ENSMUSG00000041147" /> 160 <has_text text="ENSMUSG00000041147" />
141 </assert_contents> 161 </assert_contents>
142 </output> 162 </output>
143 </test> 163 </test>
144 <test> 164 <test>
145 <param name="input_type" value="gene_tree_id" /> 165 <conditional name="input_type_conditional">
166 <param name="input_type" value="gene_tree_id" />
167 </conditional>
146 <param name="input" value="ENSGT00390000003602" /> 168 <param name="input" value="ENSGT00390000003602" />
147 <param name="output_format_selector" value="phyloxml" /> 169 <param name="output_format_selector" value="phyloxml" />
148 <param name="sequence_selector" value="protein" /> 170 <param name="sequence_selector" value="protein" />
149 <param name="aligned" value="0" /> 171 <param name="aligned" value="0" />
150 <output name="output" ftype="phyloxml"> 172 <output name="output" ftype="phyloxml">
162 <![CDATA[ 184 <![CDATA[
163 **What it does** 185 **What it does**
164 186
165 Retrieve a gene tree from Ensembl using its REST API. 187 Retrieve a gene tree from Ensembl using its REST API.
166 188
167 Uses the `"GET genetree/id"`_ and `"GET genetree/member/id"`_ API endpoint. 189 Uses the `"GET genetree/id/:id"`_ and `"GET genetree/member/id/:species/:id"`_ API endpoints.
168 190
169 .. _"GET genetree/id": https://rest.ensembl.org/documentation/info/genetree 191 .. _"GET genetree/id/:id": https://rest.ensembl.org/documentation/info/genetree
170 .. _"GET genetree/member/id": https://rest.ensembl.org/documentation/info/genetree_member_id 192 .. _"GET genetree/member/id/:species/:id": https://rest.ensembl.org/documentation/info/genetree_species_member_id
171 ]]> 193 ]]>
172 </help> 194 </help>
173 <citations> 195 <expand macro="citations" />
174 </citations>
175 </tool> 196 </tool>