Mercurial > repos > earlhaminst > ensembl_get_genetree
comparison get_genetree/get_genetree.xml @ 0:f0018341e9f6 draft
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
author | earlhaminst |
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date | Thu, 11 Aug 2016 14:29:07 -0400 |
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1 <tool id="get_genetree" name="Get gene tree by Ensembl ID" version="0.1.1"> | |
2 <description>using REST API</description> | |
3 <macros> | |
4 <xml name="sequence_conditional"> | |
5 <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 <option value="protein" selected="true">Protein</option> | |
8 <option value="cdna">cDNA</option> | |
9 <option value="none">None</option> | |
10 </param> | |
11 <when value="protein"> | |
12 <param name="aligned" type="boolean" truevalue="1" falsevalue="0" label="Return the aligned sequences instead of the original ones" help="The original sequences contain no insertions" /> | |
13 <yield /> | |
14 </when> | |
15 <when value="cdna"> | |
16 <param name="aligned" type="boolean" truevalue="1" falsevalue="0" label="Return the aligned sequences instead of the original ones" help="The original sequences contain no insertions" /> | |
17 <yield /> | |
18 </when> | |
19 <when value="none" /> | |
20 </conditional> | |
21 </xml> | |
22 </macros> | |
23 <requirements> | |
24 <requirement type="package" version="2.7">requests</requirement> | |
25 </requirements> | |
26 <command> | |
27 <![CDATA[ | |
28 python $__tool_directory__/get_genetree.py | |
29 --id_type $input_type | |
30 -i "$input" | |
31 -g $species_selector | |
32 --format ${output_format.output_format_selector} | |
33 #if $output_format.output_format_selector == 'json' | |
34 -s ${output_format.sequence.sequence_selector} | |
35 #if $output_format.sequence.sequence_selector != 'none' | |
36 -a ${output_format.sequence.aligned} | |
37 -c ${output_format.sequence.cigar} | |
38 #end if | |
39 #elif $output_format.output_format_selector == 'phyloxml' | |
40 -s ${output_format.sequence.sequence_selector} | |
41 #if $output_format.sequence.sequence_selector != 'none' | |
42 -a ${output_format.sequence.aligned} | |
43 #end if | |
44 #else | |
45 --nh_format $output_format.nh_format | |
46 #end if | |
47 > "$output" | |
48 ]]> | |
49 </command> | |
50 | |
51 <inputs> | |
52 <param name="input_type" type="select" label="Input type"> | |
53 <option value="gene_id" selected="true">Ensembl gene ID</option> | |
54 <option value="gene_tree_id">Ensembl genetree ID</option> | |
55 </param> | |
56 <param name="input" type="text" label="Ensembl ID"> | |
57 <validator type="empty_field" /> | |
58 </param> | |
59 <param name="species_selector" type="select" label="Select Species"> | |
60 <option value="ensembl" selected="true">Vertebrates</option> | |
61 <option value="ensemblgenomes">Other species</option> | |
62 </param> | |
63 <conditional name="output_format"> | |
64 <param name="output_format_selector" type="select" label="Output format"> | |
65 <option value="json" selected="true">JSON</option> | |
66 <!-- <option value="orthoxml">OrthoXML</option> --> | |
67 <option value="phyloxml">phyloXML</option> | |
68 <option value="nh">Newick</option> | |
69 </param> | |
70 <when value="json"> | |
71 <expand macro="sequence_conditional"> | |
72 <param name="cigar" type="boolean" truevalue="1" falsevalue="0" label="Output the sequences also in CIGAR format" /> | |
73 </expand> | |
74 </when> | |
75 <when value="phyloxml"> | |
76 <expand macro="sequence_conditional" /> | |
77 </when> | |
78 <when value="nh"> | |
79 <param name="nh_format" type="select" label="NH format" help="The format of a NH (New Hampshire) request"> | |
80 <option value="simple" selected="true">simple</option> | |
81 <option value="full">full</option> | |
82 <option value="display_label_composite">display_label_composite</option> | |
83 <option value="species">species</option> | |
84 <option value="species_short_name">species_short_name</option> | |
85 <option value="ncbi_taxon">ncbi_taxon</option> | |
86 <option value="ncbi_name">ncbi_name</option> | |
87 <option value="njtree">njtree</option> | |
88 <option value="phylip">phylip</option> | |
89 </param> | |
90 </when> | |
91 </conditional> | |
92 </inputs> | |
93 | |
94 <outputs> | |
95 <data name="output" format="json" label="$(tool.name) on ${input_type} ${input}"> | |
96 <change_format> | |
97 <when input="output_format.output_format_selector" value="phyloxml" format="phyloxml" /> | |
98 <when input="output_format.output_format_selector" value="nh" format="nhx" /> | |
99 </change_format> | |
100 </data> | |
101 </outputs> | |
102 | |
103 <tests> | |
104 <test> | |
105 <param name="input_type" value="gene_id" /> | |
106 <param name="input" value="ENSGALP00000027524" /> | |
107 <param name="output_format_selector" value="json" /> | |
108 <param name="sequence_selector" value="protein" /> | |
109 <param name="aligned" value="0" /> | |
110 <param name="cigar" value="0" /> | |
111 <output name="output" file="genetree.json" ftype="json" /> | |
112 </test> | |
113 <test> | |
114 <param name="input_type" value="gene_tree_id" /> | |
115 <param name="input" value="ENSGT00390000003602" /> | |
116 <param name="output_format_selector" value="json" /> | |
117 <param name="sequence_selector" value="protein" /> | |
118 <param name="aligned" value="0" /> | |
119 <param name="cigar" value="0" /> | |
120 <output name="output" file="genetree.json" fype="json" /> | |
121 </test> | |
122 <test> | |
123 <param name="input_type" value="gene_tree_id" /> | |
124 <param name="input" value="ENSGT00390000003602" /> | |
125 <param name="output_format_selector" value="phyloxml" /> | |
126 <param name="sequence_selector" value="protein" /> | |
127 <param name="aligned" value="0" /> | |
128 <output name="output" file="genetree.phyloxml" ftype="phyloxml" compare="sim_size" /> | |
129 </test> | |
130 </tests> | |
131 | |
132 <help> | |
133 <![CDATA[ | |
134 **What it does** | |
135 | |
136 Retrieve a gene tree from Ensembl using its REST API. | |
137 | |
138 Uses the `"GET genetree/id"`_ and `"GET genetree/member/id"`_ API endpoint. | |
139 | |
140 .. _"GET genetree/id": http://rest.ensembl.org/documentation/info/genetree | |
141 .. _"GET genetree/member/id": http://rest.ensembl.org/documentation/info/genetree_member_id | |
142 ]]> | |
143 </help> | |
144 <citations> | |
145 </citations> | |
146 </tool> |