Mercurial > repos > earlhaminst > ensembl_get_genetree

comparison get_genetree.xml @ 2:950d9d11b6fb draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit 099d38157cec200f0a343579ca9babcd8acb266f
author earlhaminst
date Wed, 21 Dec 2016 15:16:35 -0500
parents 98aba0efe77a
children 181e12d6ac96
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1:98aba0efe77a 2:950d9d11b6fb
1 <tool id="get_genetree" name="Get gene tree by Ensembl ID" version="0.1.1"> 1 <tool id="get_genetree" name="Get gene tree by Ensembl ID" version="0.1.2">
2 <description>using REST API</description> 2 <description>using REST API</description>
3 <macros> 3 <macros>
4 <xml name="sequence_conditional"> 4 <xml name="sequence_conditional">
5 <conditional name="sequence"> 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"> 6 <param name="sequence_selector" type="select" label="Sequence type" help="The type of sequences to bring back. If 'None', no sequence is returned">
19 <when value="none" /> 19 <when value="none" />
20 </conditional> 20 </conditional>
21 </xml> 21 </xml>
22 </macros> 22 </macros>
23 <requirements> 23 <requirements>
24 <requirement type="package" version="2.7">requests</requirement> 24 <requirement type="package" version="2.12.4">requests</requirement>
25 <requirement type="package" version="1.10.0">six</requirement>
25 </requirements> 26 </requirements>
26 <command> 27 <command>
27 <![CDATA[ 28 <![CDATA[
28 python $__tool_directory__/get_genetree.py 29 python $__tool_directory__/get_genetree.py
29 --id_type $input_type 30 --id_type $input_type
106 <param name="input" value="ENSGALP00000027524" /> 107 <param name="input" value="ENSGALP00000027524" />
107 <param name="output_format_selector" value="json" /> 108 <param name="output_format_selector" value="json" />
108 <param name="sequence_selector" value="protein" /> 109 <param name="sequence_selector" value="protein" />
109 <param name="aligned" value="0" /> 110 <param name="aligned" value="0" />
110 <param name="cigar" value="0" /> 111 <param name="cigar" value="0" />
111 <output name="output" file="genetree.json" ftype="json" /> 112 <output name="output" file="genetree.json" ftype="json" compare="sim_size" />
112 </test> 113 </test>
113 <test> 114 <test>
114 <param name="input_type" value="gene_tree_id" /> 115 <param name="input_type" value="gene_tree_id" />
115 <param name="input" value="ENSGT00390000003602" /> 116 <param name="input" value="ENSGT00390000003602" />
116 <param name="output_format_selector" value="json" /> 117 <param name="output_format_selector" value="json" />
117 <param name="sequence_selector" value="protein" /> 118 <param name="sequence_selector" value="protein" />
118 <param name="aligned" value="0" /> 119 <param name="aligned" value="0" />
119 <param name="cigar" value="0" /> 120 <param name="cigar" value="0" />
120 <output name="output" file="genetree.json" ftype="json" /> 121 <output name="output" file="genetree.json" ftype="json" compare="sim_size" />
121 </test> 122 </test>
122 <test> 123 <test>
123 <param name="input_type" value="gene_tree_id" /> 124 <param name="input_type" value="gene_tree_id" />
124 <param name="input" value="ENSGT00390000003602" /> 125 <param name="input" value="ENSGT00390000003602" />
125 <param name="output_format_selector" value="phyloxml" /> 126 <param name="output_format_selector" value="phyloxml" />