Mercurial > repos > earlhaminst > ensembl_get_sequences

comparison get_sequences.xml @ 5:0fa1d1cc417d draft

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"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit ed32f2e6d8174873cefcbe141084f857f84b0586"
author earlhaminst
date Thu, 31 Oct 2019 07:50:07 -0400
parents 3b686142e9c2
children 7af66c2b3831
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4:3b686142e9c2 5:0fa1d1cc417d
5 <requirement type="package" version="1.10.0">six</requirement> 5 <requirement type="package" version="1.10.0">six</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"> 7 <command detect_errors="exit_code">
8 <![CDATA[ 8 <![CDATA[
9 python '$__tool_directory__/get_sequences.py' 9 python '$__tool_directory__/get_sequences.py'
10 -s $species_selector
11 --expand_3prime $expand_3prime 10 --expand_3prime $expand_3prime
12 --expand_5prime $expand_5prime 11 --expand_5prime $expand_5prime
13 -t $type_selector 12 -t $type_selector
14 -i '$input' 13 -i '$input'
15 > '$output' 14 > '$output'
16 ]]> 15 ]]>
17 </command> 16 </command>
18 17
19 <inputs> 18 <inputs>
20 <param name="input" type="data" format="txt" label="List of Ensembl IDs" /> 19 <param name="input" type="data" format="txt" label="List of Ensembl IDs" />
21 <param name="species_selector" type="select" label="Select Species">
22 <option value="ensembl" selected="true">Vertebrates</option>
23 <option value="ensemblgenomes">Other species</option>
24 </param>
25 <param name="expand_3prime" type="integer" value="0" min="0" label="expand_3prime" help="Expand each sequence downstream of the sequence by this many basepairs. Only available when using genomic sequence type." /> 20 <param name="expand_3prime" type="integer" value="0" min="0" label="expand_3prime" help="Expand each sequence downstream of the sequence by this many basepairs. Only available when using genomic sequence type." />
26 <param name="expand_5prime" type="integer" value="0" min="0" label="expand_5prime" help="Expand each sequence downstream of the sequence by this many basepairs. Only available when using genomic sequence type." /> 21 <param name="expand_5prime" type="integer" value="0" min="0" label="expand_5prime" help="Expand each sequence downstream of the sequence by this many basepairs. Only available when using genomic sequence type." />
27 <param name="type_selector" type="select" label="Type" help="Type of sequence. Defaults to genomic where applicable, i.e. not translations. cDNA refers to the spliced transcript sequence with UTR; CDS refers to the spliced transcript sequence without UTR"> 22 <param name="type_selector" type="select" label="Type" help="Type of sequence. Defaults to genomic where applicable, i.e. not translations. cDNA refers to the spliced transcript sequence with UTR; CDS refers to the spliced transcript sequence without UTR">
28 <option value="genomic" selected="true">Genomic</option> 23 <option value="genomic" selected="true">Genomic</option>
29 <option value="cds">CDS</option> 24 <option value="cds">CDS</option>