Mercurial > repos > ieguinoa > data_manager_fetch_tx2gene

comparison data_manager/data_manager_fetch_tx2gene.xml @ 3:d71f65b854de draft

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author ieguinoa
date Fri, 19 Oct 2018 07:36:02 -0400
parents 7d3ffe28ff3f
children bacd91d8b05a
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2:7d3ffe28ff3f 3:d71f65b854de
1 <tool id="data_manager_fetch_tx2gene" name="Create entries in tx2gene data table" version="0.0.1" tool_type="manage_data"> 1 <tool id="data_manager_fetch_tx2gene" name="Create entries in tx2gene data table" version="0.0.1" tool_type="manage_data">
2 <description>fetching</description> 2 <description>fetching</description>
3 <requirements>
4 <requirement type="package" version="1.26.4">bioconductor-genomicfeatures</requirement>
5 <requirement type="package">r-getopt</requirement>
6 </requirements>
7
3 <command><![CDATA[ 8 <command><![CDATA[
4 python "$__tool_directory__"/data_manager_fetch_tx2gene.py "${out_file}" 9 python "$__tool_directory__"/data_manager_fetch_tx2gene.py "${out_file}"
5 --type $file_type 10 --type $file_type
6 --dbkey_description ${ dbkey.get_display_text() } 11 --dbkey_description ${ dbkey.get_display_text() }
7 --base_dir $__tool_directory__ 12 --base_dir $__tool_directory__
12 <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" /> 17 <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" />
13 <param type="text" name="sequence_name" value="" label="Name of sequence" /> 18 <param type="text" name="sequence_name" value="" label="Name of sequence" />
14 <param type="text" name="sequence_id" value="" label="ID for sequence" /> 19 <param type="text" name="sequence_id" value="" label="ID for sequence" />
15 20
16 <param name="file_type" type="select" label="Select input type: GFF/GTF file(features will be extracted to create tx2gene table) or transcript to gene table file(tab separated)"> 21 <param name="file_type" type="select" label="Select input type: GFF/GTF file(features will be extracted to create tx2gene table) or transcript to gene table file(tab separated)">
17 <option value="gff_gtf">GFF/GTF file</option> 22 <option value="gtf">GTF file</option>
23 <option value="gff3">GFF3 file</option>
18 <option value="tx2gene">tx2gene</option> 24 <option value="tx2gene">tx2gene</option>
19 </param> 25 </param>
20 <conditional name="reference_source"> 26 <conditional name="reference_source">
21 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> 27 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
22 <option value="url">URL</option> 28 <option value="url">URL</option>
23 <option value="history">History</option> 29 <option value="history">History</option>
24 <option value="directory">Directory on Server</option> 30 <option value="directory">Directory on Server</option>