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comparison load_ref_data.xml @ 0:faeb871ac76d draft

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author ieguinoa
date Tue, 25 May 2021 21:51:27 +0000
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1 <tool id="load_reference_datasets" name="Load built-in reference data to history" version="0.0.1" >
2 <command><![CDATA[
3 #if $input_source.table_type_selector == "gff":
4 out_name=\$(sed 's/ /_/g' <<< "$input_source.gff.fields.name");
5 cp $input_source.gff.fields.path \$out_name.gff;
6 #else:
7 out_name=\$(sed 's/ /_/g' <<< "$input_source.fasta.fields.name");
8 cp $input_source.fasta.fields.path \$out_name.fasta;
9 #end if
10 ]]></command>
11 <inputs>
12 <conditional name="input_source">
13 <param name="table_type_selector" type="select" label="Select the type of file you want to access">
14 <option value="gff" selected='True'>Annotations (GFF/GTF) files</option>
15 <option value="fasta">FASTA Files (Genomes files / cDNA / etc)</option>
16 </param>
17 <when value="full">
18 <param name="gff" type="select" label="Select the annotation file from the list" help="If your genome of interest is not listed contact the Galaxy admin">
19 <options from_data_table="all_gff"/>
20 </param>
21 </when>
22 <when value="fasta">
23 <param name="fasta" type="select" label="Select the FASTA file from the list" help="if your genome of interest is not listed contact the Galaxy admin">
24 <options from_data_table="all_fasta"/>
25 </param>
26
27 </when>
28 </conditional>
29 </inputs>
30 <outputs>
31 <data name="copied_file" label="">
32 <discover_datasets pattern="__designation_and_ext__" visible="true" />
33 </data>
34 </outputs>
35 <help>
36 **What it does**
37
38 This tool allows loading different built-in datasets into your history using the same data tables access that any other tool uses.
39
40
41 </help>
42 </tool>