comparison macro_lumpy_smoove.xml @ 0:ee8fc44b1655 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 515176ccca845de0b1a0c08417238bfa9ea45360"
author artbio
date Tue, 25 Aug 2020 11:35:02 -0400
parents
children 49a8a327cc72
comparison
equal deleted inserted replaced
-1:000000000000 0:ee8fc44b1655
1 <macros>
2 <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token>
3
4 <token name="@set_fasta_index@"><![CDATA[
5 #if str( $reference_source.reference_source_selector ) == "history":
6 ln -s '${reference_source.ref_file}' reference.fa &&
7 samtools faidx 'reference.fa' 2>&1 || echo "Error running samtools faidx for lumpy_smoove" >&2 &&
8 #else:
9 ln -s '${source.index.fields.path}' reference.fa &&
10 ln -s '${source.index.fields.path}.fai' reference.fa.fai &&
11 #end if
12 ]]></token>
13
14 <macro name="reference_source_conditional">
15 <conditional name="reference_source">
16 <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
17 <option value="cached">Use a built-in genome index</option>
18 <option value="history">Use a genome from history and build index</option>
19 </param>
20 <when value="cached">
21 <param name="index" type="select" label="Using built-in genome" help="Select genome from the list">
22 <options from_data_table="fasta_indexes">
23 <filter type="sort_by" column="2" />
24 <validator type="no_options" message="No indexes are available" />
25 </options>
26 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
27 </param>
28 </when>
29 <when value="history">
30 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence"
31 help="You can upload a FASTA sequence to the history and use it as reference" />
32 </when>
33 </conditional>
34 </macro>
35 </macros>