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comparison macros.xml @ 0:f7c0a0030254 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 0851e9e6d46223a8233c56f3b0bcf14e19d63916
author bgruening
date Tue, 23 May 2023 13:43:07 +0000
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children 6d8444408ff1
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-1:000000000000 0:f7c0a0030254
1 <macros>
2 <token name="@TOOL_VERSION@">1.1.0</token>
3 <token name="@VERSION_SUFFIX@">0</token>
4 <xml name="requirements">
5 <requirements>
6 <requirement type="package" version="@TOOL_VERSION@">agat</requirement>
7 <requirement type="package" version="0.34">perl-statistics-r</requirement>
8 </requirements>
9 </xml>
10 <xml name="biotools">
11 <xrefs>
12 <xref type="bio.tools">agat</xref>
13 </xrefs>
14 </xml>
15 <xml name="citations">
16 <citations>
17 <citation type="doi">10.5281/zenodo.3552717</citation>
18 </citations>
19 </xml>
20 <xml name="ANNOTATION_INPUT" token_format="gff,gtf,gff3,gff3.gz">
21 <param argument="--gff" type="data" format="@FORMAT@" label="Annotation file" help="Input GTF/GFF file" />
22 </xml>
23
24 <xml name="REFERENCE_FASTA">
25 <conditional name="reference_genome">
26 <param name="source" type="select" label="Source for the reference genome" help="Built-in references were created using default options.">
27 <option value="indexed" selected="true">Use a built-in genome</option>
28 <option value="history" selected="true">Use a genome from history</option>
29 </param>
30 <when value="indexed">
31 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team.">
32 <options from_data_table="fasta_indexes">
33 <filter type="sort_by" column="2" />
34 <validator type="no_options" message="No genomes are available for the selected input dataset" />
35 </options>
36 </param>
37 </when>
38 <when value="history">
39 <param name="history_item" type="data" format="fasta" label="Reference genome" help="A reference genome in FASTA format" />
40 </when>
41 </conditional>
42 </xml>
43 <token name="@input_annotation_single@"><![CDATA[
44 #set $input_annotation = 'annotation.' + str($tool.gff.ext)
45 ln -s '${tool.gff}' $input_annotation &&
46 ]]></token>
47 <token name="@input_reference@"><![CDATA[
48 #if $tool.reference_genome.source == 'history':
49 #set $ref_genome = 'reference.fasta'
50 ln -s -f '${tool.reference_genome.history_item}' $ref_genome &&
51 #else:
52 #set $ref_genome = $tool.reference_genome.index.fields.path
53 #end if
54 ]]></token>
55 <token name="@input_annotation_double@"><![CDATA[
56 #set $input1 = 'annotation1.' + str($tool.input_annotation1.ext)
57 #set $input2 = 'annotation2.' + str($tool.input_annotation2.ext)
58 ln -s '${tool.input_annotation1}' $input1 &&
59 ln -s '${tool.input_annotation2}' $input2 &&
60 ]]></token>
61
62
63 </macros>