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comparison macros.xml @ 0:ba3910d7bd99 draft

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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/transindel commit f102f45fafcda3ee868765784d2f69d2dcad6233-dirty"
author jjohnson
date Fri, 27 Mar 2020 10:01:26 -0400
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-1:000000000000 0:ba3910d7bd99
1 <macros>
2 <token name="@VERSION@">1.0</token>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="@VERSION@">transindel</requirement>
6 <yield/>
7 </requirements>
8 </xml>
9 <xml name="citations">
10 <citations>
11 <citation type="doi">10.1186/s12864-018-4671-4</citation>
12 <yield />
13 </citations>
14 </xml>
15 <xml name="version_command">
16 <version_command>transIndel_build_DNA.py -v</version_command>
17 </xml>
18 <xml name="reference_genome">
19 <conditional name="rfasta">
20 <param name="rfasta_source" type="select" label="Reference genome FASTA used for analyzing RNAseq data">
21 <option value="cached" selected="true">Use a built-in genome fasta</option>
22 <option value="history">Use a FASTA from history</option>
23 </param>
24 <when value="cached">
25 <param name="ref_fa_builtin" type="select" label="Select a built-in FASTA" help="If your genome of interest is not listed, contact your Galaxy administrator">
26 <options from_data_table="all_fasta">
27 <filter type="sort_by" column="2" />
28 <validator type="no_options" message="No FASTA is available for the selected input dataset" />
29 </options>
30 </param>
31 </when>
32 <when value="history">
33 <param name="ref_fa_hist" type="data" format="fasta" label="Select a history FASTA" />
34 </when>
35 </conditional>
36 </xml>
37 <xml name="reference_gtf">
38 <conditional name="rgtf">
39 <param name="rgtf_source" type="select" label="Reference GTF annotation file used for analyzing RNAseq data">
40 <option value="cached" selected="true">Use a built-in transcriptome</option>
41 <option value="history">Use a GTF from history</option>
42 </param>
43 <when value="cached">
44 <param name="ref_gtf_builtin" type="select" label="Select a built-in GTF" help="If the GTF file for your transcriptome of interest is not listed, contact your Galaxy administrator">
45 <options from_data_table="gene_sets">
46 <filter type="sort_by" column="2" />
47 <validator type="no_options" message="No GTF file is available." />
48 </options>
49 </param>
50 </when>
51 <when value="history">
52 <param name="ref_gtf_hist" type="data" format="gtf" label="Select a history GTF" />
53 </when>
54 </conditional>
55 </xml>
56
57 <xml name="build_opts" token_default_mapq_cutoff="60">
58 <param argument="--mapq_cutoff" type="integer" value="@DEFAULT_MAPQ_CUTOFF@" label="minimal MapQ in SAM for support SV event"/>
59 <param argument="--max_del_length" type="integer" value="1000000" label="maximum deletion length to be detected"/>
60 </xml>
61 <xml name="call_opts">
62 <section name="call_opts" title="transIndel_call.py options" expanded="false">
63 <param name="min_observation_count" argument="-c" type="integer" value="4" label="minimal observation count for Indel" help="(default 4)"/>
64 <param name="min_depth" argument="-d" type="integer" value="10" label="minimal depth to call Indel" help="(default 10)"/>
65 <param name="min_length" argument="-l" type="integer" value="10" label="minimal indel length to report" help="(default 10)"/>
66 <param name="min_mapq" argument="-m" type="integer" value="15" label="minimal mapq of read from BAM file to call indel" help="(default 15)"/>
67 <param name="min_allele_frequency" argument="-f" type="float" value="0.1" min="0" max="1.0" label="minimal variant allele frequency" help="(default 0.1)"/>
68 <conditional name="regions">
69 <param name="regions_source" type="select" label="limit analysis to regions">
70 <option value="none">No limit</option>
71 <option value="text">text entry</option>
72 <option value="bed">BED file</option>
73 </param>
74 <when value="none"/>
75 <when value="text">
76 <param name="target" argument="-t" type="text" value="" label="samtools region string">
77 </param>
78 </when>
79 <when value="bed">
80 <param name="target" argument="-t" type="data" format="bed" label="BED file of regions to report"/>
81 </when>
82 </conditional>
83 </section>
84 </xml>
85 <xml name="transindel_call">
86 <conditional name="transIndel_call">
87 <param name="run_transIndel_call" type="select" label="Produce a VCF file using transIndel_call.py">
88 <option value="yes">Yes</option>
89 <option value="no">No</option>
90 </param>
91 <when value="yes">
92 <yield/>
93 <expand macro="call_opts"/>
94 </when>
95 <when value="no"/>
96 </conditional>
97 </xml>
98 </macros>