Mercurial > repos > recetox > freebayes

comparison macros.xml @ 0:13bde05924da draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"
author recetox
date Fri, 14 Aug 2020 13:59:45 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:13bde05924da
1 <macros>
2 <token name="@DEPENDENCY_VERSION@">1.3.1</token>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="@DEPENDENCY_VERSION@">freebayes</requirement>
6 <requirement type="package" version="1.9">samtools</requirement>
7 <yield />
8 </requirements>
9 </xml>
10 <xml name="citations">
11 <citations>
12 <citation type="bibtex">
13 @misc{1207.3907,
14 Author = {Erik Garrison},
15 Title = {Haplotype-based variant detection from short-read sequencing},
16 Year = {2012},
17 Eprint = {arXiv:1207.3907},
18 url = {http://arxiv.org/abs/1207.3907}
19 }
20 </citation>
21 <yield />
22 </citations>
23 </xml>
24 <xml name="validation">
25 <validator type="unspecified_build" />
26 <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
27 </xml>
28 <xml name="input_bam">
29 <conditional name="batchmode">
30 <param name="processmode" type="select" label="Run in batch mode?" help="Selecting individual mode will generate one VCF dataset for each input BAM dataset. Selecting the merge option will produce one VCF dataset for all input BAM datasets" display="radio">
31 <option value="individual" selected="true">Run individually</option>
32 <option value="merge">Merge output VCFs</option>
33 </param>
34 <when value="individual">
35 <param name="input_bams" type="data" format="bam" label="BAM dataset">
36 <yield />
37 </param>
38 </when>
39 <when value="merge">
40 <param name="input_bams" type="data" format="bam" multiple="true" label="BAM dataset(s)">
41 <yield />
42 </param>
43 </when>
44 </conditional>
45 </xml>
46 <token name="@COVERAGE@">
47 --min-coverage ${coverage_options.min_coverage}
48 --skip-coverage ${coverage_options.skip_coverage}
49 --limit-coverage ${coverage_options.limit_coverage}
50 </token>
51 <xml name="par_min_cov">
52 <param name="min_coverage" argument="--min-coverage" type="integer" value="0" label="Require at least this coverage to process a site" />
53 <param name="limit_coverage" argument="--limit-coverage" type="integer" value="0" label="Downsample per-sample coverage to this level if greater than this coverage" />
54 <param name="skip_coverage" argument="--skip-coverage" type="integer" value="0" label="Skip processing of alignments overlapping positions with coverage greater than this" />
55 </xml>
56 </macros>