Mercurial > repos > devteam > freebayes
comparison macros.xml @ 28:977a5301b66d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
author | iuc |
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date | Tue, 06 Jun 2017 18:41:18 -0400 |
parents | 9f164587a92f |
children | 156b60c1530f |
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27:9f164587a92f | 28:977a5301b66d |
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1 <macros> | 1 <macros> |
2 <token name="@DEPENDENCY_VERSION@">1.1.0</token> | 2 <token name="@DEPENDENCY_VERSION@">1.1.0</token> |
3 | 3 <xml name="requirements"> |
4 <requirements> | |
5 <requirement type="package" version="@DEPENDENCY_VERSION@">freebayes</requirement> | |
6 <requirement type="package" version="0.1.19">samtools</requirement> | |
7 <yield /> | |
8 </requirements> | |
9 </xml> | |
4 <xml name="citations"> | 10 <xml name="citations"> |
5 <citations> | 11 <citations> |
6 <citation type="bibtex"> | 12 <citation type="bibtex"> |
7 @misc{1207.3907, | 13 @misc{1207.3907, |
8 Author = {Erik Garrison}, | 14 Author = {Erik Garrison}, |
18 <validator type="unspecified_build" /> | 24 <validator type="unspecified_build" /> |
19 <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." /> | 25 <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." /> |
20 </xml> | 26 </xml> |
21 <xml name="input_bam"> | 27 <xml name="input_bam"> |
22 <conditional name="batchmode"> | 28 <conditional name="batchmode"> |
23 <param name="processmode" type="select" label="Run in batch mode?" help="Selecting individual mode will generate one VCF file for each input BAM file. Selecting the merge option will produce one VCF file for all input BAM files." display="radio"> | 29 <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"> |
24 <option value="individual" selected="True">Run individually</option> | 30 <option value="individual" selected="true">Run individually</option> |
25 <option value="merge">Merge output VCFs</option> | 31 <option value="merge">Merge output VCFs</option> |
26 </param> | 32 </param> |
27 <when value="individual"> | 33 <when value="individual"> |
28 <param name="input_bams" type="data" format="bam" label="BAM file"> | 34 <param name="input_bams" type="data" format="bam" label="BAM dataset"> |
29 <yield /> | 35 <yield /> |
30 </param> | 36 </param> |
31 </when> | 37 </when> |
32 <when value="merge"> | 38 <when value="merge"> |
33 <param name="input_bams" type="data" format="bam" multiple="True" label="BAM file"> | 39 <param name="input_bams" type="data" format="bam" multiple="true" label="BAM dataset(s)"> |
34 <yield /> | 40 <yield /> |
35 </param> | 41 </param> |
36 </when> | 42 </when> |
37 </conditional> | 43 </conditional> |
38 </xml> | 44 </xml> |
39 <xml name="par_min_cov"> | 45 <xml name="par_min_cov"> |
40 <param name="min_coverage" type="integer" value="0" label="Require at least this coverage to process a site" | 46 <param name="min_coverage" argument="--coverage" type="integer" value="0" label="Require at least this coverage to process a site" /> |
41 help="default=0" argument="--coverage" /> | |
42 </xml> | 47 </xml> |
43 </macros> | 48 </macros> |