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comparison macros.xml @ 9:c07ad8a9c701 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
author iuc
date Tue, 06 Jun 2017 18:41:04 -0400
parents b0ff6447545f
children 2fb16f415220
comparison
equal deleted inserted replaced
8:b0ff6447545f 9:c07ad8a9c701
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>