Mercurial > repos > blankenberg > naive_variant_caller

comparison naive_variant_caller.xml @ 7:f297269cbcd8 draft default tip

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"planemo upload for repository https://github.com/BlankenbergLab/galaxy-tools-blankenberg/tree/master/tools/naive_variant_caller commit 6f2b4ed336036cd98c043536e45905bcd3c93044"
author blankenberg
date Thu, 05 Dec 2019 16:55:20 +0000
parents dac6381febb7
children
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6:dac6381febb7 7:f297269cbcd8
57 #end if 57 #end if
58 </command> 58 </command>
59 <inputs> 59 <inputs>
60 <conditional name="reference_source"> 60 <conditional name="reference_source">
61 <param name="reference_source_selector" type="select" label="Choose the source for the reference list"> 61 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
62 <option value="cached">Locally cached</option> 62 <option value="cached_fasta_indexes" selected="True">Locally cached</option>
63 <option value="history">History</option> 63 <option value="history">History</option>
64 <option value="cached">Locally cached (deprecated source)</option>
64 </param> 65 </param>
65 <when value="cached"> 66 <when value="cached_fasta_indexes">
67 <repeat name="input_bams" title="BAM file" min="1" >
68 <param name="input_bam" type="data" format="bam" label="BAM file">
69 <validator type="unspecified_build" />
70 <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
71 </param>
72 </repeat>
73 <param name="ref_file" type="select" label="Using reference genome" >
74 <options from_data_table="fasta_indexes">
75 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
76 </options>
77 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
78 </param>
79 </when>
80 <when value="cached"> <!-- deprecated, uses older samtools data table -->
66 <repeat name="input_bams" title="BAM file" min="1" > 81 <repeat name="input_bams" title="BAM file" min="1" >
67 <param name="input_bam" type="data" format="bam" label="BAM file"> 82 <param name="input_bam" type="data" format="bam" label="BAM file">
68 <validator type="unspecified_build" /> 83 <validator type="unspecified_build" />
69 <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="value" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select --> 84 <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="value" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
70 </param> 85 </param>