Mercurial > repos > iuc > gatk2
diff variant_eval.xml @ 13:669a23f1f4b5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit e5a5ad091c621348dc6ce2df861475ebc54a380e
author | iuc |
---|---|
date | Tue, 13 Oct 2015 17:22:38 -0400 |
parents | 0d369d08ad6e |
children |
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--- a/variant_eval.xml Thu May 14 22:47:18 2015 -0400 +++ b/variant_eval.xml Tue Oct 13 17:22:38 2015 -0400 @@ -1,4 +1,4 @@ -<tool id="gatk2_variant_eval" name="Eval Variants" version="@VERSION@.0"> +<tool id="gatk2_variant_eval" name="Eval Variants" version="@VERSION@.1"> <description></description> <macros> <import>gatk2_macros.xml</import> @@ -10,8 +10,8 @@ gatk2_wrapper.py --stdout "${output_log}" - #for $var_count, $variant in enumerate( $reference_source.variants ): - -d "--eval:input_${var_count},%(file_type)s" "${variant.input_variant}" "${variant.input_variant.ext}" "input_variants_${var_count}" + #for $var_count, $variant in enumerate( $reference_source.input_variants ): + -d "--eval:input_${var_count},%(file_type)s" "${variant}" "${variant.ext}" "input_variants_${var_count}" #end for -p ' @JAR_PATH@ @@ -100,9 +100,7 @@ <conditional name="reference_source"> <expand macro="reference_source_selector_param" /> <when value="cached"> - <repeat name="variants" title="Variant" min="1" help="-eval,--eval &lt;eval&gt;"> - <param name="input_variant" type="data" format="vcf" label="Input variant file" /> - </repeat> + <expand macro="input_variants" help="-eval,--eval &lt;eval&gt;"/> <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> <options from_data_table="gatk2_picard_indexes"> <!-- <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> --> @@ -111,9 +109,7 @@ </param> </when> <when value="history"> <!-- FIX ME!!!! --> - <repeat name="variants" title="Variant" min="1" help="-eval,--eval &lt;eval&gt;"> - <param name="input_variant" type="data" format="vcf" label="Input variant file" /> - </repeat> + <expand macro="input_variants" help="-eval,--eval &lt;eval&gt;" /> <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> </when> </conditional>