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comparison variant_eval.xml @ 13:669a23f1f4b5 draft

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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
comparison
equal deleted inserted replaced
12:86007c982f00 13:669a23f1f4b5
1 <tool id="gatk2_variant_eval" name="Eval Variants" version="@VERSION@.0"> 1 <tool id="gatk2_variant_eval" name="Eval Variants" version="@VERSION@.1">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>gatk2_macros.xml</import> 4 <import>gatk2_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
8 <command interpreter="python"> 8 <command interpreter="python">
9 #from binascii import hexlify 9 #from binascii import hexlify
10 10
11 gatk2_wrapper.py 11 gatk2_wrapper.py
12 --stdout "${output_log}" 12 --stdout "${output_log}"
13 #for $var_count, $variant in enumerate( $reference_source.variants ): 13 #for $var_count, $variant in enumerate( $reference_source.input_variants ):
14 -d "--eval:input_${var_count},%(file_type)s" "${variant.input_variant}" "${variant.input_variant.ext}" "input_variants_${var_count}" 14 -d "--eval:input_${var_count},%(file_type)s" "${variant}" "${variant.ext}" "input_variants_${var_count}"
15 #end for 15 #end for
16 -p ' 16 -p '
17 @JAR_PATH@ 17 @JAR_PATH@
18 -T "VariantEval" 18 -T "VariantEval"
19 --out "${output_report}" 19 --out "${output_report}"
98 <inputs> 98 <inputs>
99 99
100 <conditional name="reference_source"> 100 <conditional name="reference_source">
101 <expand macro="reference_source_selector_param" /> 101 <expand macro="reference_source_selector_param" />
102 <when value="cached"> 102 <when value="cached">
103 <repeat name="variants" title="Variant" min="1" help="-eval,--eval &amp;lt;eval&amp;gt;"> 103 <expand macro="input_variants" help="-eval,--eval &amp;lt;eval&amp;gt;"/>
104 <param name="input_variant" type="data" format="vcf" label="Input variant file" />
105 </repeat>
106 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;"> 104 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
107 <options from_data_table="gatk2_picard_indexes"> 105 <options from_data_table="gatk2_picard_indexes">
108 <!-- <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> --> 106 <!-- <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> -->
109 </options> 107 </options>
110 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 108 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
111 </param> 109 </param>
112 </when> 110 </when>
113 <when value="history"> <!-- FIX ME!!!! --> 111 <when value="history"> <!-- FIX ME!!!! -->
114 <repeat name="variants" title="Variant" min="1" help="-eval,--eval &amp;lt;eval&amp;gt;"> 112 <expand macro="input_variants" help="-eval,--eval &amp;lt;eval&amp;gt;" />
115 <param name="input_variant" type="data" format="vcf" label="Input variant file" />
116 </repeat>
117 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" /> 113 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
118 </when> 114 </when>
119 </conditional> 115 </conditional>
120 116
121 <repeat name="comp_rod_bind" title="Comparison Reference-Ordered Data (ROD) file" help="-comp,--comp &amp;lt;comp&amp;gt;"> 117 <repeat name="comp_rod_bind" title="Comparison Reference-Ordered Data (ROD) file" help="-comp,--comp &amp;lt;comp&amp;gt;">