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comparison variant_filtration.xml @ 2:8bcc13094767 draft

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Uploaded
author iuc
date Sat, 18 Jan 2014 07:21:33 -0500
parents 340633249b3d
children f244b8209eb8
comparison
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1:f760c0de8e3a 2:8bcc13094767
12 -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" 12 -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
13 -p ' 13 -p '
14 @JAR_PATH@ 14 @JAR_PATH@
15 -T "VariantFiltration" 15 -T "VariantFiltration"
16 \$GATK2_SITE_OPTIONS 16 \$GATK2_SITE_OPTIONS
17
18 @THREADS@
19 17
20 -o "${output_vcf}" 18 -o "${output_vcf}"
21 19
22 #if $reference_source.reference_source_selector != "history": 20 #if $reference_source.reference_source_selector != "history":
23 -R "${reference_source.ref_file.fields.path}" 21 -R "${reference_source.ref_file.fields.path}"
81 79
82 80
83 81
84 <conditional name="mask_rod_bind_type"> 82 <conditional name="mask_rod_bind_type">
85 <param name="mask_rod_bind_type_selector" type="select" label="Provide a Mask reference-ordered data file"> 83 <param name="mask_rod_bind_type_selector" type="select" label="Provide a Mask reference-ordered data file">
86 <option value="set_mask" selected="True">Set maskP</option> 84 <option value="set_mask" selected="True">Set mask</option>
87 <option value="exclude_mask">Don't set mask</option> 85 <option value="exclude_mask">Don't set mask</option>
88 </param> 86 </param>
89 <when value="exclude_mask"> 87 <when value="exclude_mask">
90 <!-- Do nothing here --> 88 <!-- Do nothing here -->
91 </when> 89 </when>