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comparison variant_validate.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
equal deleted inserted replaced
1:f760c0de8e3a 2:8bcc13094767
12 @JAR_PATH@ 12 @JAR_PATH@
13 -T "ValidateVariants" 13 -T "ValidateVariants"
14 14
15 \$GATK2_SITE_OPTIONS 15 \$GATK2_SITE_OPTIONS
16 16
17 @THREADS@
18
19 #if $reference_source.reference_source_selector != "history": 17 #if $reference_source.reference_source_selector != "history":
20 -R "${reference_source.ref_file.fields.path}" 18 -R "${reference_source.ref_file.fields.path}"
21 #end if 19 #end if
22 ${warn_on_errors} 20 ${warn_on_errors}
23 ${do_not_validate_filtered_records} 21 ${do_not_validate_filtered_records}
24 ' 22 '
25 23 @DBSNP_OPTIONS@
26 #if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp':
27 -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}"
28 #end if
29 24
30 #include source=$standard_gatk_options# 25 #include source=$standard_gatk_options#
31 </command> 26 </command>
32 <inputs> 27 <inputs>
33 28
45 <when value="history"> <!-- FIX ME!!!! --> 40 <when value="history"> <!-- FIX ME!!!! -->
46 <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &amp;lt;variant&amp;gt;" /> 41 <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &amp;lt;variant&amp;gt;" />
47 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" /> 42 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
48 </when> 43 </when>
49 </conditional> 44 </conditional>
50 45 <expand macro="dbsnp_param" />
51 <conditional name="dbsnp_rod_bind_type">
52 <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file" help="-D,--dbsnp &amp;lt;dbsnp&amp;gt;">
53 <option value="set_dbsnp" selected="True">Set dbSNP</option>
54 <option value="exclude_dbsnp">Don't set dbSNP</option>
55 </param>
56 <when value="exclude_dbsnp">
57 <!-- Do nothing here -->
58 </when>
59 <when value="set_dbsnp">
60 <param name="dbsnp_input_rod" type="data" format="vcf" label="ROD file" />
61 <param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="ROD Name"/>
62 </when>
63 </conditional>
64 46
65 <param name="warn_on_errors" type="boolean" checked="False" truevalue="-warnOnErrors" falsevalue="" label="instead of terminating the run at the first error, print warning messages for each error seen." help="-warnOnErrors,--warnOnErrors"/> 47 <param name="warn_on_errors" type="boolean" checked="False" truevalue="-warnOnErrors" falsevalue="" label="instead of terminating the run at the first error, print warning messages for each error seen." help="-warnOnErrors,--warnOnErrors"/>
66 <param name="do_not_validate_filtered_records" type="boolean" checked="False" truevalue="-doNotValidateFilteredRecords" falsevalue="" label="do not try to validate records that are FILTERed." help="-doNotValidateFilteredRecords,--doNotValidateFilteredRecords"/> 48 <param name="do_not_validate_filtered_records" type="boolean" checked="False" truevalue="-doNotValidateFilteredRecords" falsevalue="" label="do not try to validate records that are FILTERed." help="-doNotValidateFilteredRecords,--doNotValidateFilteredRecords"/>
67 49
68 <expand macro="gatk_param_type_conditional" /> 50 <expand macro="gatk_param_type_conditional" />
76 <param name="reference_source_selector" value="history" /> 58 <param name="reference_source_selector" value="history" />
77 <param name="ref_file" value="phiX.fasta" ftype="fasta" /> 59 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
78 <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" /> 60 <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" />
79 <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" /> 61 <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" />
80 <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" /> 62 <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
63 <param name="dbsnp_rod_name" value="dbsnp" />
81 <param name="warn_on_errors" value="True"/> 64 <param name="warn_on_errors" value="True"/>
82 <param name="do_not_validate_filtered_records" /> 65 <param name="do_not_validate_filtered_records" />
83 <param name="gatk_param_type_selector" value="basic" /> 66 <param name="gatk_param_type_selector" value="basic" />
84 <output name="output_log" file="gatk/gatk_validate_variants/gatk_validate_variants_out_1.log.contains" compare="contains" /> 67 <output name="output_log" file="gatk/gatk_validate_variants/gatk_validate_variants_out_1.log.contains" compare="contains" />
85 </test> 68 </test>