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comparison variant_validate.xml @ 6:35c00763cb5c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
author iuc
date Mon, 04 Jun 2018 05:38:15 -0400
parents f244b8209eb8
children
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equal deleted inserted replaced
5:84584664264c 6:35c00763cb5c
1 <tool id="gatk2_variant_validate" name="Validate Variants" version="@VERSION@.0"> 1 <tool id="gatk2_variant_validate" name="Validate Variants" version="@VERSION@.0">
2 <description></description> 2 <description></description>
3 <expand macro="requirements" />
4 <macros> 3 <macros>
5 <import>gatk2_macros.xml</import> 4 <import>gatk2_macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="requirements" />
7 <expand macro="version_command" />
7 <command interpreter="python"> 8 <command interpreter="python">
8 gatk2_wrapper.py 9 gatk2_wrapper.py
9 --stdout "${output_log}" 10 --stdout "${output_log}"
10 -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" 11 -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
11 -p ' 12 -p '
12 @JAR_PATH@ 13 @JAR_PATH@
13 -T "ValidateVariants" 14 -T "ValidateVariants"
14 15
15 \$GATK2_SITE_OPTIONS 16 \$GATK2_SITE_OPTIONS
16 17
17 #if $reference_source.reference_source_selector != "history": 18 #if $reference_source.reference_source_selector != "history":
18 -R "${reference_source.ref_file.fields.path}" 19 -R "${reference_source.ref_file.fields.path}"
19 #end if 20 #end if
20 ${warn_on_errors} 21 ${warn_on_errors}
21 ${do_not_validate_filtered_records} 22 ${do_not_validate_filtered_records}
22 ' 23 '
23 @DBSNP_OPTIONS@ 24 @DBSNP_OPTIONS@
24 25
25 #include source=$standard_gatk_options# 26 #include source=$standard_gatk_options#
26 </command> 27 </command>
27 <inputs> 28 <inputs>
28 29
29 <conditional name="reference_source"> 30 <conditional name="reference_source">
30 <expand macro="reference_source_selector_param" /> 31 <expand macro="reference_source_selector_param" />
31 <when value="cached"> 32 <when value="cached">
32 <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &amp;lt;variant&amp;gt;" /> 33 <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &amp;lt;variant&amp;gt;" />
33 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;"> 34 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
41 <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &amp;lt;variant&amp;gt;" /> 42 <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &amp;lt;variant&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;" /> 43 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
43 </when> 44 </when>
44 </conditional> 45 </conditional>
45 <expand macro="dbsnp_param" /> 46 <expand macro="dbsnp_param" />
46 47
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"/> 48 <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"/>
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"/> 49 <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"/>
49 50
50 <expand macro="gatk_param_type_conditional" /> 51 <expand macro="gatk_param_type_conditional" />
51 52
52 </inputs> 53 </inputs>
53 <outputs> 54 <outputs>
54 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> 55 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
55 </outputs> 56 </outputs>
56 <tests> 57 <tests>