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annotate variant_combine.xml @ 6:35c00763cb5c draft default tip
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 |
| rev | line source |
|---|---|
| 4 | 1 <tool id="gatk2_variant_combine" name="Combine Variants" version="@VERSION@.0"> |
| 0 | 2 <description></description> |
| 3 <macros> | |
| 4 <import>gatk2_macros.xml</import> | |
| 5 </macros> | |
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
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changeset
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6 <expand macro="requirements" /> |
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
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changeset
|
7 <expand macro="version_command" /> |
| 0 | 8 <command interpreter="python"> |
| 9 gatk2_wrapper.py | |
| 10 --stdout "${output_log}" | |
| 11 | |
| 12 #set $priority_order = [] | |
| 13 #for $input_variant in $reference_source.input_variants: | |
| 14 -d "--variant:${input_variant.input_variant_name},%(file_type)s" "${input_variant.input_variant}" "${input_variant.input_variant.ext}" "input_variant_${input_variant.input_variant_name}" | |
| 15 #set $input_variant_name = str( $input_variant.input_variant_name ) | |
| 16 #assert $input_variant_name not in $priority_order, "Variant Names must be unique" ##this should be handled by a validator | |
| 17 #silent $priority_order.append( $input_variant_name ) | |
| 18 #end for | |
| 19 -p ' | |
| 20 @JAR_PATH@ | |
| 21 -T "CombineVariants" | |
| 22 --out "${output_variants}" | |
| 23 \$GATK2_SITE_OPTIONS | |
| 24 | |
| 25 @THREADS@ | |
| 26 | |
| 27 #if $reference_source.reference_source_selector != "history": | |
| 28 -R "${reference_source.ref_file.fields.path}" | |
| 29 #end if | |
| 30 --genotypemergeoption "${genotype_merge_option}" | |
| 31 --rod_priority_list "${ ','.join( $priority_order ) }" | |
| 32 ' | |
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
33 |
| 0 | 34 #include source=$standard_gatk_options# |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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35 |
| 0 | 36 ##start analysis specific options |
| 37 #if $analysis_param_type.analysis_param_type_selector == "advanced": | |
| 38 -p ' | |
| 39 --filteredrecordsmergetype "${analysis_param_type.filtered_records_merge_type}" | |
| 40 ${analysis_param_type.print_complex_merges} | |
| 41 ${analysis_param_type.filtered_are_uncalled} | |
| 42 ${analysis_param_type.minimal_vcf} | |
| 43 ${analysis_param_type.assume_identical_samples} | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
44 |
| 0 | 45 #if str( $analysis_param_type.set_key ): |
| 46 --setKey "${analysis_param_type.set_key}" | |
| 47 #end if | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
48 |
| 0 | 49 --minimumN "${analysis_param_type.minimum_n}" |
| 50 ' | |
| 51 #end if | |
| 52 </command> | |
| 53 <inputs> | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
54 |
| 0 | 55 <conditional name="reference_source"> |
| 56 <expand macro="reference_source_selector_param" /> | |
| 57 <when value="cached"> | |
| 58 <repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here (-V,--variant &lt;variant&gt;)"> | |
| 59 <param name="input_variant" type="data" format="vcf" label="Input variant file" /> | |
| 60 <param name="input_variant_name" type="text" value="" label="Variant name" help="Names must be unique"> | |
| 61 <validator type="length" min="1" message="You must provide a unique name for this set of variants" /> | |
| 62 </param> | |
| 63 </repeat> | |
| 64 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> | |
| 65 <options from_data_table="gatk2_picard_indexes"> | |
| 66 <!-- <filter type="data_meta" key="dbkey" ref="input_variants.input_variant" column="dbkey"/> --> | |
| 67 </options> | |
| 68 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 69 </param> | |
| 70 </when> | |
| 71 <when value="history"> <!-- FIX ME!!!! --> | |
| 72 <repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here (-V,--variant &lt;variant&gt;)"> | |
| 73 <param name="input_variant" type="data" format="vcf" label="Input variant file" /> | |
| 74 <param name="input_variant_name" type="text" value="" label="Variant name" help="Names must be unique"> | |
| 75 <validator type="length" min="1" message="You must provide a unique name for this set of variants" /> | |
| 76 </param> | |
| 77 </repeat> | |
| 78 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> | |
| 79 </when> | |
| 80 </conditional> | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
81 |
| 0 | 82 <param name="genotype_merge_option" type="select" label="How should we merge genotype records across records for samples shared across the ROD files" help="-genotypeMergeOptions,--genotypemergeoption &lt;genotypemergeoption&gt;" > |
| 83 <option value="UNIQUIFY" /> | |
| 84 <option value="PRIORITIZE" selected="true"/> | |
| 85 <option value="UNSORTED" /> | |
| 86 <option value="REQUIRE_UNIQUE" /> | |
| 87 </param> | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
88 |
| 0 | 89 <expand macro="gatk_param_type_conditional" /> |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
90 |
| 0 | 91 <expand macro="analysis_type_conditional"> |
| 92 <param name="filtered_records_merge_type" type="select" label="How should we deal with records seen at the same site in the VCF, but with different FILTER fields?" help="-filteredRecordsMergeType,--filteredrecordsmergetype &lt;filteredrecordsmergetype&gt;" > | |
| 93 <option value="KEEP_IF_ANY_UNFILTERED" selected="true"/> | |
| 94 <option value="KEEP_IF_ALL_UNFILTERED" /> | |
| 95 </param> | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
96 |
| 0 | 97 <param name="print_complex_merges" checked="false" type="boolean" truevalue="--printComplexMerges" falsevalue="" label="Print out interesting sites requiring complex compatibility merging" help="-printComplexMerges,--printComplexMerges" /> |
| 98 <param name="filtered_are_uncalled" checked="false" type="boolean" truevalue="--filteredAreUncalled" falsevalue="" label="If true, then filtered VCFs are treated as uncalled, so that filtered set annotation don't appear in the combined VCF" help="-filteredAreUncalled,--filteredAreUncalled" /> | |
| 99 <param name="minimal_vcf" checked="false" type="boolean" truevalue="--minimalVCF" falsevalue="" label="If true, then the output VCF will contain no INFO or genotype INFO field" help="-minimalVCF,--minimalVCF" /> | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
100 |
| 0 | 101 <param name="set_key" type="text" value="" label="Key, by default set, in the INFO key=value tag emitted describing which set the combined VCF record came from." help="-setKey,--setKey &lt;setKey&gt;"/> |
| 102 <param name="assume_identical_samples" checked="false" type="boolean" truevalue="--assumeIdenticalSamples" falsevalue="" label="If true, assume input VCFs have identical sample sets and disjoint calls so that one can simply perform a merge sort to combine the VCFs into one, drastically reducing the runtime." help="-assumeIdenticalSamples,--assumeIdenticalSamples" /> | |
| 103 <param name="minimum_n" type="integer" value="1" label="Combine variants and output site only if variant is present in at least N input files." help="-minN,--minimumN &lt;minimumN&gt;"/> | |
| 104 </expand> | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
105 |
| 0 | 106 </inputs> |
| 107 <outputs> | |
| 108 <data format="vcf" name="output_variants" label="${tool.name} on ${on_string} (variants)" /> | |
| 109 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> | |
| 110 </outputs> | |
| 111 <tests> | |
| 112 <test> | |
| 113 <param name="reference_source_selector" value="history" /> | |
| 114 <param name="ref_file" value="phiX.fasta" ftype="fasta" /> | |
| 115 <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" /> | |
| 116 <param name="input_variant_name" value="from_variant_annotator" /> | |
| 117 <param name="genotype_merge_option" value="PRIORITIZE" /> | |
| 118 <param name="gatk_param_type_selector" value="basic" /> | |
| 119 <param name="analysis_param_type_selector" value="basic" /> | |
| 120 <output name="output_variants" file="gatk/gatk_variant_combine/gatk_variant_combine_out_1.vcf" lines_diff="4" /> | |
| 121 <output name="output_log" file="gatk/gatk_variant_combine/gatk_variant_combine_out_1.log.contains" compare="contains" /> | |
| 122 </test> | |
| 123 </tests> | |
| 124 <help> | |
| 125 **What it does** | |
| 126 | |
| 127 Combines VCF records from different sources; supports both full merges and set unions. Merge: combines multiple records into a single one; if sample names overlap then they are uniquified. Union: assumes each rod represents the same set of samples (although this is not enforced); using the priority list (if provided), emits a single record instance at every position represented in the rods. | |
| 128 | |
| 129 For more information on using the CombineVariants module, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_CombineVariants.html>`_. | |
| 130 | |
| 131 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_. | |
| 132 | |
| 133 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_. | |
| 134 | |
| 135 ------ | |
| 136 | |
| 137 **Inputs** | |
| 138 | |
| 139 GenomeAnalysisTK: CombineVariants accepts variant files as input. | |
| 140 | |
| 141 ------ | |
| 142 | |
| 143 **Outputs** | |
| 144 | |
| 145 The output is a combined vcf file. | |
| 146 | |
| 147 | |
| 148 Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats. | |
| 149 | |
| 150 ------- | |
| 151 | |
| 152 **Settings**:: | |
| 153 | |
| 154 out File to which variants should be written | |
| 155 genotypemergeoption How should we merge genotype records for samples shared across the ROD files? (UNIQUIFY|PRIORITIZE|UNSORTED|REQUIRE_UNIQUE) | |
| 156 filteredrecordsmergetype How should we deal with records seen at the same site in the VCF, but with different FILTER fields? KEEP_IF_ANY_UNFILTERED PASSes the record if any record is unfiltered, KEEP_IF_ALL_UNFILTERED requires all records to be unfiltered (KEEP_IF_ANY_UNFILTERED|KEEP_IF_ALL_UNFILTERED) | |
| 157 rod_priority_list When taking the union of variants containing genotypes: a comma-separated string describing the priority ordering for the genotypes as far as which record gets emitted; a complete priority list MUST be provided | |
| 158 printComplexMerges Print out interesting sites requiring complex compatibility merging | |
| 159 filteredAreUncalled If true, then filtered VCFs are treated as uncalled, so that filtered set annotation don't appear in the combined VCF | |
| 160 minimalVCF If true, then the output VCF will contain no INFO or genotype INFO field | |
| 161 setKey Key, by default set, in the INFO key=value tag emitted describing which set the combined VCF record came from. Set to null if you don't want the set field emitted. | |
| 162 assumeIdenticalSamples If true, assume input VCFs have identical sample sets and disjoint calls so that one can simply perform a merge sort to combine the VCFs into one, drastically reducing the runtime. | |
| 163 minimumN Combine variants and output site only if variant is present in at least N input files. | |
| 164 | |
| 165 @CITATION_SECTION@ | |
| 166 </help> | |
| 4 | 167 <expand macro="citations" /> |
| 0 | 168 </tool> |