Mercurial > repos > iuc > gatk2
annotate variant_filtration.xml @ 15:a3247b69fa59 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 898393cb5c244c8fab2e965f003ae3991bcb655e
| author | iuc |
|---|---|
| date | Mon, 04 Apr 2016 06:33:05 -0400 |
| parents | 0d369d08ad6e |
| children |
| rev | line source |
|---|---|
| 6 | 1 <tool id="gatk2_variant_filtration" name="Variant Filtration" version="@VERSION@.0"> |
| 0 | 2 <description>on VCF files</description> |
| 3 <macros> | |
| 4 <import>gatk2_macros.xml</import> | |
| 5 </macros> | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
6 <expand macro="requirements" /> |
|
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
7 <expand macro="version_command" /> |
| 1 | 8 <command interpreter="python"> |
| 9 #from binascii import hexlify | |
| 10 | |
| 11 gatk2_wrapper.py | |
| 12 --stdout "${output_log}" | |
| 13 -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" | |
| 14 -p ' | |
| 15 @JAR_PATH@ | |
| 0 | 16 -T "VariantFiltration" |
| 17 \$GATK2_SITE_OPTIONS | |
| 18 | |
| 19 -o "${output_vcf}" | |
| 1 | 20 |
| 0 | 21 #if $reference_source.reference_source_selector != "history": |
| 22 -R "${reference_source.ref_file.fields.path}" | |
| 23 #end if | |
| 24 ' | |
| 25 #for $variant_filter in $variant_filters: | |
| 26 #set $variant_filter = "--%sExpression '%s' --%sName '%s'" % ( str( $variant_filter.is_genotype_filter ), str( $variant_filter.filter_expression ), str( $variant_filter.is_genotype_filter ), str( $variant_filter.filter_name ) ) | |
| 27 -o '${ hexlify( $variant_filter ) }' | |
| 28 #end for | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
29 |
| 0 | 30 #if str( $mask_rod_bind_type.mask_rod_bind_type_selector ) == 'set_mask': |
| 31 -d "--mask:${mask_rod_bind_type.mask_rod_name},%(file_type)s" "${mask_rod_bind_type.input_mask_rod}" "${mask_rod_bind_type.input_mask_rod.ext}" "input_mask_${mask_rod_bind_type.mask_rod_name}" | |
| 32 -p ' | |
| 33 --maskExtension "${mask_rod_bind_type.mask_extension}" | |
| 34 --maskName "${mask_rod_bind_type.mask_rod_name}" | |
| 35 ' | |
| 36 #end if | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
37 |
| 0 | 38 #include source=$standard_gatk_options# |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
39 |
| 0 | 40 ##start analysis specific options |
| 41 #if $cluster_snp_type.cluster_snp_type_selector == "cluster_snp": | |
| 42 -p ' | |
| 43 --clusterSize "${cluster_snp_type.cluster_size}" | |
| 44 --clusterWindowSize "${cluster_snp_type.cluster_window_size}" | |
| 45 ' | |
| 46 #end if | |
| 47 -p '${missing_values_in_expressions_should_evaluate_as_failing}' | |
| 48 </command> | |
| 49 <inputs> | |
| 50 <conditional name="reference_source"> | |
| 51 <expand macro="reference_source_selector_param" /> | |
| 52 <when value="cached"> | |
| 53 <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &lt;variant&gt;" /> | |
| 54 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> | |
| 55 <options from_data_table="gatk2_picard_indexes"> | |
| 56 <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> | |
| 57 </options> | |
| 58 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 59 </param> | |
| 60 </when> | |
| 61 <when value="history"> <!-- FIX ME!!!! --> | |
| 62 <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &lt;variant&gt;" /> | |
| 63 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> | |
| 64 </when> | |
| 65 </conditional> | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
66 |
| 0 | 67 <repeat name="variant_filters" title="Variant Filters"> |
| 68 <param name="filter_expression" value="AB < 0.2 || MQ0 > 50" type="text" label="Filter expression" help="JEXL formatted expressions (-filter,--filterExpression &lt;filterExpression&gt;)"> | |
| 69 <sanitizer> | |
| 70 <valid initial="string.printable"> | |
| 71 <remove value="'"/> | |
| 72 </valid> | |
| 73 <mapping initial="none"/> | |
| 74 </sanitizer> | |
| 75 </param> | |
| 76 <param name="filter_name" value="custom_filter" type="text" label="Filter name" help="-filterName,--filterName &lt;filterName&gt;"/> | |
| 77 <param name="is_genotype_filter" type="boolean" truevalue="genotypeFilter" falsevalue="filter" label="Use filter at the individual sample level" help="Use -G_filter,--genotypeFilterExpression &lt;genotypeFilterExpression&gt; and -G_filterName,--genotypeFilterName &lt;genotypeFilterName&gt; for filter type" /> | |
| 78 </repeat> | |
| 79 | |
| 80 <conditional name="mask_rod_bind_type"> | |
| 81 <param name="mask_rod_bind_type_selector" type="select" label="Provide a Mask reference-ordered data file"> | |
| 4 | 82 <option value="set_mask" selected="True">Set mask</option> |
| 0 | 83 <option value="exclude_mask">Don't set mask</option> |
| 84 </param> | |
| 85 <when value="exclude_mask"> | |
| 86 <!-- Do nothing here --> | |
| 87 </when> | |
| 88 <when value="set_mask"> | |
| 89 <param name="input_mask_rod" type="data" format="bed,gatk_dbsnp,vcf" label="Mask ROD file" help="--mask &lt;mask&gt;" /> | |
| 90 <param name="mask_rod_name" type="text" value="Mask" label="Mask Name" help="-maskName,--maskName &lt;maskName&gt;"/> | |
| 91 <param name="mask_extension" type="integer" value="0" label="Mask Extension" help="-maskExtend,--maskExtension &lt;maskExtension&gt;"/> | |
| 92 </when> | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
93 </conditional> |
|
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
94 |
| 0 | 95 <expand macro="gatk_param_type_conditional" /> |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
96 |
| 0 | 97 <conditional name="cluster_snp_type"> |
| 98 <param name="cluster_snp_type_selector" type="select" label="Cluster SNPs"> | |
| 99 <option value="cluster_snp">Cluster SNPs</option> | |
| 100 <option value="do_not_cluster_snp" selected="True">Do not cluster SNPs</option> | |
| 101 </param> | |
| 102 <when value="do_not_cluster_snp"> | |
| 103 <!-- Do nothing here --> | |
| 104 </when> | |
| 105 <when value="cluster_snp"> | |
| 106 <param name="cluster_size" type="integer" value="3" label="The number of SNPs which make up a cluster" help="-cluster,--clusterSize &lt;clusterSize&gt;"/> | |
| 107 <param name="cluster_window_size" type="integer" value="0" label="The window size (in bases) in which to evaluate clustered SNPs" help="-window,--clusterWindowSize &lt;clusterWindowSize&gt;"/> | |
| 108 </when> | |
| 109 </conditional> | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
110 |
| 0 | 111 <param name="missing_values_in_expressions_should_evaluate_as_failing" type="boolean" truevalue="--missingValuesInExpressionsShouldEvaluateAsFailing" falsevalue="" label="Should missing values be considered failing the expression" help="--missingValuesInExpressionsShouldEvaluateAsFailing" /> |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
112 |
| 0 | 113 </inputs> |
| 114 <outputs> | |
| 115 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" /> | |
| 116 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> | |
| 117 </outputs> | |
| 118 <tests> | |
| 119 <test> | |
| 120 <param name="reference_source_selector" value="history" /> | |
| 121 <param name="ref_file" value="phiX.fasta" ftype="fasta" /> | |
| 122 <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" /> | |
| 123 <param name="filter_expression" value="MQ < 37.74 || MQ0 > 50" /> | |
| 124 <param name="filter_name" value="Galaxy_filter" /> | |
| 125 <param name="is_genotype_filter" /> | |
| 126 <param name="mask_rod_bind_type_selector" value="set_mask" /> | |
| 127 <param name="input_mask_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" /> | |
| 128 <param name="mask_rod_name" value="." /> | |
| 129 <param name="mask_extension" value="0" /> | |
| 130 <param name="gatk_param_type_selector" value="basic" /> | |
| 131 <param name="cluster_snp_type_selector" value="do_not_cluster_snp" /> | |
| 132 <param name="missing_values_in_expressions_should_evaluate_as_failing" /> | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
133 <output name="output_vcf" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" lines_diff="4" /> |
| 0 | 134 <output name="output_log" file="gatk/gatk_variant_filtration/gatk_variant_filtration_out_1.log.contains" compare="contains" /> |
| 135 </test> | |
| 136 </tests> | |
| 137 <help> | |
| 138 **What it does** | |
| 139 | |
| 140 Filters variant calls using a number of user-selectable, parameterizable criteria. | |
| 141 | |
| 142 For more information on using the VariantFiltration module, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_filters_VariantFiltration.html>`_. | |
| 143 | |
| 144 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_. | |
| 145 | |
| 146 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_. | |
| 147 | |
| 148 ------ | |
| 149 | |
| 150 **Inputs** | |
| 151 | |
| 152 GenomeAnalysisTK: VariantFiltration accepts a VCF input file. | |
| 153 | |
| 154 | |
| 155 **Outputs** | |
| 156 | |
| 157 The output is in VCF format. | |
| 158 | |
| 159 Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats. | |
| 160 | |
| 161 ------- | |
| 162 | |
| 163 **Settings**:: | |
| 164 | |
| 165 | |
| 166 filterExpression One or more expression used with INFO fields to filter (see wiki docs for more info) | |
| 167 filterName Names to use for the list of filters (must be a 1-to-1 mapping); this name is put in the FILTER field for variants that get filtered | |
| 168 genotypeFilterExpression One or more expression used with FORMAT (sample/genotype-level) fields to filter (see wiki docs for more info) | |
| 169 genotypeFilterName Names to use for the list of sample/genotype filters (must be a 1-to-1 mapping); this name is put in the FILTER field for variants that get filtered | |
| 170 clusterSize The number of SNPs which make up a cluster (see also --clusterWindowSize); [default:3] | |
| 171 clusterWindowSize The window size (in bases) in which to evaluate clustered SNPs (to disable the clustered SNP filter, set this value to less than 1); [default:0] | |
| 172 maskName The text to put in the FILTER field if a 'mask' rod is provided and overlaps with a variant call; [default:'Mask'] | |
| 173 missingValuesInExpressionsShouldEvaluateAsFailing When evaluating the JEXL expressions, should missing values be considered failing the expression (by default they are considered passing)? | |
| 174 | |
| 175 @CITATION_SECTION@ | |
| 176 </help> | |
| 6 | 177 <expand macro="citations" /> |
| 0 | 178 </tool> |