Mercurial > repos > iuc > gatk2
comparison variant_filtration.xml @ 6:35c00763cb5c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
author | iuc |
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date | Mon, 04 Jun 2018 05:38:15 -0400 |
parents | f244b8209eb8 |
children |
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5:84584664264c | 6:35c00763cb5c |
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1 <tool id="gatk2_variant_filtration" name="Variant Filtration" version="@VERSION@.0"> | 1 <tool id="gatk2_variant_filtration" name="Variant Filtration" version="@VERSION@.0"> |
2 <description>on VCF files</description> | 2 <description>on VCF files</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 #from binascii import hexlify | 9 #from binascii import hexlify |
9 | 10 |
10 gatk2_wrapper.py | 11 gatk2_wrapper.py |
11 --stdout "${output_log}" | 12 --stdout "${output_log}" |
23 ' | 24 ' |
24 #for $variant_filter in $variant_filters: | 25 #for $variant_filter in $variant_filters: |
25 #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 ) ) | 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( $variant_filter.filter_name ) ) |
26 -o '${ hexlify( $variant_filter ) }' | 27 -o '${ hexlify( $variant_filter ) }' |
27 #end for | 28 #end for |
28 | 29 |
29 #if str( $mask_rod_bind_type.mask_rod_bind_type_selector ) == 'set_mask': | 30 #if str( $mask_rod_bind_type.mask_rod_bind_type_selector ) == 'set_mask': |
30 -d "--mask:${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_${mask_rod_bind_type.mask_rod_name}" | 31 -d "--mask:${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_${mask_rod_bind_type.mask_rod_name}" |
31 -p ' | 32 -p ' |
32 --maskExtension "${mask_rod_bind_type.mask_extension}" | 33 --maskExtension "${mask_rod_bind_type.mask_extension}" |
33 --maskName "${mask_rod_bind_type.mask_rod_name}" | 34 --maskName "${mask_rod_bind_type.mask_rod_name}" |
34 ' | 35 ' |
35 #end if | 36 #end if |
36 | 37 |
37 #include source=$standard_gatk_options# | 38 #include source=$standard_gatk_options# |
38 | 39 |
39 ##start analysis specific options | 40 ##start analysis specific options |
40 #if $cluster_snp_type.cluster_snp_type_selector == "cluster_snp": | 41 #if $cluster_snp_type.cluster_snp_type_selector == "cluster_snp": |
41 -p ' | 42 -p ' |
42 --clusterSize "${cluster_snp_type.cluster_size}" | 43 --clusterSize "${cluster_snp_type.cluster_size}" |
43 --clusterWindowSize "${cluster_snp_type.cluster_window_size}" | 44 --clusterWindowSize "${cluster_snp_type.cluster_window_size}" |
60 <when value="history"> <!-- FIX ME!!!! --> | 61 <when value="history"> <!-- FIX ME!!!! --> |
61 <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &lt;variant&gt;" /> | 62 <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &lt;variant&gt;" /> |
62 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> | 63 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> |
63 </when> | 64 </when> |
64 </conditional> | 65 </conditional> |
65 | 66 |
66 | |
67 <repeat name="variant_filters" title="Variant Filters"> | 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;)"> | 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> | 69 <sanitizer> |
70 <valid initial="string.printable"> | 70 <valid initial="string.printable"> |
71 <remove value="'"/> | 71 <remove value="'"/> |
74 </sanitizer> | 74 </sanitizer> |
75 </param> | 75 </param> |
76 <param name="filter_name" value="custom_filter" type="text" label="Filter name" help="-filterName,--filterName &lt;filterName&gt;"/> | 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" /> | 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> | 78 </repeat> |
79 | |
80 | 79 |
81 | |
82 <conditional name="mask_rod_bind_type"> | 80 <conditional name="mask_rod_bind_type"> |
83 <param name="mask_rod_bind_type_selector" type="select" label="Provide a Mask reference-ordered data file"> | 81 <param name="mask_rod_bind_type_selector" type="select" label="Provide a Mask reference-ordered data file"> |
84 <option value="set_mask" selected="True">Set mask</option> | 82 <option value="set_mask" selected="True">Set mask</option> |
85 <option value="exclude_mask">Don't set mask</option> | 83 <option value="exclude_mask">Don't set mask</option> |
86 </param> | 84 </param> |
90 <when value="set_mask"> | 88 <when value="set_mask"> |
91 <param name="input_mask_rod" type="data" format="bed,gatk_dbsnp,vcf" label="Mask ROD file" help="--mask &lt;mask&gt;" /> | 89 <param name="input_mask_rod" type="data" format="bed,gatk_dbsnp,vcf" label="Mask ROD file" help="--mask &lt;mask&gt;" /> |
92 <param name="mask_rod_name" type="text" value="Mask" label="Mask Name" help="-maskName,--maskName &lt;maskName&gt;"/> | 90 <param name="mask_rod_name" type="text" value="Mask" label="Mask Name" help="-maskName,--maskName &lt;maskName&gt;"/> |
93 <param name="mask_extension" type="integer" value="0" label="Mask Extension" help="-maskExtend,--maskExtension &lt;maskExtension&gt;"/> | 91 <param name="mask_extension" type="integer" value="0" label="Mask Extension" help="-maskExtend,--maskExtension &lt;maskExtension&gt;"/> |
94 </when> | 92 </when> |
95 </conditional> | 93 </conditional> |
96 | 94 |
97 | |
98 <expand macro="gatk_param_type_conditional" /> | 95 <expand macro="gatk_param_type_conditional" /> |
99 | 96 |
100 <conditional name="cluster_snp_type"> | 97 <conditional name="cluster_snp_type"> |
101 <param name="cluster_snp_type_selector" type="select" label="Cluster SNPs"> | 98 <param name="cluster_snp_type_selector" type="select" label="Cluster SNPs"> |
102 <option value="cluster_snp">Cluster SNPs</option> | 99 <option value="cluster_snp">Cluster SNPs</option> |
103 <option value="do_not_cluster_snp" selected="True">Do not cluster SNPs</option> | 100 <option value="do_not_cluster_snp" selected="True">Do not cluster SNPs</option> |
104 </param> | 101 </param> |
108 <when value="cluster_snp"> | 105 <when value="cluster_snp"> |
109 <param name="cluster_size" type="integer" value="3" label="The number of SNPs which make up a cluster" help="-cluster,--clusterSize &lt;clusterSize&gt;"/> | 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;"/> |
110 <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;"/> | 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;"/> |
111 </when> | 108 </when> |
112 </conditional> | 109 </conditional> |
113 | 110 |
114 <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" /> | 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" /> |
115 | 112 |
116 </inputs> | 113 </inputs> |
117 <outputs> | 114 <outputs> |
118 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" /> | 115 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" /> |
119 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> | 116 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> |
120 </outputs> | 117 </outputs> |
131 <param name="mask_rod_name" value="." /> | 128 <param name="mask_rod_name" value="." /> |
132 <param name="mask_extension" value="0" /> | 129 <param name="mask_extension" value="0" /> |
133 <param name="gatk_param_type_selector" value="basic" /> | 130 <param name="gatk_param_type_selector" value="basic" /> |
134 <param name="cluster_snp_type_selector" value="do_not_cluster_snp" /> | 131 <param name="cluster_snp_type_selector" value="do_not_cluster_snp" /> |
135 <param name="missing_values_in_expressions_should_evaluate_as_failing" /> | 132 <param name="missing_values_in_expressions_should_evaluate_as_failing" /> |
136 <output name="output_vcf" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" lines_diff="4" /> | 133 <output name="output_vcf" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" lines_diff="4" /> |
137 <output name="output_log" file="gatk/gatk_variant_filtration/gatk_variant_filtration_out_1.log.contains" compare="contains" /> | 134 <output name="output_log" file="gatk/gatk_variant_filtration/gatk_variant_filtration_out_1.log.contains" compare="contains" /> |
138 </test> | 135 </test> |
139 </tests> | 136 </tests> |
140 <help> | 137 <help> |
141 **What it does** | 138 **What it does** |