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comparison variant_annotator.xml @ 1:c8752e31f496 draft

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Uploaded
author bgruening
date Tue, 26 Nov 2013 06:10:20 -0500
parents 9ad15075b9fa
children e67da4f2c9bf
comparison
equal deleted inserted replaced
0:9ad15075b9fa 1:c8752e31f496
2 <description></description> 2 <description></description>
3 <expand macro="requirements" /> 3 <expand macro="requirements" />
4 <macros> 4 <macros>
5 <import>gatk2_macros.xml</import> 5 <import>gatk2_macros.xml</import>
6 </macros> 6 </macros>
7 <command interpreter="python">gatk2_wrapper.py 7 <command interpreter="python">
8 ##--max_jvm_heap_fraction "1" 8 gatk2_wrapper.py
9 --stdout "${output_log}" 9 --stdout "${output_log}"
10 #if str( $reference_source.input_bam ) != "None": 10 #if str( $reference_source.input_bam ) != "None":
11 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input" 11 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
12 #if str( $reference_source.input_bam.metadata.bam_index ) != "None": 12 #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
13 -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index 13 -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
14 #end if 14 #end if
15 #end if 15 #end if
16 -d "--variant" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" 16 -d "--variant" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
17 -p ' 17 -p '
18 @JAR_PATH@ 18 @JAR_PATH@
19 ##--list
20 -T "VariantAnnotator" 19 -T "VariantAnnotator"
21 \$GATK2_SITE_OPTIONS 20 \$GATK2_SITE_OPTIONS
22 21
23 @THREADS@ 22 @THREADS@
24 23
25 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
26 #if $reference_source.reference_source_selector != "history": 24 #if $reference_source.reference_source_selector != "history":
27 -R "${reference_source.ref_file.fields.path}" 25 -R "${reference_source.ref_file.fields.path}"
28 #end if 26 #end if
29 -o "${output_vcf}" 27 -o "${output_vcf}"
30 #if str( $annotations_type.annotations_type_selector ) == "use_all_annotations": 28 #if str( $annotations_type.annotations_type_selector ) == "use_all_annotations":
90 <inputs> 88 <inputs>
91 <conditional name="reference_source"> 89 <conditional name="reference_source">
92 <expand macro="reference_source_selector_param" /> 90 <expand macro="reference_source_selector_param" />
93 <when value="cached"> 91 <when value="cached">
94 <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&amp;gt;"/> 92 <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&amp;gt;"/>
95 <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." help="--intervals"/> 93 <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." help="-BTI variant"/>
96 <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations. (-I,--input_file &amp;lt;input_file&amp;gt;)" > 94 <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations. (-I,--input_file &amp;lt;input_file&amp;gt;)" >
97 <validator type="unspecified_build" /> 95 <validator type="unspecified_build" />
98 <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select --> 96 <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
99 </param> 97 </param>
100 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;"> 98 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
104 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 102 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
105 </param> 103 </param>
106 </when> 104 </when>
107 <when value="history"> <!-- FIX ME!!!! --> 105 <when value="history"> <!-- FIX ME!!!! -->
108 <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&amp;gt;"/> 106 <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&amp;gt;"/>
109 <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." help="--intervals"/> 107 <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." help="-BTI variant"/>
110 <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations. (-I,--input_file &amp;lt;input_file&amp;gt;)" > 108 <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations. (-I,--input_file &amp;lt;input_file&amp;gt;)" />
111 </param>
112 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" /> 109 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
113 </when> 110 </when>
114 </conditional> 111 </conditional>
115 <conditional name="annotations_type"> 112 <conditional name="annotations_type">
116 <param name="annotations_type_selector" type="select" label="Use all possible annotations"> 113 <param name="annotations_type_selector" type="select" label="Use all possible annotations">
158 <param name="resource_input_rod" type="data" format="vcf" label="ROD file" /> 155 <param name="resource_input_rod" type="data" format="vcf" label="ROD file" />
159 <param name="resource_rod_name" type="text" value="Unnamed" label="ROD Name"/> 156 <param name="resource_rod_name" type="text" value="Unnamed" label="ROD Name"/>
160 </repeat> 157 </repeat>
161 158
162 <conditional name="snpEff_rod_bind_type"> 159 <conditional name="snpEff_rod_bind_type">
163 <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file" help="-snpEffFile,--snpEffFile &amp;lt;snpEffFile&amp;gt;"> 160 <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file (VCF)" help="-snpEffFile,--snpEffFile &amp;lt;snpEffFile&amp;gt;">
164 <option value="set_snpEff">Set snpEff</option> 161 <option value="set_snpEff">Set snpEff</option>
165 <option value="exclude_snpEff" selected="True">Don't set snpEff</option> 162 <option value="exclude_snpEff" selected="True">Don't set snpEff</option>
166 </param> 163 </param>
167 <when value="exclude_snpEff"> 164 <when value="exclude_snpEff">
168 <!-- Do nothing here --> 165 <!-- Do nothing here -->