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comparison variant_annotator.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_annotator" name="Variant Annotator" version="@VERSION@.0"> 1 <tool id="gatk2_variant_annotator" name="Variant Annotator" 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 #if str( $reference_source.input_bam ) != "None": 11 #if str( $reference_source.input_bam ) != "None":
11 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input" 12 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
44 #end for 45 #end for
45 ' 46 '
46 #if $reference_source.input_variant_bti: 47 #if $reference_source.input_variant_bti:
47 -d "--intervals" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant_bti" 48 -d "--intervals" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant_bti"
48 #end if 49 #end if
49 50
50 #for $rod_binding in $comp_rod_bind: 51 #for $rod_binding in $comp_rod_bind:
51 -d "--comp:${rod_binding.comp_rod_name},%(file_type)s" "${rod_binding.comp_input_rod}" "${rod_binding.comp_input_rod.ext}" "input_comp_${rod_binding.comp_rod_name}" 52 -d "--comp:${rod_binding.comp_rod_name},%(file_type)s" "${rod_binding.comp_input_rod}" "${rod_binding.comp_input_rod.ext}" "input_comp_${rod_binding.comp_rod_name}"
52 #end for 53 #end for
53 54
54 @DBSNP_OPTIONS@ 55 @DBSNP_OPTIONS@
55 56
56 #for $rod_binding in $resource_rod_bind: 57 #for $rod_binding in $resource_rod_bind:
57 -d "--resource:${rod_binding.resource_rod_name},%(file_type)s" "${rod_binding.resource_input_rod}" "${rod_binding.resource_input_rod.ext}" "input_resource_${rod_binding.resource_rod_name}" 58 -d "--resource:${rod_binding.resource_rod_name},%(file_type)s" "${rod_binding.resource_input_rod}" "${rod_binding.resource_input_rod.ext}" "input_resource_${rod_binding.resource_rod_name}"
58 #end for 59 #end for
59 60
60 #if str( $snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff': 61 #if str( $snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff':
61 -p '--annotation "SnpEff"' 62 -p '--annotation "SnpEff"'
62 -d "--snpEffFile:${snpEff_rod_bind_type.snpEff_rod_name},%(file_type)s" "${snpEff_rod_bind_type.snpEff_input_rod}" "${snpEff_rod_bind_type.snpEff_input_rod.ext}" "input_snpEff_${snpEff_rod_bind_type.snpEff_rod_name}" 63 -d "--snpEffFile:${snpEff_rod_bind_type.snpEff_rod_name},%(file_type)s" "${snpEff_rod_bind_type.snpEff_input_rod}" "${snpEff_rod_bind_type.snpEff_input_rod.ext}" "input_snpEff_${snpEff_rod_bind_type.snpEff_rod_name}"
63 #else: 64 #else:
64 -p '--excludeAnnotation "SnpEff"' 65 -p '--excludeAnnotation "SnpEff"'
65 #end if 66 #end if
66 67
67 #for $expression in $expressions: 68 #for $expression in $expressions:
68 -p '--expression "${expression.expression}"' 69 -p '--expression "${expression.expression}"'
69 #end for 70 #end for
70 71
71 #include source=$standard_gatk_options# 72 #include source=$standard_gatk_options#
72 73
73 -p ' 74 -p '
74 #if str( $annotation_group ) != "None": 75 #if str( $annotation_group ) != "None":
75 #for $group in str( $annotation_group ).split( ',' ): 76 #for $group in str( $annotation_group ).split( ',' ):
76 --group "${group}" 77 --group "${group}"
77 #end for 78 #end for
122 <filter type="static_value" value="VariantAnnotator" column="tools_valid_for"/> 123 <filter type="static_value" value="VariantAnnotator" column="tools_valid_for"/>
123 </options> 124 </options>
124 </param> 125 </param>
125 </when> 126 </when>
126 </conditional> 127 </conditional>
127 128
128 <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &amp;lt;annotation&amp;gt;"> 129 <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &amp;lt;annotation&amp;gt;">
129 <param name="additional_annotation_name" type="text" value="" label="Annotation name" /> 130 <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
130 </repeat> 131 </repeat>
131 132
132 <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data" help="-comp,--comp &amp;lt;comp&amp;gt;"> 133 <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data" help="-comp,--comp &amp;lt;comp&amp;gt;">
133 <param name="comp_input_rod" type="data" format="vcf" label="ROD file" /> 134 <param name="comp_input_rod" type="data" format="vcf" label="ROD file" />
134 <param name="comp_rod_name" type="text" value="Unnamed" label="ROD Name"/> 135 <param name="comp_rod_name" type="text" value="Unnamed" label="ROD Name"/>
135 </repeat> 136 </repeat>
136 <expand macro="dbsnp_param" /> 137 <expand macro="dbsnp_param" />
137 138
138 <repeat name="resource_rod_bind" title="Binding for reference-ordered resource data" help="-resource,--resource &amp;lt;resource&amp;gt;"> 139 <repeat name="resource_rod_bind" title="Binding for reference-ordered resource data" help="-resource,--resource &amp;lt;resource&amp;gt;">
139 <param name="resource_input_rod" type="data" format="vcf" label="ROD file" /> 140 <param name="resource_input_rod" type="data" format="vcf" label="ROD file" />
140 <param name="resource_rod_name" type="text" value="Unnamed" label="ROD Name"/> 141 <param name="resource_rod_name" type="text" value="Unnamed" label="ROD Name"/>
141 </repeat> 142 </repeat>
142 143
143 <conditional name="snpEff_rod_bind_type"> 144 <conditional name="snpEff_rod_bind_type">
144 <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;"> 145 <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;">
145 <option value="set_snpEff">Set snpEff</option> 146 <option value="set_snpEff">Set snpEff</option>
146 <option value="exclude_snpEff" selected="True">Don't set snpEff</option> 147 <option value="exclude_snpEff" selected="True">Don't set snpEff</option>
147 </param> 148 </param>
151 <when value="set_snpEff"> 152 <when value="set_snpEff">
152 <param name="snpEff_input_rod" type="data" format="vcf" label="ROD file" /> 153 <param name="snpEff_input_rod" type="data" format="vcf" label="ROD file" />
153 <param name="snpEff_rod_name" type="hidden" value="snpEff" label="ROD Name"/> 154 <param name="snpEff_rod_name" type="hidden" value="snpEff" label="ROD Name"/>
154 </when> 155 </when>
155 </conditional> 156 </conditional>
156 157
157 <repeat name="expressions" title="Expression" help="-E,--expression &amp;lt;expression&amp;gt;"> 158 <repeat name="expressions" title="Expression" help="-E,--expression &amp;lt;expression&amp;gt;">
158 <param name="expression" type="text" value="" label="Expression"/> 159 <param name="expression" type="text" value="" label="Expression"/>
159 </repeat> 160 </repeat>
160 161
161 <expand macro="gatk_param_type_conditional" /> 162 <expand macro="gatk_param_type_conditional" />
162 163
163 <param name="annotation_group" type="select" multiple="True" display="checkboxes" label="annotation interfaces/groups to apply to variant calls" help="-G,--group &amp;lt;group&amp;gt;"> 164 <param name="annotation_group" type="select" multiple="True" display="checkboxes" label="annotation interfaces/groups to apply to variant calls" help="-G,--group &amp;lt;group&amp;gt;">
164 <option value="RodRequiringAnnotation">RodRequiringAnnotation</option> 165 <option value="RodRequiringAnnotation">RodRequiringAnnotation</option>
165 <option value="Standard">Standard</option> 166 <option value="Standard">Standard</option>
166 <option value="Experimental">Experimental</option> 167 <option value="Experimental">Experimental</option>
167 <option value="WorkInProgress">WorkInProgress</option> 168 <option value="WorkInProgress">WorkInProgress</option>
174 <options from_data_table="gatk2_annotations"> 175 <options from_data_table="gatk2_annotations">
175 <filter type="multiple_splitter" column="tools_valid_for" separator=","/> 176 <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
176 <filter type="static_value" value="VariantAnnotator" column="tools_valid_for"/> 177 <filter type="static_value" value="VariantAnnotator" column="tools_valid_for"/>
177 </options> 178 </options>
178 </param> 179 </param>
179 180
180 </inputs> 181 </inputs>
181 <outputs> 182 <outputs>
182 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" /> 183 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" />
183 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> 184 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
184 </outputs> 185 </outputs>
195 <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" /> 196 <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" />
196 <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" /> 197 <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
197 <param name="dbsnp_rod_name" value="dbsnp" /> 198 <param name="dbsnp_rod_name" value="dbsnp" />
198 <param name="snpEff_rod_bind_type_selector" value="exclude_snpEff" /> 199 <param name="snpEff_rod_bind_type_selector" value="exclude_snpEff" />
199 <param name="gatk_param_type_selector" value="basic" /> 200 <param name="gatk_param_type_selector" value="basic" />
200 <output name="output_vcf" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" lines_diff="4" /> 201 <output name="output_vcf" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" lines_diff="4" />
201 <output name="output_log" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.log.contains" compare="contains" /> 202 <output name="output_log" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.log.contains" compare="contains" />
202 <param name="comp_rod_bind" value="0" /> 203 <param name="comp_rod_bind" value="0" />
203 <param name="resource_rod_bind" value="0" /> 204 <param name="resource_rod_bind" value="0" />
204 <param name="expressions" value="0" /> 205 <param name="expressions" value="0" />
205 <!-- <param name="annotation_group" /> --> 206 <!-- <param name="annotation_group" /> -->