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comparison bcftools_annotate.xml @ 9:a80ec64f9101 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
author iuc
date Mon, 29 Jul 2019 18:11:40 -0400
parents 2f09d9744e0b
children 8e01baf41774
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8:2f09d9744e0b 9:a80ec64f9101
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy2">
3 <description>Annotate and edit VCF/BCF files</description> 3 <description>Annotate and edit VCF/BCF files</description>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">annotate</token> 5 <token name="@EXECUTABLE@">annotate</token>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
12 @PREPARE_INPUT_FILE@ 12 @PREPARE_INPUT_FILE@
13 #set $annotation_file = None 13 #set $annotation_file = None
14 #set $annotation_hdr = None 14 #set $annotation_hdr = None
15 #set $section = $sec_annofile 15 #set $section = $sec_annofile
16 #if $section.annofile.anno_fmt == 'vcf': 16 #if $section.annofile.anno_fmt == 'vcf':
17 #set $annotation_file = 'annotations.vcf.gz' 17 #if $section.annofile.annotations.is_of_type('vcf')
18 bgzip -c "$section.annofile.annotations" > $annotation_file && 18 #set $annotation_file = 'annotations.vcf.gz'
19 bcftools index $annotation_file && 19 bgzip -c "$section.annofile.annotations" > $annotation_file &&
20 bcftools index $annotation_file &&
21 #elif $section.annofile.annotations.is_of_type('bcf')
22 #set $annotation_file = 'annotations.bcf'
23 ln -s '$section.annofile.annotations' $annotation_file &&
24 #if $section.annofile.annotations.metadata.bcf_index:
25 ln -s '${section.annofile.annotations.metadata.bcf_index}' ${annotation_file}.csi &&
26 #else
27 bcftools index $annotation_file &&
28 #end if
29 #end if
20 #elif $section.annofile.anno_fmt == 'tab': 30 #elif $section.annofile.anno_fmt == 'tab':
21 #if $section.annofile.annotations.is_of_type('bed') 31 #if $section.annofile.annotations.is_of_type('bed')
22 #set $annotation_file = 'annotations.bed.gz' 32 #set $annotation_file = 'annotations.bed.gz'
23 bgzip -c "$section.annofile.annotations" > $annotation_file && 33 bgzip -c "$section.annofile.annotations" > $annotation_file &&
24 tabix -s 1 -b 2 -e 3 $annotation_file && 34 tabix -s 1 -b 2 -e 3 $annotation_file &&
95 <option value="vcf">From a VCF/BCF file</option> 105 <option value="vcf">From a VCF/BCF file</option>
96 <option value="tab">From a BED or tab-delimited file</option> 106 <option value="tab">From a BED or tab-delimited file</option>
97 </param> 107 </param>
98 <when value="none"/> 108 <when value="none"/>
99 <when value="vcf"> 109 <when value="vcf">
100 <param name="annotations" type="data" format="vcf" label="Annotations VCF"/> 110 <param name="annotations" type="data" format="vcf,bcf" label="Annotations VCF"/>
101 </when> 111 </when>
102 <when value="tab"> 112 <when value="tab">
103 <param name="annotations" type="data" format="tabular,bed" label="Annotations"> 113 <param name="annotations" type="data" format="tabular,bed" label="Annotations">
104 <help><![CDATA[ 114 <help><![CDATA[
105 BED, or a tab-delimited file with mandatory columns CHROM, POS (or, alternatively, FROM and TO), 115 BED, or a tab-delimited file with mandatory columns CHROM, POS (or, alternatively, FROM and TO),
194 <has_text text="STR=testSNP" /> 204 <has_text text="STR=testSNP" />
195 </assert_contents> 205 </assert_contents>
196 </output> 206 </output>
197 </test> 207 </test>
198 <test> 208 <test>
209 <param name="input_file" ftype="vcf" value="annotate.vcf" />
210 <param name="anno_fmt" value="vcf" />
211 <param name="annotations" value="annots.bcf" />
212 <param name="columns" value="STR,ID,QUAL,FILTER" />
213 <param name="output_type" value="v" />
214 <output name="output_file">
215 <assert_contents>
216 <has_text text="idIndel" />
217 <has_text text="STR=testSNP" />
218 </assert_contents>
219 </output>
220 </test>
221 <test>
199 <param name="input_file" ftype="vcf" value="annotate2.vcf" /> 222 <param name="input_file" ftype="vcf" value="annotate2.vcf" />
200 <param name="anno_fmt" value="vcf" /> 223 <param name="anno_fmt" value="vcf" />
201 <param name="annotations" value="annots2.vcf" /> 224 <param name="annotations" value="annots2.vcf" />
202 <param name="columns" value="ID,QUAL,FILTER,INFO,FMT" /> 225 <param name="columns" value="ID,QUAL,FILTER,INFO,FMT" />
203 <param name="output_type" value="v" /> 226 <param name="output_type" value="v" />