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comparison bcftools_annotate.xml @ 17:28647eee857d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ccc967cdce26379110361f8dea521bade23f8612"
author iuc
date Tue, 08 Mar 2022 17:26:56 +0000
parents a974b56e4c43
children 65d418d476a5
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16:a974b56e4c43 17:28647eee857d
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@"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1">
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>
15 #set $annotation_hdr = None 15 #set $annotation_hdr = None
16 #set $section = $sec_annofile 16 #set $section = $sec_annofile
17 #if $section.annofile.anno_fmt == 'vcf': 17 #if $section.annofile.anno_fmt == 'vcf':
18 #if $section.annofile.annotations.is_of_type('vcf') 18 #if $section.annofile.annotations.is_of_type('vcf')
19 #set $annotation_file = 'annotations.vcf.gz' 19 #set $annotation_file = 'annotations.vcf.gz'
20 bgzip -c "$section.annofile.annotations" > $annotation_file && 20 bgzip -c '$section.annofile.annotations' > $annotation_file &&
21 bcftools index $annotation_file && 21 bcftools index $annotation_file &&
22 #elif $section.annofile.annotations.is_of_type('bcf') 22 #elif $section.annofile.annotations.is_of_type('bcf')
23 #set $annotation_file = 'annotations.bcf' 23 #set $annotation_file = 'annotations.bcf'
24 ln -s '$section.annofile.annotations' $annotation_file && 24 ln -s '$section.annofile.annotations' $annotation_file &&
25 #if $section.annofile.annotations.metadata.bcf_index: 25 #if $section.annofile.annotations.metadata.bcf_index:
29 #end if 29 #end if
30 #end if 30 #end if
31 #elif $section.annofile.anno_fmt == 'tab': 31 #elif $section.annofile.anno_fmt == 'tab':
32 #if $section.annofile.annotations.is_of_type('bed') 32 #if $section.annofile.annotations.is_of_type('bed')
33 #set $annotation_file = 'annotations.bed.gz' 33 #set $annotation_file = 'annotations.bed.gz'
34 bgzip -c "$section.annofile.annotations" > $annotation_file && 34 bgzip -c '$section.annofile.annotations' > $annotation_file &&
35 tabix -s 1 -b 2 -e 3 $annotation_file && 35 tabix -s 1 -b 2 -e 3 $annotation_file &&
36 #else: 36 #else:
37 #set $annotation_file = 'annotations.tab.gz' 37 #set $annotation_file = 'annotations.tab.gz'
38 bgzip -c "$section.annofile.annotations" > $annotation_file && 38 bgzip -c '$section.annofile.annotations' > $annotation_file &&
39 tabix -s 1 -b 2 -e 2 $annotation_file && 39 tabix -s 1 -b 2 -e 2 $annotation_file &&
40 #end if 40 #end if
41 #if $section.annofile.header_file: 41 #if $section.annofile.header_file:
42 #set $annotation_hdr = $section.annofile.header_file 42 #set $annotation_hdr = $section.annofile.header_file
43 #elif $section.annofile.header_lines: 43 #elif $section.annofile.header_lines:
44 #set $annotation_hdr = 'annotation.hdr' 44 #set $annotation_hdr = 'annotation.hdr'
45 grep '^\#\#INFO' ${hdr_file} > $annotation_hdr && 45 grep '^\#\#INFO' '${hdr_file}' > $annotation_hdr &&
46 #end if 46 #end if
47 #end if 47 #end if
48 #set $section = $sec_restrict 48 #set $section = $sec_restrict
49 49
50 bcftools @EXECUTABLE@ 50 bcftools @EXECUTABLE@
51 @PREPARE_REGIONS_FILE@ 51 @PREPARE_REGIONS_FILE@
52 52
53 #set $section = $sec_annofile 53 #set $section = $sec_annofile
54 @COLUMNS@ 54 @COLUMNS@
55 #if $annotation_file: 55 #if $annotation_file:
56 --annotations "${annotation_file}" 56 --annotations '${annotation_file}'
57 #end if 57 #end if
58 #if $annotation_hdr: 58 #if $annotation_hdr:
59 --header-lines "${annotation_hdr}" 59 --header-lines '${annotation_hdr}'
60 #end if 60 #end if
61 61
62 #if $section.set_id: 62 #if $section.set_id:
63 --set-id "${section.set_id}" 63 --set-id '${section.set_id}'
64 #end if 64 #end if
65 #if $section.mark_sites: 65 #if $section.mark_sites:
66 --mark-sites "${section.mark_sites}" 66 --mark-sites '${section.mark_sites}'
67 #end if 67 #end if
68 68
69 #set $section = $sec_annotate 69 #set $section = $sec_annotate
70 #if $section.rename_chrs: 70 #if $section.rename_chrs:
71 --rename-chrs "${section.rename_chrs}" 71 --rename-chrs '${section.rename_chrs}'
72 #end if 72 #end if
73 #if $section.remove: 73 #if $section.remove:
74 --remove "${section.remove}" 74 --remove '${section.remove}'
75 #end if 75 #end if
76 76
77 ## Default section 77 ## Default section
78 #set $section = $sec_restrict 78 #set $section = $sec_restrict
79 @INCLUDE@ 79 @INCLUDE@
116 BED, or a tab-delimited file with mandatory columns CHROM, POS (or, alternatively, FROM and TO), 116 BED, or a tab-delimited file with mandatory columns CHROM, POS (or, alternatively, FROM and TO),
117 optional columns REF and ALT, and arbitrary number of annotation columns. 117 optional columns REF and ALT, and arbitrary number of annotation columns.
118 Note that in case of tab-delimited file, the coordinates POS, FROM and TO are one-based and inclusive. 118 Note that in case of tab-delimited file, the coordinates POS, FROM and TO are one-based and inclusive.
119 ]]></help> 119 ]]></help>
120 </param> 120 </param>
121 <param name="header_file" type="data" format="txt" label="Header Lines File" optional="True" help="lines which should be appended to the VCF header" /> 121 <param name="header_file" type="data" format="txt" label="Header Lines File" optional="true" help="lines which should be appended to the VCF header" />
122 <param name="header_lines" type="text" area="True" label="Header Lines" optional="True" help="lines which should be appended to the VCF header" > 122 <param name="header_lines" type="text" area="true" label="Header Lines" optional="true" help="lines which should be appended to the VCF header" >
123 <help><![CDATA[ 123 <help><![CDATA[
124 ##INFO=<ID=NUMERIC_TAG,Number=1,Type=Integer,Description="Example header line"> 124 ##INFO=<ID=NUMERIC_TAG,Number=1,Type=Integer,Description="Example header line">
125 ##INFO=<ID=STRING_TAG,Number=1,Type=String,Description="Yet another header line"> 125 ##INFO=<ID=STRING_TAG,Number=1,Type=String,Description="Yet another header line">
126 ]]></help> 126 ]]></help>
127 <sanitizer sanitize="False"/> 127 <sanitizer sanitize="False"/>
128 </param> 128 </param>
129 </when> 129 </when>
130 </conditional> 130 </conditional>
131 <param name="mark_sites" type="text" value="" label="Mark Sites TAG" 131 <param argument="--mark-sites" type="text" value="" label="Mark Sites TAG"
132 help="add INFO/TAG flag to sites which are (&quot;+&quot;) or are not (&quot;-&quot;) listed in the annotations file" /> 132 help="add INFO/TAG flag to sites which are (&quot;+&quot;) or are not (&quot;-&quot;) listed in the annotations file" />
133 <param name="set_id" type="text" value="" optional="true" label="Set Id"> 133 <param argument="--set-id" type="text" value="" optional="true" label="Set Id">
134 <help>Assign ID on the fly using the given format. 134 <help>Assign ID on the fly using the given format.
135 By default all existing IDs are replaced. 135 By default all existing IDs are replaced.
136 If the format string is preceded by "+", only missing IDs will be set. 136 If the format string is preceded by "+", only missing IDs will be set.
137 For example: '%CHROM\_%POS\_%REF\_%FIRST_ALT' 137 For example: '%CHROM\_%POS\_%REF\_%FIRST_ALT'
138 </help> 138 </help>
139 <sanitizer sanitize="False"/> 139 <sanitizer sanitize="False"/>
140 <validator type="regex" message="">^([+]?(%[A-Z]+)(\_%[A-Z]+)*)?$</validator> 140 <validator type="regex" message="">^([+]?(%[A-Z_]+)(\\_%[A-Z_]+)*)?$</validator>
141 </param> 141 </param>
142 </section> 142 </section>
143 <section name="sec_annotate" expanded="false" title="Change Annotations"> 143 <section name="sec_annotate" expanded="false" title="Change Annotations">
144 <param name="remove" type="text" value="" label="Remove annotations" optional="true"> 144 <param argument="--remove" type="text" value="" label="Remove annotations" optional="true">
145 <help><![CDATA[ 145 <help><![CDATA[
146 List of annotations to remove. 146 List of annotations to remove.
147 Use "FILTER" to remove all filters or "FILTER/SomeFilter" to remove a specific filter. 147 Use "FILTER" to remove all filters or "FILTER/SomeFilter" to remove a specific filter.
148 Similarly, "INFO" can be used to remove all INFO tags and "FORMAT" to remove all FORMAT tags except GT. 148 Similarly, "INFO" can be used to remove all INFO tags and "FORMAT" to remove all FORMAT tags except GT.
149 To remove all INFO tags except "FOO" and "BAR", use "^INFO/FOO,INFO/BAR" (and similarly for FORMAT and FILTER). 149 To remove all INFO tags except "FOO" and "BAR", use "^INFO/FOO,INFO/BAR" (and similarly for FORMAT and FILTER).
150 "INFO" can be abbreviated to "INF" and "FORMAT" to "FMT". 150 "INFO" can be abbreviated to "INF" and "FORMAT" to "FMT".
151 ]]></help> 151 ]]></help>
152 <validator type="regex" message="">^(\^?[A-Z]+(/\w+)?(,\^?[A-Z]+(/\w+)?)*)?$</validator> 152 <validator type="regex" message="">^(\^?[A-Z]+(/\w+)?(,\^?[A-Z]+(/\w+)?)*)?$</validator>
153 </param> 153 </param>
154 <param name="rename_chrs" type="data" format="tabular" label="Rename CHROM" optional="True" 154 <param argument="--rename-chrs" type="data" format="tabular" label="Rename CHROM" optional="true"
155 help="rename chromosomes according to the map in file, with old_name new_name pairs separated by whitespaces, each on a separate line." /> 155 help="rename chromosomes according to the map in file, with old_name new_name pairs separated by whitespaces, each on a separate line." />
156 </section> 156 </section>
157 <section name="sec_restrict" expanded="false" title="Restrict to"> 157 <section name="sec_restrict" expanded="false" title="Restrict to">
158 <expand macro="macro_include" /> 158 <expand macro="macro_include" />
159 <expand macro="macro_exclude" /> 159 <expand macro="macro_exclude" />
180 </assert_contents> 180 </assert_contents>
181 </output> 181 </output>
182 </test> 182 </test>
183 <test> 183 <test>
184 <param name="input_file" ftype="vcf" value="annotate.vcf" /> 184 <param name="input_file" ftype="vcf" value="annotate.vcf" />
185 <param name="anno_fmt" value="tab" /> 185 <section name="sec_annofile">
186 <param name="annotations" value="annotate2.tab" /> 186 <param name="columns" value="CHROM,FROM,TO,T_STR" />
187 <param name="header_file" value="annotate.hdr" /> 187 <conditional name="annofile">
188 <param name="columns" value="CHROM,FROM,TO,T_STR" /> 188 <param name="anno_fmt" value="tab" />
189 <param name="annotations" value="annotate2.tab" />
190 <param name="header_file" value="annotate.hdr" />
191 </conditional>
192 <param name="set_id" value="%CHROM\_%POS\_%REF\_%FIRST_ALT" />
193 </section>
189 <param name="output_type" value="v" /> 194 <param name="output_type" value="v" />
190 <output name="output_file"> 195 <output name="output_file">
191 <assert_contents> 196 <assert_contents>
192 <has_text text="T_STR=region_3000150_3106154" /> 197 <has_text text="T_STR=region_3000150_3106154" />
198 <has_text text="1_3062915_GTTT_G" />
193 </assert_contents> 199 </assert_contents>
194 </output> 200 </output>
195 </test> 201 </test>
196 <test> 202 <test>
197 <param name="input_file" ftype="vcf" value="annotate.vcf" /> 203 <param name="input_file" ftype="vcf" value="annotate.vcf" />