Mercurial > repos > iuc > bcftools_annotate

comparison bcftools_annotate.xml @ 3:12c14f97429b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
author iuc
date Tue, 31 Jan 2017 12:41:19 -0500
parents e58e34d48868
children 7b10a015526e
comparison
equal deleted inserted replaced
2:06a488b9cd34 3:12c14f97429b
11 @PREPARE_ENV@ 11 @PREPARE_ENV@
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 #set $annotation_file = 'annotations.vcf.gz'
18 bgzip -c "$section.annofile.annotations" > $annotation_file && 18 bgzip -c "$section.annofile.annotations" > $annotation_file &&
19 bcftools index $annotation_file && 19 bcftools index $annotation_file &&
20 #elif $section.annofile.anno_fmt == 'tab': 20 #elif $section.annofile.anno_fmt == 'tab':
21 #if $section.annofile.annotations.ext == 'bed' 21 #if $section.annofile.annotations.is_of_type('bed')
22 #set $annotation_file = 'annotations.bed.gz' 22 #set $annotation_file = 'annotations.bed.gz'
23 bgzip -c "$section.annofile.annotations" > $annotation_file && 23 bgzip -c "$section.annofile.annotations" > $annotation_file &&
24 tabix -s 1 -b 2 -e 3 $annotation_file && 24 tabix -s 1 -b 2 -e 3 $annotation_file &&
25 #else: 25 #else:
26 #set $annotation_file = 'annotations.tab.gz' 26 #set $annotation_file = 'annotations.tab.gz'
85 <inputs> 85 <inputs>
86 <expand macro="macro_input" /> 86 <expand macro="macro_input" />
87 <section name="sec_annofile" expanded="false" title="Add Annotations"> 87 <section name="sec_annofile" expanded="false" title="Add Annotations">
88 <expand macro="macro_columns" /> 88 <expand macro="macro_columns" />
89 <conditional name="annofile"> 89 <conditional name="annofile">
90 <param name="anno_fmt" type="select" label="Annotations File"> 90 <param name="anno_fmt" type="select" label="Annotations File">
91 <option value="none">None</option> 91 <option value="none">None</option>
92 <option value="vcf">From a VCF/BCF file</option> 92 <option value="vcf">From a VCF/BCF file</option>
93 <option value="tab">From a BED or tab-delimited file</option> 93 <option value="tab">From a BED or tab-delimited file</option>
94 </param> 94 </param>
95 <when value="none"/> 95 <when value="none"/>
97 <param name="annotations" type="data" format="vcf" label="Annotations VCF"/> 97 <param name="annotations" type="data" format="vcf" label="Annotations VCF"/>
98 </when> 98 </when>
99 <when value="tab"> 99 <when value="tab">
100 <param name="annotations" type="data" format="tabular,bed" label="Annotations"> 100 <param name="annotations" type="data" format="tabular,bed" label="Annotations">
101 <help><![CDATA[ 101 <help><![CDATA[
102 BED, or a tab-delimited file with mandatory columns CHROM, POS (or, alternatively, FROM and TO), 102 BED, or a tab-delimited file with mandatory columns CHROM, POS (or, alternatively, FROM and TO),
103 optional columns REF and ALT, and arbitrary number of annotation columns. 103 optional columns REF and ALT, and arbitrary number of annotation columns.
104 Note that in case of tab-delimited file, the coordinates POS, FROM and TO are one-based and inclusive. 104 Note that in case of tab-delimited file, the coordinates POS, FROM and TO are one-based and inclusive.
105 ]]></help> 105 ]]></help>
106 </param> 106 </param>
107 <param name="header_file" type="data" format="txt" label="Header Lines File" optional="True" help="lines which should be appended to the VCF header" /> 107 <param name="header_file" type="data" format="txt" label="Header Lines File" optional="True" help="lines which should be appended to the VCF header" />
108 <param name="header_lines" type="text" area="True" label="Header Lines" optional="True" help="lines which should be appended to the VCF header" > 108 <param name="header_lines" type="text" area="True" label="Header Lines" optional="True" help="lines which should be appended to the VCF header" >
109 <help><![CDATA[ 109 <help><![CDATA[
112 ]]></help> 112 ]]></help>
113 <sanitizer sanitize="False"/> 113 <sanitizer sanitize="False"/>
114 </param> 114 </param>
115 </when> 115 </when>
116 </conditional> 116 </conditional>
117 <param name="mark_sites" type="text" value="" label="Mark Sites TAG" 117 <param name="mark_sites" type="text" value="" label="Mark Sites TAG"
118 help="add INFO/TAG flag to sites which are (&quot;+&quot;) or are not (&quot;-&quot;) listed in the annotations file" /> 118 help="add INFO/TAG flag to sites which are (&quot;+&quot;) or are not (&quot;-&quot;) listed in the annotations file" />
119 <param name="set_id" type="text" value="" optional="true" label="Set Id"> 119 <param name="set_id" type="text" value="" optional="true" label="Set Id">
120 <help>Assign ID on the fly using the given format. 120 <help>Assign ID on the fly using the given format.
121 By default all existing IDs are replaced. 121 By default all existing IDs are replaced.
122 If the format string is preceded by "+", only missing IDs will be set. 122 If the format string is preceded by "+", only missing IDs will be set.
123 For example: '%CHROM\_%POS\_%REF\_%FIRST_ALT' 123 For example: '%CHROM\_%POS\_%REF\_%FIRST_ALT'
124 </help> 124 </help>
125 <sanitizer sanitize="False"/> 125 <sanitizer sanitize="False"/>
126 <validator type="regex" message="">^([+]?(%[A-Z]+)(\_%[A-Z]+)*)?$</validator> 126 <validator type="regex" message="">^([+]?(%[A-Z]+)(\_%[A-Z]+)*)?$</validator>
127 </param> 127 </param>
128 </section> 128 </section>
129 <section name="sec_annotate" expanded="false" title="Change Annotations"> 129 <section name="sec_annotate" expanded="false" title="Change Annotations">
130 <param name="remove" type="text" value="" label="Remove annotations" optional="true"> 130 <param name="remove" type="text" value="" label="Remove annotations" optional="true">
131 <help><![CDATA[ 131 <help><![CDATA[
132 List of annotations to remove. 132 List of annotations to remove.
133 Use "FILTER" to remove all filters or "FILTER/SomeFilter" to remove a specific filter. 133 Use "FILTER" to remove all filters or "FILTER/SomeFilter" to remove a specific filter.
134 Similarly, "INFO" can be used to remove all INFO tags and "FORMAT" to remove all FORMAT tags except GT. 134 Similarly, "INFO" can be used to remove all INFO tags and "FORMAT" to remove all FORMAT tags except GT.
135 To remove all INFO tags except "FOO" and "BAR", use "^INFO/FOO,INFO/BAR" (and similarly for FORMAT and FILTER). 135 To remove all INFO tags except "FOO" and "BAR", use "^INFO/FOO,INFO/BAR" (and similarly for FORMAT and FILTER).
136 "INFO" can be abbreviated to "INF" and "FORMAT" to "FMT". 136 "INFO" can be abbreviated to "INF" and "FORMAT" to "FMT".
137 ]]></help> 137 ]]></help>
138 <validator type="regex" message="">^(\^?[A-Z]+(/\w+)?(,\^?[A-Z]+(/\w+)?)*)?$</validator> 138 <validator type="regex" message="">^(\^?[A-Z]+(/\w+)?(,\^?[A-Z]+(/\w+)?)*)?$</validator>
139 </param> 139 </param>
140 <param name="rename_chrs" type="data" format="tabular" label="Rename CHROM" optional="True" 140 <param name="rename_chrs" type="data" format="tabular" label="Rename CHROM" optional="True"
141 help="rename chromosomes according to the map in file, with old_name new_name pairs separated by whitespaces, each on a separate line." /> 141 help="rename chromosomes according to the map in file, with old_name new_name pairs separated by whitespaces, each on a separate line." />
142 </section> 142 </section>
143 <section name="sec_restrict" expanded="false" title="Restrict to"> 143 <section name="sec_restrict" expanded="false" title="Restrict to">
144 <expand macro="macro_include" /> 144 <expand macro="macro_include" />
145 <expand macro="macro_exclude" /> 145 <expand macro="macro_exclude" />