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comparison bcftools_concat.xml @ 8:62ca6da715bf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
author iuc
date Thu, 21 Feb 2019 16:06:33 -0500
parents 2d95ed0b720a
children 398d2ccc4233
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7:f430a1ec7ee4 8:62ca6da715bf
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="@VERSION@.1"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@">
3 <description>Concatenate or combine VCF/BCF files</description> 3 <description>Concatenate or combine VCF/BCF files</description>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">concat</token> 5 <token name="@EXECUTABLE@">concat</token>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
17 17
18 ## Default section 18 ## Default section
19 #set $section = $sec_default 19 #set $section = $sec_default
20 20
21 #if $section.mode.naive == "yes": 21 #if $section.mode.naive == "yes":
22 --naive 22 --naive
23 #else: 23 #else:
24 #if $section.mode.overlaps.allow_overlaps == 'yes': 24 #if $section.mode.overlaps.allow_overlaps == 'yes':
25 --allow-overlaps 25 --allow-overlaps
26 #if $section.mode.overlaps.rm_dups: 26 #if $section.mode.overlaps.rm_dups:
27 --rm-dups $section.mode.overlaps.rm_dups 27 --rm-dups $section.mode.overlaps.rm_dups
28 #end if
28 #end if 29 #end if
29 #end if 30 ${section.mode.ligate}
30 ${section.mode.ligate}
31 #end if 31 #end if
32 ${section.compact_PS} 32 ${section.compact_PS}
33 #if $section.min_PQ: 33 #if str($section.min_PQ):
34 --min-PQ "${section.min_PQ}" 34 --min-PQ ${section.min_PQ}
35 #end if 35 #end if
36 36
37 #set $section = $sec_restrict 37 #set $section = $sec_restrict
38 @REGIONS@ 38 @REGIONS@
39 39
40 @OUTPUT_TYPE@ 40 @OUTPUT_TYPE@
41 @THREADS@ 41 @THREADS@
42 42
43 ## Primary Input/Outputs 43 ## Primary Input/Outputs
44 @INPUT_FILES@ 44 @INPUT_FILES@
45 #if $sec_default.mode.naive == "yes" and $output_type == 'v': 45 #if $sec_default.mode.naive == "yes" and $output_type == 'v':
46 > output.gz && bcftools index output.gz && bcftools view -O v -o '$output_file' output.gz 46 > output.gz && bcftools index output.gz && bcftools view -O v -o '$output_file' output.gz
47 #else: 47 #else:
48 > '$output_file' 48 > '$output_file'
49 #end if 49 #end if
50 ]]> 50 ]]></command>
51 </command>
52 <inputs> 51 <inputs>
53 <expand macro="macro_inputs" /> 52 <expand macro="macro_inputs" />
54 <section name="sec_restrict" expanded="false" title="Restrict to"> 53 <section name="sec_restrict" expanded="false" title="Restrict to">
55 <expand macro="macro_regions" /> 54 <expand macro="macro_regions" />
56 </section> 55 </section>
57 <section name="sec_default" expanded="true" title="Concat Options"> 56 <section name="sec_default" expanded="true" title="Concat Options">
58 <conditional name="mode"> 57 <conditional name="mode">
59 <param name="naive" type="select" label="naive concat"> 58 <param name="naive" type="select" label="naive concat">
60 <help><![CDATA[ 59 <help><![CDATA[
61 --naive concatenates VCF or BCF files without recompression. This can be used used to combine results that were generated separately for each chromosome. This is very fast but requires that all files are of the same type (all VCF or all BCF) and have the same headers. This is because all tags and chromosome names in the BCF body rely on the implicit order of the contig and tag definitions in the header. Currently no sanity checks are in place. Dangerous, use with caution. 60 --naive concatenates VCF or BCF files without recompression. This can be used used to combine results that were generated separately for each chromosome. This is very fast but requires that all files are of the same type (all VCF or all BCF) and have the same headers. This is because all tags and chromosome names in the BCF body rely on the implicit order of the contig and tag definitions in the header. Currently no sanity checks are in place. Dangerous, use with caution.
62 ]]></help> 61 ]]></help>
63 <option value="no">No </option> 62 <option value="no">No </option>
64 <option value="yes">Yes </option> 63 <option value="yes">Yes </option>
65 </param> 64 </param>
66 <when value="yes"/> 65 <when value="yes"/>
67 <when value="no"> 66 <when value="no">
68 <conditional name="overlaps"> 67 <conditional name="overlaps">
69 <param name="allow_overlaps" type="select" label="Allow Overlaps"> 68 <param name="allow_overlaps" type="select" label="Allow Overlaps">
70 <help> 69 <help>
71 First coordinate of the next file can precede last record of the current file. 70 First coordinate of the next file can precede last record of the current file.
72 </help> 71 </help>
73 <option value="yes">Yes </option> 72 <option value="yes">Yes </option>
74 <option value="no">No </option> 73 <option value="no">No </option>
75 </param> 74 </param>
76 <when value="yes"> 75 <when value="yes">
77 <param name="rm_dups" type="select" label="Remove duplicate" optional="True" > 76 <param name="rm_dups" type="select" label="Remove duplicate" optional="true">
78 <help><![CDATA[ 77 <help><![CDATA[
79 Output duplicate records present in multiple files only once: 78 Output duplicate records present in multiple files only once:
80 rm-dups <snps|indels|both|all|none> 79 rm-dups <snps|indels|both|all|none>
81 ]]></help> 80 ]]></help>
82 <option value="snps">snps - SNP records</option> 81 <option value="snps">snps - SNP records</option>
83 <option value="indels">indels - indel records</option> 82 <option value="indels">indels - indel records</option>
84 <option value="both">both - both SNP and indel records</option> 83 <option value="both">both - both SNP and indel records</option>
86 <option value="none">none - output multiple records instead</option> 85 <option value="none">none - output multiple records instead</option>
87 </param> 86 </param>
88 </when> 87 </when>
89 <when value="no"/> 88 <when value="no"/>
90 </conditional> 89 </conditional>
91 <param name="ligate" type="boolean" truevalue="--ligate" falsevalue="" label="Ligate" 90 <param name="ligate" type="boolean" truevalue="--ligate" falsevalue="" label="Ligate"
92 help="Ligate phased VCFs by matching phase at overlapping haplotypes" /> 91 help="Ligate phased VCFs by matching phase at overlapping haplotypes" />
93 </when> 92 </when>
94 </conditional> 93 </conditional>
95 <param name="compact_PS" type="boolean" truevalue="--compact-PS" falsevalue="" label="Compact Ps" 94 <param name="compact_PS" type="boolean" truevalue="--compact-PS" falsevalue="" label="Compact Ps"
96 help="Do not output PS tag at each site, only at the start of a new phase set block." /> 95 help="Do not output PS tag at each site, only at the start of a new phase set block." />
97 <param name="min_PQ" type="integer" label="Min Pq" value="30" optional="True" 96 <param name="min_PQ" type="integer" label="Min Pq" value="30" optional="true"
98 help="Break phase set if phasing quality is lower than &lt;int&gt;" /> 97 help="Break phase set if phasing quality is lower than &lt;int&gt;" />
99 </section> 98 </section>
100 <expand macro="macro_select_output_type" /> 99 <expand macro="macro_select_output_type" />
101 </inputs> 100 </inputs>
102 <outputs> 101 <outputs>
103 <expand macro="macro_vcf_output"/> 102 <expand macro="macro_vcf_output"/>
104 </outputs> 103 </outputs>
105 <tests> 104 <tests>
106 <test> 105 <test>
107 <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf" /> 106 <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf" />
108 <param name="output_type" value="v" /> 107 <param name="output_type" value="v" />
109 <output name="output_file"> 108 <output name="output_file">
110 <assert_contents> 109 <assert_contents>
111 <has_text_matching expression="1\t100"/> 110 <has_text_matching expression="1\t100"/>
112 <has_text_matching expression="3\t192"/> 111 <has_text_matching expression="3\t192"/>
113 </assert_contents> 112 </assert_contents>
114 </output> 113 </output>
115 </test> 114 </test>
116 <test> 115 <test>
117 <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf" /> 116 <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf" />
118 <param name="naive" value="yes" /> 117 <param name="naive" value="yes" />
119 <param name="output_type" value="v" /> 118 <param name="output_type" value="v" />
120 <output name="output_file"> 119 <output name="output_file">
121 <assert_contents> 120 <assert_contents>
122 <has_text_matching expression="1\t100"/> 121 <has_text_matching expression="1\t100"/>
123 <has_text_matching expression="3\t192"/> 122 <has_text_matching expression="3\t192"/>
124 </assert_contents> 123 </assert_contents>
125 </output> 124 </output>
126 </test> 125 </test>
127 <test> 126 <test>
128 <param name="input_files" ftype="vcf" value="concat.2.b.vcf,concat.2.a.vcf" /> 127 <param name="input_files" ftype="vcf" value="concat.2.b.vcf,concat.2.a.vcf" />
129 <param name="allow_overlaps" value="yes" /> 128 <param name="allow_overlaps" value="yes" />
130 <param name="output_type" value="v" /> 129 <param name="output_type" value="v" />
131 <output name="output_file"> 130 <output name="output_file">
132 <assert_contents> 131 <assert_contents>
133 <has_text_matching expression="2\t140\t.\tA\tG"/> 132 <has_text_matching expression="2\t140\t.\tA\tG"/>
134 <has_text_matching expression="2\t140\t.\tGT\tG"/> 133 <has_text_matching expression="2\t140\t.\tGT\tG"/>
135 </assert_contents> 134 </assert_contents>
136 </output> 135 </output>
137 </test> 136 </test>
138 <test> 137 <test>
139 <param name="input_files" ftype="vcf" value="concat.2.b.vcf,concat.2.a.vcf" /> 138 <param name="input_files" ftype="vcf" value="concat.2.b.vcf,concat.2.a.vcf" />
140 <param name="allow_overlaps" value="yes" /> 139 <param name="allow_overlaps" value="yes" />
141 <param name="rm_dups" value="none" /> 140 <param name="rm_dups" value="none" />
142 <param name="output_type" value="v" /> 141 <param name="output_type" value="v" />
143 <output name="output_file"> 142 <output name="output_file">
153 ===================================== 152 =====================================
154 153
155 Concatenate or combine VCF/BCF files. All source files must have the same sample columns appearing in the same order. The program can be used, for example, to concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel VCF into one. The input files must be sorted by chr and position. The files must be given in the correct order to produce sorted VCF on output unless the -a, --allow-overlaps option is specified. 154 Concatenate or combine VCF/BCF files. All source files must have the same sample columns appearing in the same order. The program can be used, for example, to concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel VCF into one. The input files must be sorted by chr and position. The files must be given in the correct order to produce sorted VCF on output unless the -a, --allow-overlaps option is specified.
156 155
157 156
158 Naive concatenation is useful when using a galaxy workflow that splits a BAM file by chromosome, processes each in parallel, then bcftools concat merges the results into a single VCF file: 157 Naive concatenation is useful when using a galaxy workflow that splits a BAM file by chromosome, processes each in parallel, then bcftools concat merges the results into a single VCF file:
159 158
160 BAM -> bamtools split => bcftools mpileup => bcftools call => bcftools concat -> VCF 159 BAM -> bamtools split => bcftools mpileup => bcftools call => bcftools concat -> VCF
161 160
162 161
163 @REGIONS_HELP@ 162 @REGIONS_HELP@
164 163
165 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ 164 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
166 165
167 @BCFTOOLS_WIKI@ 166 @BCFTOOLS_WIKI@
168 ]]> 167 ]]></help>
169 </help>
170 <expand macro="citations" /> 168 <expand macro="citations" />
171 </tool> 169 </tool>