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comparison merge.xml @ 2:148389992630 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
author iuc
date Fri, 22 Jan 2021 14:32:24 +0000
parents 97c7441aed0d
children 1efb2b927957
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1:97c7441aed0d 2:148389992630
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="delly_merge" name="Delly merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01"> 2 <tool id="delly_merge" name="Delly merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
3 <description>structural variants across/within VCF/BCF file(s)</description> 3 <description>structural variants across/within BCF/VCF file(s)</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 ## initialize 10 ## initialize
11 #for $i, $current in enumerate($samples) 11 #for $i, $current in enumerate($input)
12 #if $current.is_of_type('vcf') 12 #if $current.is_of_type('vcf')
13 bcftools view -Ob '$current' > 'sample_${i}.bcf.gz' && 13 bcftools view -Ob '$current' > 'input_${i}.bcf.gz' &&
14 bcftools index 'sample_${i}.bcf.gz' && 14 bcftools index 'input_${i}.bcf.gz' &&
15 #else 15 #else
16 ln -s '${current}' 'sample_${i}.bcf.gz' && 16 ln -s '${current}' 'input_${i}.bcf.gz' &&
17 ln -s '${current.metadata.bcf_index}' 'sample_${i}.bcf.gz.csi' && 17 ln -s '${current.metadata.bcf_index}' 'input_${i}.bcf.gz.csi' &&
18 #end if 18 #end if
19 #end for 19 #end for
20 20
21 ## run 21 ## run
22 delly merge 22 delly merge
25 --chunks $generic.chunks 25 --chunks $generic.chunks
26 --vaf $generic.vaf 26 --vaf $generic.vaf
27 --coverage $generic.coverage 27 --coverage $generic.coverage
28 --minsize $generic.minsize 28 --minsize $generic.minsize
29 --maxsize $generic.maxsize 29 --maxsize $generic.maxsize
30 $generic.cnvmode
30 $generic.precise 31 $generic.precise
31 $generic.pass 32 $generic.pass
32 ## overlap options 33 ## overlap options
33 --bp-offset $overlap.bpoffset 34 --bp-offset $overlap.bpoffset
34 --rec-overlap $overlap.recoverlap 35 --rec-overlap $overlap.recoverlap
35 ## samples 36 ## input
36 #for $i, $current in enumerate($samples) 37 #for $i, $current in enumerate($input)
37 'sample_${i}.bcf.gz' 38 'input_${i}.bcf.gz'
38 #end for 39 #end for
39 40
40 ## postprocessing 41 ## postprocessing
41 @LOG@ 42 @LOG@
42 @VCF@ 43 @VCF@
43 ]]></command> 44 ]]></command>
44 <inputs> 45 <inputs>
45 <expand macro="samples" format="bcf,vcf"/> 46 <expand macro="input" format="bcf,vcf" multiple="true" label="Select input files"/>
46 <section name="generic" title="Generic options" expanded="true"> 47 <section name="generic" title="Generic options" expanded="true">
47 <param argument="--chunks" type="integer" value="500" label="Set maximum chunk size to merge groups of BCF files"/> 48 <param argument="--chunks" type="integer" value="500" label="Set maximum chunk size to merge groups of BCF files"/>
48 <param argument="--vaf" type="float" value="0.15" min="0.0" max="1.0" label="Set minimum fractional ALT support"/> 49 <param argument="--vaf" type="float" value="0.15" min="0.0" max="1.0" label="Set minimum fractional ALT support"/>
49 <param argument="--coverage" type="integer" value="10" label="Set minimum coverage"/> 50 <expand macro="coverage" label="Set minimum coverage"/>
50 <expand macro="minsize"/> 51 <expand macro="minsize" default="0" label="Set minimum SV size"/>
51 <expand macro="maxsize"/> 52 <expand macro="maxsize" default="1000000" label="Set maximum SV size"/>
53 <param argument="--cnvmode" type="boolean" truevalue="--cnvmode" falsevalue="" label="Merge Delly CNV files?"/>
52 <param argument="--precise" type="boolean" truevalue="--precise" falsevalue="" label="Filter sites for PRECISE?"/> 54 <param argument="--precise" type="boolean" truevalue="--precise" falsevalue="" label="Filter sites for PRECISE?"/>
53 <param argument="--pass" type="boolean" truevalue="--pass" falsevalue="" label="Filter sites for PASS?"/> 55 <expand macro="pass"/>
54 </section> 56 </section>
55 <section name="overlap" title="Overlap options" expanded="true"> 57 <section name="overlap" title="Overlap options" expanded="true">
56 <param name="bpoffset" type="integer" value="1000" label="Set maximum breakpoint offset" help="(--bp-offset)"/> 58 <param name="bpoffset" type="integer" value="1000" label="Set maximum breakpoint offset" help="(--bp-offset)"/>
57 <param name="recoverlap" type="float" value="0.8" label="Set minimum reciprocal overlap" help="(--rec-overlap)"/> 59 <param name="recoverlap" type="float" value="0.8" label="Set minimum reciprocal overlap" help="(--rec-overlap)"/>
58 </section> 60 </section>
59 <section name="oo" title="Output options"> 61 <section name="oo" title="Output options" expanded="true">
60 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)"> 62 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
61 <option value="bcf" selected="true">BCF</option> 63 <option value="bcf" selected="true">BCF</option>
64 <option value="log">Log</option>
62 <option value="vcf">VCF</option> 65 <option value="vcf">VCF</option>
63 <option value="log">Log</option>
64 </param> 66 </param>
65 </section> 67 </section>
66 </inputs> 68 </inputs>
67 <outputs> 69 <outputs>
68 <expand macro="vcf"/>
69 <expand macro="bcf"/> 70 <expand macro="bcf"/>
70 <expand macro="log"/> 71 <expand macro="log"/>
72 <expand macro="vcf"/>
71 </outputs> 73 </outputs>
72 <tests> 74 <tests>
73 <!-- #1 default, bcf --> 75 <!-- #1 bcf, default -->
74 <test expect_num_outputs="2"> 76 <test expect_num_outputs="2">
75 <param name="samples" value="call_1.bcf.gz,call_2.bcf.gz"/> 77 <param name="input" value="call_1.bcf.gz,call_2.bcf.gz"/>
76 <section name="oo"> 78 <section name="oo">
77 <param name="out" value="vcf,bcf"/> 79 <param name="out" value="vcf,bcf"/>
78 </section> 80 </section>
79 <output name="out_bcf"> 81 <output name="out_bcf">
80 <assert_contents> 82 <assert_contents>
87 <has_line line="##fileformat=VCFv4.2"/> 89 <has_line line="##fileformat=VCFv4.2"/>
88 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO"/> 90 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO"/>
89 </assert_contents> 91 </assert_contents>
90 </output> 92 </output>
91 </test> 93 </test>
92 <!-- #2 bcf--> 94 <!-- #2 bcf -->
93 <test expect_num_outputs="3"> 95 <test expect_num_outputs="3">
94 <param name="samples" value="call_1.bcf.gz,call_2.bcf.gz"/> 96 <param name="input" value="call_1.bcf.gz,call_2.bcf.gz"/>
95 <section name="generic"> 97 <section name="generic">
96 <param name="chunks" value="500"/> 98 <param name="chunks" value="500"/>
97 <param name="vaf" value="0.16"/> 99 <param name="vaf" value="0.16"/>
98 <param name="coverage" value="10"/> 100 <param name="coverage" value="10"/>
99 <param name="minsize" value="0"/> 101 <param name="minsize" value="0"/>
100 <param name="maxsize" value="1000000"/> 102 <param name="maxsize" value="1000000"/>
103 <param name="cnvmode" value="true"/>
101 <param name="precise" value="true"/> 104 <param name="precise" value="true"/>
102 <param name="pass" value="true"/> 105 <param name="pass" value="true"/>
103 </section> 106 </section>
104 <section name="overlap"> 107 <section name="overlap">
105 <param name="bp-offset" value="1000"/> 108 <param name="bp-offset" value="1000"/>
108 <section name="oo"> 111 <section name="oo">
109 <param name="out" value="vcf,bcf,log"/> 112 <param name="out" value="vcf,bcf,log"/>
110 </section> 113 </section>
111 <output name="out_bcf"> 114 <output name="out_bcf">
112 <assert_contents> 115 <assert_contents>
113 <has_size value="1851" delta="10"/> 116 <has_size value="1021" delta="10"/>
114 </assert_contents>
115 </output>
116 <output name="out_vcf">
117 <assert_contents>
118 <has_n_lines n="128"/>
119 <has_line line="##fileformat=VCFv4.2"/>
120 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO"/>
121 <has_text_matching expression="chr5&#009;75911568.+"/>
122 </assert_contents> 117 </assert_contents>
123 </output> 118 </output>
124 <output name="out_log"> 119 <output name="out_log">
125 <assert_contents> 120 <assert_contents>
126 <has_text_matching expression=".+Done\."/> 121 <has_text_matching expression=".+Done\."/>
127 </assert_contents> 122 </assert_contents>
128 </output> 123 </output>
124 <output name="out_vcf">
125 <assert_contents>
126 <has_n_lines n="108"/>
127 <has_line line="##fileformat=VCFv4.2"/>
128 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO"/>
129 </assert_contents>
130 </output>
129 </test> 131 </test>
130 <!-- #3 default, vcf --> 132 <!-- #3 vcf, default -->
131 <test expect_num_outputs="2"> 133 <test expect_num_outputs="2">
132 <param name="samples" value="call_1.vcf.gz,call_2.vcf.gz"/> 134 <param name="input" value="call_1.vcf.gz,call_2.vcf.gz"/>
133 <section name="oo"> 135 <section name="oo">
134 <param name="out" value="vcf,bcf"/> 136 <param name="out" value="vcf,bcf"/>
135 </section> 137 </section>
136 <output name="out_bcf"> 138 <output name="out_bcf">
137 <assert_contents> 139 <assert_contents>
152 154
153 **What it does** 155 **What it does**
154 156
155 @WID@ 157 @WID@
156 158
157 Delly *merge* merges SV sites into a unified site list.
158
159 **Input** 159 **Input**
160 160
161 BCF or VCF files. 161 Delly *merge* requires BCF or VCF files.
162 162
163 **Output** 163 **Output**
164 164
165 A single BCF file. 165 A single file in BCF/VCF format. Additionally a log file is provided.
166 166
167 .. class:: infomark 167 .. class:: infomark
168 168
169 **References** 169 **References**
170 170