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comparison lumpy_smoove.xml @ 4:49da975ba395 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
author artbio
date Thu, 27 Aug 2020 17:14:25 -0400
parents 65b400409455
children bd4135caa3fa
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3:65b400409455 4:49da975ba395
1 <tool id="lumpy_smoove" name="lumpy_smoove" version="0.5.0"> 1 <tool id="lumpy_smoove" name="lumpy_smoove" version="0.6.0">
2 <description>find structural variants using the smoove workflow</description> 2 <description>find structural variants using the smoove workflow</description>
3 <macros> 3 <macros>
4 <import>macro_lumpy_smoove.xml</import> 4 <import>macro_lumpy_smoove.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
10 <exit_code range="1:" level="fatal" description="Tool exception" /> 10 <exit_code range="1:" level="fatal" description="Tool exception" />
11 </stdio> 11 </stdio>
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 @pipefail@ 13 @pipefail@
14 @set_fasta_index@ 14 @set_fasta_index@
15 ln -s $normal_bam normal.bam && 15 #if $set_plan.plan_choice=='pair':
16 ln -s $tumor_bam tumor.bam && 16 ln -s $set_plan.normal_bam normal.bam &&
17 samtools index -@ \${GALAXY_SLOTS:-4} normal.bam && 17 ln -f -s $set_plan.normal_bam.metadata.bam_index normal.bam.bai &&
18 samtools index -@ \${GALAXY_SLOTS:-4} tumor.bam && 18 ln -s $set_plan.tumor_bam tumor.bam &&
19 ln -f -s $set_plan.tumor_bam.metadata.bam_index tumor.bam.bai &&
20 #else
21 ln -s $set_plan.single_bam single.bam &&
22 ln -f -s $set_plan.single_bam.metadata.bam_index single.bam.bai &&
23 #end if
19 24
20 smoove call --name output 25 smoove call --name output
21 #if $set_exclusion.choices=="yes": 26 #if $set_exclusion.choices=="yes":
22 --exclude $bedmask 27 --exclude $bedmask
23 #end if 28 #end if
25 --processes \${GALAXY_SLOTS:-4} 30 --processes \${GALAXY_SLOTS:-4}
26 --genotype 31 --genotype
27 #if $prpos=="no": 32 #if $prpos=="no":
28 --removepr 33 --removepr
29 #end if 34 #end if
30 normal.bam tumor.bam && 35 *.bam &&
31 ls -latr && 36 ls -latr &&
32 gunzip output-smoove.genotyped.vcf.gz 37 gunzip output-smoove.genotyped.vcf.gz
33 38
34 ]]></command> 39 ]]></command>
35 <inputs> 40 <inputs>
36 <expand macro="reference_source_conditional" /> 41 <expand macro="reference_source_conditional" />
37 <param format="bam" name="normal_bam" type="data" label="BAM alignments from the normal sample"/> 42 <conditional name="set_plan">
38 <param format="bam" name="tumor_bam" type="data" label="BAM alignments from the tumor sample"/> 43 <param name="plan_choice" type="select" label="Analyse a single Bam or a pair of Bam (eg normal/tumor)" display="radio">
44 <option value="pair" selected="true">A pair of Bam files</option>
45 <option value="single">A single Bam</option>
46 </param>
47 <when value="pair">
48 <param format="bam" name="normal_bam" type="data" label="BAM alignment from the normal sample"/>
49 <param format="bam" name="tumor_bam" type="data" label="BAM alignment from the tumor sample"/>
50 </when>
51 <when value="single">
52 <param format="bam" name="single_bam" type="data" label="BAM alignment from a single sample"/>
53 </when>
54 </conditional>
55
56
39 <conditional name="set_exclusion"> 57 <conditional name="set_exclusion">
40 <param name="choices" type="select" label="exclude regions with a bed file" display="radio"> 58 <param name="choices" type="select" label="exclude regions with a bed file" display="radio">
41 <option value="no" selected="true">No</option> 59 <option value="no" selected="true">No</option>
42 <option value="yes">Yes</option> 60 <option value="yes">Yes</option>
43 </param> 61 </param>
64 <param name="normal_bam" value="celegans_RG_1.bam"/> 82 <param name="normal_bam" value="celegans_RG_1.bam"/>
65 <param name="tumor_bam" value="celegans_RG_2.bam"/> 83 <param name="tumor_bam" value="celegans_RG_2.bam"/>
66 <param name="choices" value="yes"/> 84 <param name="choices" value="yes"/>
67 <param name="bedmask" value="exclude.bed"/> 85 <param name="bedmask" value="exclude.bed"/>
68 <param name="prpos" value="no"/> 86 <param name="prpos" value="no"/>
69 <output name="vcf_call" ftype="vcf" file="result-1.vcf" lines_diff="6"/> 87 <output name="vcf_call" ftype="vcf" file="result-1.vcf" lines_diff="8"/>
70 </test> 88 </test>
71 <test> 89 <test>
72 <param name="reference_source_selector" value="history" /> 90 <param name="reference_source_selector" value="history" />
73 <param name="ref_file" value="chrI-ce11.fa"/> 91 <param name="ref_file" value="chrI-ce11.fa"/>
74 <param name="normal_bam" value="celegans_RG_1.bam"/> 92 <param name="normal_bam" value="celegans_RG_1.bam"/>
75 <param name="tumor_bam" value="celegans_RG_2.bam"/> 93 <param name="tumor_bam" value="celegans_RG_2.bam"/>
76 <param name="choices" value="no"/> 94 <param name="choices" value="no"/>
77 <param name="prpos" value="no"/> 95 <param name="prpos" value="no"/>
78 <output name="vcf_call" ftype="vcf" file="result-2.vcf" lines_diff="6"/> 96 <output name="vcf_call" ftype="vcf" file="result-2.vcf" lines_diff="8"/>
79 </test> 97 </test>
80 <test> 98 <test>
81 <param name="reference_source_selector" value="history" /> 99 <param name="reference_source_selector" value="history" />
82 <param name="ref_file" value="chrI-ce11.fa"/> 100 <param name="ref_file" value="chrI-ce11.fa"/>
83 <param name="normal_bam" value="celegans_RG_2.bam"/> 101 <param name="normal_bam" value="celegans_RG_2.bam"/>
84 <param name="tumor_bam" value="celegans_RG_1.bam"/> 102 <param name="tumor_bam" value="celegans_RG_1.bam"/>
85 <param name="choices" value="no"/> 103 <param name="choices" value="no"/>
86 <param name="prpos" value="no"/> 104 <param name="prpos" value="no"/>
87 <output name="vcf_call" ftype="vcf" file="result-3.vcf" lines_diff="6"/> 105 <output name="vcf_call" ftype="vcf" file="result-3.vcf" lines_diff="8"/>
88 </test> 106 </test>
89 <test> 107 <test>
90 <param name="reference_source_selector" value="history" /> 108 <param name="reference_source_selector" value="history" />
91 <param name="ref_file" value="chrI-ce11.fa"/> 109 <param name="ref_file" value="chrI-ce11.fa"/>
92 <param name="normal_bam" value="celegans_RG_1.bam"/> 110 <param name="normal_bam" value="celegans_RG_1.bam"/>
93 <param name="tumor_bam" value="celegans_RG_2.bam"/> 111 <param name="tumor_bam" value="celegans_RG_2.bam"/>
94 <param name="choices" value="no"/> 112 <param name="choices" value="no"/>
95 <param name="prpos" value="yes"/> 113 <param name="prpos" value="yes"/>
96 <output name="vcf_call" ftype="vcf" file="result-4.vcf" lines_diff="6"/> 114 <output name="vcf_call" ftype="vcf" file="result-4.vcf" lines_diff="8"/>
97 </test> 115 </test>
98 116 <test>
117 <param name="reference_source_selector" value="history" />
118 <param name="plan_choice" value="single" />
119 <param name="ref_file" value="chrI-ce11.fa"/>
120 <param name="single_bam" value="celegans_RG_1.bam"/>
121 <param name="choices" value="no"/>
122 <param name="prpos" value="no"/>
123 <output name="vcf_call" ftype="vcf" file="result-5.vcf" lines_diff="8"/>
124 </test>
99 </tests> 125 </tests>
100 126
101 <help> 127 <help>
102 **smoove** simplifies and speeds calling and genotyping SVs for short reads. It also improves 128 **smoove** simplifies and speeds calling and genotyping SVs for short reads. It also improves
103 specificity by removing many spurious alignment signals that are indicative of low-level 129 specificity by removing many spurious alignment signals that are indicative of low-level
142 168
143 5. sort, compress, and index final VCF (but this galaxy wrapper is uncompression the gzip_vcf output) 169 5. sort, compress, and index final VCF (but this galaxy wrapper is uncompression the gzip_vcf output)
144 170
145 **Input(s)** 171 **Input(s)**
146 172
147 * BAM files: One Bam for normal sample and one Bam for tumor sample. Only BAM alignments produced by BWA-mem have been tested with this tool 173 * BAM files: Either a pair of Bam files (e.g. normal vs tumor sample) or a single Bam file.
174 Only BAM alignments produced by BWA-mem have been tested with this tool
148 175
149 .. class:: warningmark 176 .. class:: warningmark
150 177
151 It is mandatory for proper run of svtyper that **BAM files contain read group information**, 178 It is mandatory for proper run of svtyper that **BAM files contain read group information**,
152 ie the @RG tag is present and filled in each BAM 179 ie the @RG tag is present and filled in each BAM file
153 180
154 181
155 * A bed file describing the regions to exclude from the analysis 182 * A bed file describing the regions to exclude from the analysis
156 * Additional options*: refer to smoove GitHub repository_ and the lumpy publication (doi 10.1186/gb-2014-15-6-r84) 183 * Additional options*: refer to smoove GitHub repository_ and the lumpy publication (doi 10.1186/gb-2014-15-6-r84)
157 184