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comparison lumpy_smoove.xml @ 5:bd4135caa3fa draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
author artbio
date Fri, 25 Sep 2020 10:43:20 +0000
parents 49da975ba395
children ad8853ee9909
comparison
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4:49da975ba395 5:bd4135caa3fa
1 <tool id="lumpy_smoove" name="lumpy_smoove" version="0.6.0"> 1 <tool id="lumpy_smoove" name="lumpy_smoove" version="0.2.5+galaxy5">
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>
15 #if $set_plan.plan_choice=='pair': 15 #if $set_plan.plan_choice=='pair':
16 ln -s $set_plan.normal_bam normal.bam && 16 ln -s $set_plan.normal_bam normal.bam &&
17 ln -f -s $set_plan.normal_bam.metadata.bam_index normal.bam.bai && 17 ln -f -s $set_plan.normal_bam.metadata.bam_index normal.bam.bai &&
18 ln -s $set_plan.tumor_bam 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 && 19 ln -f -s $set_plan.tumor_bam.metadata.bam_index tumor.bam.bai &&
20 #else 20 #elif $set_plan.plan_choice=='single':
21 ln -s $set_plan.single_bam single.bam && 21 ln -s $set_plan.single_bam single.bam &&
22 ln -f -s $set_plan.single_bam.metadata.bam_index single.bam.bai && 22 ln -f -s $set_plan.single_bam.metadata.bam_index single.bam.bai &&
23 #else:
24 #for $sample in $set_plan.cohort:
25 ln -s $sample ${sample.element_identifier}.bam &&
26 ln -f -s $sample.metadata.bam_index ${sample.element_identifier}.bam.bai &&
27 #end for
28 ls -la &&
23 #end if 29 #end if
24 30
25 smoove call --name output 31 smoove call --name output
26 #if $set_exclusion.choices=="yes": 32 #if $set_exclusion.choices=="yes":
27 --exclude $bedmask 33 --exclude $bedmask
41 <expand macro="reference_source_conditional" /> 47 <expand macro="reference_source_conditional" />
42 <conditional name="set_plan"> 48 <conditional name="set_plan">
43 <param name="plan_choice" type="select" label="Analyse a single Bam or a pair of Bam (eg normal/tumor)" display="radio"> 49 <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> 50 <option value="pair" selected="true">A pair of Bam files</option>
45 <option value="single">A single Bam</option> 51 <option value="single">A single Bam</option>
52 <option value="cohort">a small cohort of Bam files (less than ~40)</option>
46 </param> 53 </param>
47 <when value="pair"> 54 <when value="pair">
48 <param format="bam" name="normal_bam" type="data" label="BAM alignment from the normal sample"/> 55 <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"/> 56 <param format="bam" name="tumor_bam" type="data" label="BAM alignment from the tumor sample"/>
50 </when> 57 </when>
51 <when value="single"> 58 <when value="single">
52 <param format="bam" name="single_bam" type="data" label="BAM alignment from a single sample"/> 59 <param format="bam" name="single_bam" type="data" label="BAM alignment from a single sample"/>
60 </when>
61 <when value="cohort">
62 <param name="cohort" type="data_collection" format="bam" label="A collection of bam files" multiple="true"/>
53 </when> 63 </when>
54 </conditional> 64 </conditional>
55 65
56 66
57 <conditional name="set_exclusion"> 67 <conditional name="set_exclusion">
75 <data format="vcf" name="vcf_call" label="lumpy-smoove Variant Calling" from_work_dir="./output-smoove.genotyped.vcf" /> 85 <data format="vcf" name="vcf_call" label="lumpy-smoove Variant Calling" from_work_dir="./output-smoove.genotyped.vcf" />
76 </outputs> 86 </outputs>
77 87
78 <tests> 88 <tests>
79 <test> 89 <test>
90
91 <conditional name="set_plan">
92 <param name="plan_choice" value="cohort"/>
93 <param name="cohort">
94 <collection type="list">
95 <element name="1" ftype="bam" value="celegans_RG_1.bam"/>
96 <element name="2" ftype="bam" value="celegans_RG_2.bam"/>
97 </collection>
98 </param>
99 </conditional>
100 <param name="reference_source_selector" value="history" />
101 <param name="ref_file" value="chrI-ce11.fa"/>
102 <param name="choices" value="yes"/>
103 <param name="bedmask" value="exclude.bed"/>
104 <param name="prpos" value="no"/>
105 <output name="vcf_call" ftype="vcf" file="result-6.vcf" lines_diff="8"/>
106 </test>
107 <test>
80 <param name="reference_source_selector" value="history" /> 108 <param name="reference_source_selector" value="history" />
81 <param name="ref_file" value="chrI-ce11.fa"/> 109 <param name="ref_file" value="chrI-ce11.fa"/>
82 <param name="normal_bam" value="celegans_RG_1.bam"/> 110 <param name="normal_bam" value="celegans_RG_1.bam"/>
83 <param name="tumor_bam" value="celegans_RG_2.bam"/> 111 <param name="tumor_bam" value="celegans_RG_2.bam"/>
84 <param name="choices" value="yes"/> 112 <param name="choices" value="yes"/>
130 noise and often contribute to spurious calls. 158 noise and often contribute to spurious calls.
131 159
132 There is a blog-post describing smoove in more detail 160 There is a blog-post describing smoove in more detail
133 here: https://brentp.github.io/post/smoove/ 161 here: https://brentp.github.io/post/smoove/
134 162
135 Currently, this Galaxy tool only wraps smoove for 2 samples (bam normal and tumor inputs), 163 Currently, this Galaxy tool only wraps smoove for 1, 2 (bam normal and tumor inputs) or
164 a small collection of samples (&lt;40),
136 which translates in the command line:: 165 which translates in the command line::
137 166
138 <![CDATA[smoove call --name my-cohort --exclude $bed --fasta $fasta -p $threads --genotype [--removepr] /path/to/*.bam]]> 167 <![CDATA[smoove call --name my-cohort --exclude $bed --fasta $fasta -p $threads --genotype [--removepr] /path/to/*.bam]]>
139 168
140 169