Mercurial > repos > artbio > lumpy_smoove
comparison lumpy_smoove.xml @ 5:bd4135caa3fa draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 627bb5344b7d86c0b7ca7235ea3636269613dc32"
author | artbio |
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date | Fri, 25 Sep 2020 10:43:20 +0000 |
parents | 49da975ba395 |
children | ad8853ee9909 |
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4:49da975ba395 | 5:bd4135caa3fa |
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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 (<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 |