Mercurial > repos > iuc > vsnp_add_zero_coverage

comparison vsnp_add_zero_coverage.xml @ 9:40b97055bb99 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
author iuc
date Fri, 10 Jun 2022 06:08:02 +0000
parents 6dc6dd4666e3
children
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8:18b59c38017e 9:40b97055bb99
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <expand macro="biopython_requirement"/> 7 <expand macro="biopython_requirement"/>
8 <expand macro="openpyxl_requirement"/> 8 <expand macro="openpyxl_requirement"/>
9 <expand macro="pandas_requirement"/> 9 <expand macro="pandas_requirement"/>
10 <requirement type="package" version="0.16.0.1">pysam</requirement> 10 <requirement type="package" version="0.19.1">pysam</requirement>
11 </requirements> 11 </requirements>
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 #import re 13 #import re
14 14
15 ## The identifer for both of the following files is likely the same 15 ## The identifer for both of the following files is likely the same
18 ln -s '${bam_input}' '${bam_identifier}' && 18 ln -s '${bam_input}' '${bam_identifier}' &&
19 #set vcf_identifier = re.sub('[^\s\w\-]', '_', str($vcf_input.element_identifier)) + '.vcf' 19 #set vcf_identifier = re.sub('[^\s\w\-]', '_', str($vcf_input.element_identifier)) + '.vcf'
20 ln -s '${vcf_input}' '${vcf_identifier}' && 20 ln -s '${vcf_input}' '${vcf_identifier}' &&
21 21
22 python '$__tool_directory__/vsnp_add_zero_coverage.py' 22 python '$__tool_directory__/vsnp_add_zero_coverage.py'
23 --dbkey '$bam_input.metadata.dbkey'
23 --bam_input '$bam_identifier' 24 --bam_input '$bam_identifier'
24 --vcf_input '$vcf_identifier' 25 --vcf_input '$vcf_identifier'
25 #if str($reference_cond.reference_source) == 'cached' 26 #if str($reference_cond.reference_source) == 'cached'
26 --reference '$reference_cond.reference.fields.path' 27 --reference '$reference_cond.reference.fields.path'
27 #else: 28 #else:
59 <param name="reference_source" value="history"/> 60 <param name="reference_source" value="history"/>
60 <param name="reference" value="NC_002945v4.fasta" ftype="fasta"/> 61 <param name="reference" value="NC_002945v4.fasta" ftype="fasta"/>
61 <output name="output_vcf" ftype="vcf"> 62 <output name="output_vcf" ftype="vcf">
62 <assert_contents> 63 <assert_contents>
63 <has_size value="259726"/> 64 <has_size value="259726"/>
65 <has_text text="##fileformat=VCFv4.2"/>
64 </assert_contents> 66 </assert_contents>
65 </output> 67 </output>
66 <output name="output_metrics" ftype="tabular"> 68 <output name="output_metrics" ftype="tabular">
67 <assert_contents> 69 <assert_contents>
68 <has_size value="109"/> 70 <has_size value="190"/>
71 <has_text text="# BAM File"/>
69 </assert_contents> 72 </assert_contents>
70 </output> 73 </output>
71 </test> 74 </test>
72 <test expect_num_outputs="2"> 75 <test expect_num_outputs="2">
73 <param name="bam_input" value="bam_input.bam" ftype="bam" dbkey="89"/> 76 <param name="bam_input" value="bam_input.bam" ftype="bam" dbkey="89"/>
74 <param name="vcf_input" value="vcf_input.vcf" ftype="vcf" dbkey="89"/> 77 <param name="vcf_input" value="vcf_input.vcf" ftype="vcf" dbkey="89"/>
75 <param name="reference_source" value="cached"/> 78 <param name="reference_source" value="cached"/>
76 <output name="output_vcf" ftype="vcf"> 79 <output name="output_vcf" ftype="vcf">
77 <assert_contents> 80 <assert_contents>
78 <has_size value="259726"/> 81 <has_size value="259726"/>
82 <has_text text="##fileformat=VCFv4.2"/>
79 </assert_contents> 83 </assert_contents>
80 </output> 84 </output>
81 <output name="output_metrics" ftype="tabular"> 85 <output name="output_metrics" ftype="tabular">
82 <assert_contents> 86 <assert_contents>
83 <has_size value="109"/> 87 <has_size value="190"/>
88 <has_text text="# BAM File"/>
84 </assert_contents> 89 </assert_contents>
85 </output> 90 </output>
86 </test> 91 </test>
87 </tests> 92 </tests>
88 <help> 93 <help>
90 95
91 Accepts a combination of single BAM and associated VCF files (or associated collections of each) to produce a VCF file for each 96 Accepts a combination of single BAM and associated VCF files (or associated collections of each) to produce a VCF file for each
92 combination whose positions with no coverage are represented as "N". These outputs are restricted to SNPs and those regions 97 combination whose positions with no coverage are represented as "N". These outputs are restricted to SNPs and those regions
93 along the reference with no coverage. 98 along the reference with no coverage.
94 99
95 A metrics file is produced for each combination which provides the number of good SNPs, the average coverage and the genome 100 A metrics file is produced for each combination which provides the reference length, genome coverage, average coverage,
96 coverage percentage. 101 total zero coverage, zero coverage percent and quality SNPs.
97 102
98 **Required Options** 103 **Required Options**
99 104
100 * **Choose the source for the reference genome** - select "locally cached" if the reference associated with the BAM and VCF files is available within the Galaxy environment or "from history" to select the reference from the current history. 105 * **Choose the source for the reference genome** - select "locally cached" if the reference associated with the BAM and VCF files is available within the Galaxy environment or "from history" to select the reference from the current history.
101 </help> 106 </help>