Mercurial > repos > iuc > vsnp_add_zero_coverage

annotate vsnp_add_zero_coverage.xml @ 6:9ddeef840a07 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
author iuc
date Tue, 16 Nov 2021 08:26:14 +0000
parents 5a5cf6f024bf
children 6dc6dd4666e3
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1 <tool id="vsnp_add_zero_coverage" name="vSNP: add zero coverage" version="@WRAPPER_VERSION@.2+galaxy0" profile="@PROFILE@">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="3.0.7">openpyxl</requirement>
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8 <requirement type="package" version="1.79">biopython</requirement>
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9 <requirement type="package" version="1.3.0">pandas</requirement>
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10 <requirement type="package" version="0.16.0.1">pysam</requirement>
0
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11 </requirements>
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12 <command detect_errors="exit_code"><![CDATA[
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13 #import re
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15 ## The identifer for both of the following files is likely the same
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16 ## string, so we append a file extension to allow for both links.
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17 #set bam_identifier = re.sub('[^\s\w\-]', '_', str($bam_input.element_identifier)) + '.bam'
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18 ln -s '${bam_input}' '${bam_identifier}' &&
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19 #set vcf_identifier = re.sub('[^\s\w\-]', '_', str($vcf_input.element_identifier)) + '.vcf'
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20 ln -s '${vcf_input}' '${vcf_identifier}' &&
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21
0
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22 python '$__tool_directory__/vsnp_add_zero_coverage.py'
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23 --bam_input '$bam_identifier'
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24 --vcf_input '$vcf_identifier'
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25 #if str($reference_cond.reference_source) == 'cached'
0
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26 --reference '$reference_cond.reference.fields.path'
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27 #else:
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28 --reference '$reference_cond.reference'
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29 #end if
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30 --output_metrics '$output_metrics'
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31 --output_vcf '$output_vcf'
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32 ]]></command>
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33 <inputs>
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34 <param name="bam_input" type="data" format="bam" label="BAM file"/>
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35 <param name="vcf_input" type="data" format="vcf" label="VCF file"/>
0
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36 <conditional name="reference_cond">
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37 <expand macro="param_reference_source"/>
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38 <when value="cached">
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39 <param name="reference" type="select" label="Using reference genome">
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40 <options from_data_table="fasta_indexes">
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41 <filter type="data_meta" column="1" key="dbkey" ref="bam_input"/>
3
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42 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected BAM file"/>
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43 </options>
0
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44 </param>
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45 </when>
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46 <when value="history">
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47 <param name="reference" type="data" format="fasta,fasta.gz" label="Using reference genome"/>
0
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48 </when>
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49 </conditional>
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50 </inputs>
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51 <outputs>
3
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52 <data name="output_vcf" format="vcf" label="${tool.name} on ${on_string} (filtered VCF)"/>
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53 <data name="output_metrics" format="tabular" label="${tool.name} on ${on_string} (metrics)"/>
0
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54 </outputs>
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55 <tests>
3
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56 <test expect_num_outputs="2">
0
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57 <param name="bam_input" value="bam_input.bam" ftype="bam" dbkey="89"/>
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58 <param name="vcf_input" value="vcf_input.vcf" ftype="vcf" dbkey="89"/>
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59 <param name="reference_source" value="history"/>
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60 <param name="reference" value="NC_002945v4.fasta" ftype="fasta"/>
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61 <output name="output_vcf" value="output_vcf.vcf" ftype="vcf" compare="contains"/>
3
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62 <output name="output_metrics" file="output_metrics.tabular" ftype="tabular"/>
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63 </test>
3
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64 <test expect_num_outputs="2">
0
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65 <param name="bam_input" value="bam_input.bam" ftype="bam" dbkey="89"/>
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66 <param name="vcf_input" value="vcf_input.vcf" ftype="vcf" dbkey="89"/>
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67 <param name="reference_source" value="cached"/>
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68 <output name="output_vcf" value="output_vcf.vcf" ftype="vcf" compare="contains"/>
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69 <output name="output_metrics" file="output_metrics.tabular" ftype="tabular" compare="contains"/>
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70 </test>
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71 </tests>
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72 <help>
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73 **What it does**
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74
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75 Accepts a combination of single BAM and associated VCF files (or associated collections of each) to produce a VCF file for each
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76 combination whose positions with no coverage are represented as "N". These outputs are restricted to SNPs and those regions
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77 along the reference with no coverage.
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78
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79 A metrics file is produced for each combination which provides the number of good SNPs, the average coverage and the genome
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80 coverage percentage.
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81
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82 **Required Options**
0ad85e7db2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 6a0c9a857c1f4638ef18e106b1f8c0681303acc5"
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83
0ad85e7db2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 6a0c9a857c1f4638ef18e106b1f8c0681303acc5"
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84 * **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.
0ad85e7db2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 6a0c9a857c1f4638ef18e106b1f8c0681303acc5"
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85 </help>
0ad85e7db2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 6a0c9a857c1f4638ef18e106b1f8c0681303acc5"
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86 <expand macro="citations" />
0ad85e7db2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 6a0c9a857c1f4638ef18e106b1f8c0681303acc5"
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87 </tool>
0ad85e7db2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 6a0c9a857c1f4638ef18e106b1f8c0681303acc5"
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88