Mercurial > repos > iuc > vsnp_add_zero_coverage

annotate vsnp_add_zero_coverage.xml @ 4:e12ccc57875c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit a80e3713d10fafef22e964198d59251adf955812"
author iuc
date Thu, 14 Jan 2021 09:11:12 +0000
parents 2e863710a2f0
children 5a5cf6f024bf
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1 <tool id="vsnp_add_zero_coverage" name="vSNP: add zero coverage" version="@WRAPPER_VERSION@.2" 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="1.76">biopython</requirement>
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8 <requirement type="package" version="0.25.3">pandas</requirement>
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9 <requirement type="package" version="0.15.4">pysam</requirement>
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10 </requirements>
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11 <command detect_errors="exit_code"><![CDATA[
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12 #import re
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13
2e863710a2f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2e312886647244b416c64eca91e1a61dd1be939b"
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14 ## The identifer for both of the following files is likely the same
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15 ## string, so we append a file extension to allow for both links.
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16 #set bam_identifier = re.sub('[^\s\w\-]', '_', str($bam_input.element_identifier)) + '.bam'
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17 ln -s '${bam_input}' '${bam_identifier}' &&
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18 #set vcf_identifier = re.sub('[^\s\w\-]', '_', str($vcf_input.element_identifier)) + '.vcf'
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19 ln -s '${vcf_input}' '${vcf_identifier}' &&
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20
0
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21 python '$__tool_directory__/vsnp_add_zero_coverage.py'
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22 --bam_input '$bam_identifier'
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23 --vcf_input '$vcf_identifier'
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24 #if str($reference_cond.reference_source) == 'cached'
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25 --reference '$reference_cond.reference.fields.path'
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26 #else:
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27 --reference '$reference_cond.reference'
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28 #end if
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29 --output_metrics '$output_metrics'
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30 --output_vcf '$output_vcf'
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31 ]]></command>
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32 <inputs>
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33 <param name="bam_input" type="data" format="bam" label="BAM file"/>
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34 <param name="vcf_input" type="data" format="vcf" label="VCF file"/>
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35 <conditional name="reference_cond">
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36 <expand macro="param_reference_source"/>
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37 <when value="cached">
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38 <param name="reference" type="select" label="Using reference genome">
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39 <options from_data_table="fasta_indexes">
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40 <filter type="data_meta" column="1" key="dbkey" ref="bam_input"/>
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41 <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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42 </options>
0
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43 </param>
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44 </when>
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45 <when value="history">
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46 <param name="reference" type="data" format="fasta,fasta.gz" label="Using reference genome">
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47 <validator type="no_options" message="The current history does not include a fasta dataset"/>
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48 </param>
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49 </when>
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50 </conditional>
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51 </inputs>
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52 <outputs>
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53 <data name="output_vcf" format="vcf" label="${tool.name} on ${on_string} (filtered VCF)"/>
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54 <data name="output_metrics" format="tabular" label="${tool.name} on ${on_string} (metrics)"/>
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55 </outputs>
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56 <tests>
3
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57 <test expect_num_outputs="2">
0
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58 <param name="bam_input" value="bam_input.bam" ftype="bam" dbkey="89"/>
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59 <param name="vcf_input" value="vcf_input.vcf" ftype="vcf" dbkey="89"/>
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60 <param name="reference_source" value="history"/>
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61 <param name="reference" value="NC_002945v4.fasta" ftype="fasta"/>
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62 <output name="output_vcf" value="output_vcf.vcf" ftype="vcf" compare="contains"/>
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63 <output name="output_metrics" file="output_metrics.tabular" ftype="tabular"/>
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64 </test>
3
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65 <test expect_num_outputs="2">
0
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66 <param name="bam_input" value="bam_input.bam" ftype="bam" dbkey="89"/>
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67 <param name="vcf_input" value="vcf_input.vcf" ftype="vcf" dbkey="89"/>
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68 <param name="reference_source" value="cached"/>
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69 <output name="output_vcf" value="output_vcf.vcf" ftype="vcf" compare="contains"/>
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70 <output name="output_metrics" file="output_metrics.tabular" ftype="tabular" compare="contains"/>
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71 </test>
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72 </tests>
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73 <help>
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74 **What it does**
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75
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76 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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77 combination whose positions with no coverage are represented as "N". These outputs are restricted to SNPs and those regions
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78 along the reference with no coverage.
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79
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80 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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81 coverage percentage.
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82
0ad85e7db2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 6a0c9a857c1f4638ef18e106b1f8c0681303acc5"
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83 **Required Options**
0ad85e7db2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 6a0c9a857c1f4638ef18e106b1f8c0681303acc5"
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84
0ad85e7db2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 6a0c9a857c1f4638ef18e106b1f8c0681303acc5"
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85 * **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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86 </help>
0ad85e7db2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 6a0c9a857c1f4638ef18e106b1f8c0681303acc5"
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87 <expand macro="citations" />
0ad85e7db2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 6a0c9a857c1f4638ef18e106b1f8c0681303acc5"
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88 </tool>
0ad85e7db2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 6a0c9a857c1f4638ef18e106b1f8c0681303acc5"
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89