Mercurial > repos > iuc > vsnp_add_zero_coverage

annotate 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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6dc6dd4666e3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
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1 <tool id="vsnp_add_zero_coverage" name="vSNP: add zero coverage" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" 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 <expand macro="biopython_requirement"/>
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8 <expand macro="openpyxl_requirement"/>
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9 <expand macro="pandas_requirement"/>
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10 <requirement type="package" version="0.19.1">pysam</requirement>
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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 '$__tool_directory__/vsnp_add_zero_coverage.py'
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23 --dbkey '$bam_input.metadata.dbkey'
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24 --bam_input '$bam_identifier'
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25 --vcf_input '$vcf_identifier'
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26 #if str($reference_cond.reference_source) == 'cached'
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27 --reference '$reference_cond.reference.fields.path'
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28 #else:
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29 --reference '$reference_cond.reference'
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30 #end if
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31 --output_metrics '$output_metrics'
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32 --output_vcf '$output_vcf'
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33 ]]></command>
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34 <inputs>
3
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35 <param name="bam_input" type="data" format="bam" label="BAM file"/>
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36 <param name="vcf_input" type="data" format="vcf" label="VCF file"/>
0
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37 <conditional name="reference_cond">
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38 <expand macro="param_reference_source"/>
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39 <when value="cached">
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40 <param name="reference" type="select" label="Using reference genome">
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41 <options from_data_table="fasta_indexes">
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42 <filter type="data_meta" column="1" key="dbkey" ref="bam_input"/>
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43 <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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44 </options>
0
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45 </param>
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46 </when>
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47 <when value="history">
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48 <param name="reference" type="data" format="fasta,fasta.gz" label="Using reference genome"/>
0
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49 </when>
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50 </conditional>
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51 </inputs>
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52 <outputs>
3
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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" ftype="vcf">
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63 <assert_contents>
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64 <has_size value="259726"/>
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65 <has_text text="##fileformat=VCFv4.2"/>
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66 </assert_contents>
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67 </output>
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68 <output name="output_metrics" ftype="tabular">
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69 <assert_contents>
9
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70 <has_size value="190"/>
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71 <has_text text="# BAM File"/>
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72 </assert_contents>
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73 </output>
0
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74 </test>
3
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75 <test expect_num_outputs="2">
0
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76 <param name="bam_input" value="bam_input.bam" ftype="bam" dbkey="89"/>
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77 <param name="vcf_input" value="vcf_input.vcf" ftype="vcf" dbkey="89"/>
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78 <param name="reference_source" value="cached"/>
7
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79 <output name="output_vcf" ftype="vcf">
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80 <assert_contents>
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81 <has_size value="259726"/>
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82 <has_text text="##fileformat=VCFv4.2"/>
7
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83 </assert_contents>
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84 </output>
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85 <output name="output_metrics" ftype="tabular">
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86 <assert_contents>
9
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87 <has_size value="190"/>
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88 <has_text text="# BAM File"/>
7
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89 </assert_contents>
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90 </output>
0
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91 </test>
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92 </tests>
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93 <help>
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94 **What it does**
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95
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96 Accepts a combination of single BAM and associated VCF files (or associated collections of each) to produce a VCF file for each
0ad85e7db2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 6a0c9a857c1f4638ef18e106b1f8c0681303acc5"
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97 combination whose positions with no coverage are represented as "N". These outputs are restricted to SNPs and those regions
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98 along the reference with no coverage.
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99
9
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100 A metrics file is produced for each combination which provides the reference length, genome coverage, average coverage,
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101 total zero coverage, zero coverage percent and quality SNPs.
0
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102
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103 **Required Options**
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104
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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.
0ad85e7db2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 6a0c9a857c1f4638ef18e106b1f8c0681303acc5"
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106 </help>
7
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107 <expand macro="citations"/>
0
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108 </tool>
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109