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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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2
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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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6
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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>
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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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14
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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
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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'
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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"/>
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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"/>
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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>
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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">
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48 <validator type="no_options" message="The current history does not include a fasta dataset"/>
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49 </param>
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50 </when>
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51 </conditional>
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52 </inputs>
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53 <outputs>
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2
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54 <data name="output_vcf" format="vcf" label="${tool.name} on ${on_string} (filtered VCF)"/>
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55 <data name="output_metrics" format="tabular" label="${tool.name} on ${on_string} (metrics)"/>
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56 </outputs>
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57 <tests>
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58 <test expect_num_outputs="2">
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59 <param name="bam_input" value="bam_input.bam" ftype="bam" dbkey="89"/>
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60 <param name="vcf_input" value="vcf_input.vcf" ftype="vcf" dbkey="89"/>
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61 <param name="reference_source" value="history"/>
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62 <param name="reference" value="NC_002945v4.fasta" ftype="fasta"/>
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63 <output name="output_vcf" value="output_vcf.vcf" ftype="vcf" compare="contains"/>
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64 <output name="output_metrics" file="output_metrics.tabular" ftype="tabular"/>
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65 </test>
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66 <test expect_num_outputs="2">
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67 <param name="bam_input" value="bam_input.bam" ftype="bam" dbkey="89"/>
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68 <param name="vcf_input" value="vcf_input.vcf" ftype="vcf" dbkey="89"/>
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69 <param name="reference_source" value="cached"/>
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70 <output name="output_vcf" value="output_vcf.vcf" ftype="vcf" compare="contains"/>
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71 <output name="output_metrics" file="output_metrics.tabular" ftype="tabular" compare="contains"/>
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72 </test>
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73 </tests>
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74 <help>
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75 **What it does**
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76
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77 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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78 combination whose positions with no coverage are represented as "N". These outputs are restricted to SNPs and those regions
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79 along the reference with no coverage.
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80
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81 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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82 coverage percentage.
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83
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84 **Required Options**
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85
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86 * **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.
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87 </help>
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88 <expand macro="citations" />
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89 </tool>
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90
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