annotate vsnp_statistics.xml @ 25:b908bb18008a draft

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author greg
date Thu, 16 Sep 2021 00:56:07 +0000
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1 <tool id="vsnp_statistics" name="vSNP: statistics" 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 <expand macro="biopython_requirement"/>
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8 <expand macro="numpy_requirement"/>
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9 <expand macro="openpyxl_requirement"/>
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10 <expand macro="pandas_requirement"/>
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11 <expand macro="xlrd_requirement"/>
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12 </requirements>
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13 <command detect_errors="exit_code"><![CDATA[
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14 #import re
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15
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16 #if $input_type_cond.input_type in ["single", "pair"]:
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17 #set read1 = $input_type_cond.read1
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18 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
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19 ln -s '${read1}' '${read1_identifier}' &&
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20 #if $input_type_cond.input_type == "pair":
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21 #set read2 = $input_type_cond.read2
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22 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
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23 ln -s '${read2}' '${read2_identifier}' &&
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24 #end if
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25 #else:
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26 #set identifier = re.sub('[^\s\w\-]', '_', str($input_type_cond.reads_collection.element_identifier))
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27 #set read1 = $input_type_cond.reads_collection.forward
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28 #set read1_identifier = $identifier + '_R1'
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29 ln -s '${read1}' '${read1_identifier}' &&
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30 #set read2 = $input_type_cond.reads_collection.reverse
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31 #set read2_identifier = $identifier + '_R2'
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32 ln -s '${read2}' '${read2_identifier}' &&
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33 #end if
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34
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35 python '$__tool_directory__/vsnp_statistics.py'
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36 --read1 '${read1_identifier}'
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37 #if $input_type_cond.input_type in ["pair", "paired"]:
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38 --read2 '${read2_identifier}'
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39 #end if
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40 #if $read1.is_of_type('fastqsanger.gz'):
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41 --gzipped
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42 #end if
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43 --dbkey '$samtools_idxstats.metadata.dbkey'
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44 --samtools_idxstats '$samtools_idxstats'
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45 --vsnp_azc_metrics '$vsnp_azc_metrics'
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46 --output '$output'
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47 ]]></command>
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48 <inputs>
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49 <conditional name="input_type_cond">
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50 <param name="input_type" type="select" label="Choose the category of the files to be analyzed">
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51 <option value="single" selected="true">Single files</option>
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52 <option value="paired">Paired reads</option>
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53 <option value="pair">Paired reads in separate data sets</option>
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54 </param>
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55 <when value="single">
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56 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/>
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57 </when>
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58 <when value="paired">
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59 <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/>
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60 </when>
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61 <when value="pair">
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62 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/>
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63 <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Read2 fastq file"/>
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64 </when>
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65 </conditional>
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66 <param name="samtools_idxstats" type="data" format="tabular" label="Samtools idxstats file"/>
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67 <param name="vsnp_azc_metrics" type="data" format="tabular" label="vSNP: add zero coverage metrics file"/>
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68 </inputs>
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69 <outputs>
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70 <data name="output" format="tabular"/>
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71 </outputs>
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72 <tests>
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73 <!-- A single fastq file -->
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74 <test expect_num_outputs="1">
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75 <param name="input_type" value="single"/>
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76 <param name="read1" value="Mcap_Deer_DE_SRR650221.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/>
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77 <param name="samtools_idxstats" value="samtools_idxstats1.tabular" ftype="tabular" dbkey="89"/>
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78 <param name="vsnp_azc_metrics" value="add_zc_metrics1.tabular" ftype="tabular" dbkey="89"/>
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79 <output name="output" file="vsnp_statistics1.tabular" ftype="tabular" compare="contains"/>
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80 </test>
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81 <!-- A set of paired fastq files -->
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82 <test expect_num_outputs="1">
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83 <param name="input_type" value="pair"/>
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84 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/>
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85 <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/>
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86 <param name="samtools_idxstats" value="samtools_idxstats2.tabular" ftype="tabular" dbkey="89"/>
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87 <param name="vsnp_azc_metrics" value="add_zc_metrics2.tabular" ftype="tabular" dbkey="89"/>
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88 <output name="output" file="vsnp_statistics2.tabular" ftype="tabular" compare="contains"/>
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89 </test>
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90 <!-- A collection of paired fastq files -->
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91 <test expect_num_outputs="1">
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92 <param name="input_type" value="paired"/>
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93 <param name="reads_collection">
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94 <collection type="paired">
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95 <element name="forward" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
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96 <element name="reverse" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz"/>
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97 </collection>
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98 </param>
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99 <param name="samtools_idxstats" value="samtools_idxstats5.tabular" ftype="tabular" dbkey="89"/>
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100 <param name="vsnp_azc_metrics" value="add_zc_metrics5.tabular" ftype="tabular" dbkey="89"/>
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101 <output name="output" file="vsnp_statistics4.tabular" ftype="tabular" compare="contains"/>
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102 </test>
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103 </tests>
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104 <help>
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105 **What it does**
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106
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107 Accepts associated fastq files, SAMtools idxstats files and **vSNP: add zero coverage** metrics files and extracts information from them
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108 to produce a tabular file containing statistics for each sample. The samples can be a single read, a single set of paired reads in
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109 separate datasets or a collection of paired reads. The output statistics include reference, file size, mean read length, mean read quality,
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110 reads passing Q30, total reads, all mapped reads, unmapped reads, unmapped reads percentage of total, reference with coverage, average depth
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111 of coverage and good SNP count.
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112 </help>
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113 <expand macro="citations"/>
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114 </tool>
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115