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annotate distance.xml @ 4:8cdffc02d2e2 draft

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planemo upload for repository https://github.com/phac-nml/quasitools commit 19e0f266ee455b82432e2d7b987b35de8c7a14d5
author nml
date Wed, 25 Apr 2018 10:38:00 -0400
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1 <tool id="distance" name="Quasispecies Distance" version="0.1.0">
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2 <description>Calculate the evolutionary distance between viral quasispecies.</description>
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3 <requirements>
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4 <requirement type="package" version="0.3.1">quasitools</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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8 #for $bam_file in $bam_files
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9 ln -s $bam_file '${bam_file.name}' &&
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10 ln -s $bam_file.metadata.bam_index '${bam_file.name}.bai' &&
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11 #end for
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13 quasitools distance $ref_file
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15 #for $bam_file in $bam_files
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16 '${bam_file.name}'
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17 #end for
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19 -o matrix.csv
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21 $normalize
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23 #if $low_coverage.coverage_selector == 'keep':
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24 -k
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25 #else if $low_coverage.coverage_selector == 'remove':
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26 -r
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27 #else if $low_coverage.coverage_selector == 'truncate':
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28 -t
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29 #end if
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31 #if $select_range.manual_input == 'select_range':
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32 -s $select_range.start
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33 -e $select_range.end
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34 #end if
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36 $output_similarity
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38 ]]></command>
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39 <inputs>
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40 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
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41 <param name="bam_files" type="data" format="bam" optional="false" multiple="true" label="BAM files" min="2" help="At least two BAM files are required to perform quasispecies distance comparison."/>
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42 <param name="normalize" type="boolean" truevalue="-n" falsevalue="-dn" checked="True" label="Normalize pileups" help="Normalize read count data so that the read counts per 4-tuple (A, C, T, G) sum to one."/>
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43 <param name="output_similarity" type="boolean" truevalue="-os" falsevalue="-od" checked="False" label="Output cosine similarity instead of angular cosine distance." help="Cosine similarity is not a distance metric." />
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44 <conditional name="low_coverage">
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45 <param name="coverage_selector" type="select" label="Choose how to treat zero coverage positions.">
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46 <option value="remove" selected = "true">Remove all zero coverage positions.</option>
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47 <option value="keep">Keep all zero coverage positions.</option>
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48 <option value="truncate">Truncate zero coverage positions at start and end of pileup.</option>
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49 </param>
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50 <when value="remove">
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51 </when>
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52 <when value="keep">
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53 </when>
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54 <when value="truncate">
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55 </when>
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56 </conditional>
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57 <conditional name="select_range">
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58 <param name="manual_input" type="select" label="Select pileup range." help="Currently only supports selection of custom start and end position for one single reference.">
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59 <option value="keep_range" selected = "true">Use original pileup for distance calculation.</option>
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60 <option value="select_range">Manually select pileup's start and end position for distance calculation.</option>
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61 </param>
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62 <when value="select_range">
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63 <param name="start" type="integer" optional="false" min="1" value="1" label="Select one-indexed start base position." help="Positions before start position will be ignored in the distance calculation." />
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64 <param name="end" type="integer" optional="false" min="1" value="1" label="Select one-indexed end base position." help="Positions after end position will be ignored in the distance calculation." />
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65 </when>
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66 <when value="keep_range">
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67 </when>
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68 </conditional>
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69 </inputs>
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70 <outputs>
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71 <data format="csv" name="matrix" from_work_dir="matrix.csv" />
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72 </outputs>
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73 <tests>
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74 <test>
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75 <param name="ref_file" value="hxb2_pol.fas" />
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76 <param name="bam_files" value="quasi1.bam,quasi2.bam" />
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77 <param name="normalize" value="-n" />
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78 <param name="coverage_selector" value="truncate" />
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79 <param name="manual_input" value="keep_range" />
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80 <param name="output_similarity" value="-od" />
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81 <output name="matrix" ftype="csv" >
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82 <assert_contents>
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83 <has_text_matching expression="Quasispecies"/>
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84 </assert_contents>
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85 </output>
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86 </test>
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87 </tests>
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88 <help><![CDATA[
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89
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90 Quasispecies Distance
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91 =====================
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92
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93 Determines the evolutionary distance between viral quasispecies.
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94 Uses the angular cosine distance function by default.
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95
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96 ------
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97 Inputs
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98 ------
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99
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100 1. FASTA Consensus file
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101 2. Two or more BAM files (otherwise tool will throw an error)
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102
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103 ----------
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104 Parameters
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105 ----------
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106 1. Normalize pileup (True or False)
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107 2. Select custom start and end position. Currently only supports selection of custom start and end position for one single reference.
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108 3. Choose how to treat zero coverage regions (keep, remove all, or truncate)
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109
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110 -------
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111 Outputs
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112 -------
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113
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114 CSV containing distance matrix.
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115
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116 ]]></help>
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117 <citations>
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118 <citation type="bibtex">
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119 @misc{GitHubquasitoolsdistance,
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120 title = {quasitools distance},
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121 publisher = {phac-nml},
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122 journal = {GitHub repository},
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123 url = {https://github.com/phac-nml/quasitools},
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124 }
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125 </citation>
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126 </citations>
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127 </tool>