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annotate distance.xml @ 6:9fb9fed71486 draft

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planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
author nml
date Fri, 12 Oct 2018 09:16:03 -0400
parents b69e898b8109
children dcd43b402eb3
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1 <tool id="distance" name="Quasispecies Distance" version="0.4.2">
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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="0.4.2">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 This tool determines the cosine relatedness between viral quasispecies, reporting either angular cosine distance or cosine similarity as measures of relatedness. These measures of relatedness should be understood as approximations for evolutionary distance and might be useful for performing clustering.
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95 ------
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96 Inputs
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97 ------
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98
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99 1. A reference FASTA.
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100 2. At least two BAM files generated in coordination with the above reference.
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101
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102 ----------
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103 Parameters
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104 ----------
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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 A CSV file containing a matrix of similarities or distances, as requested by the user.
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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>