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annotate distance.xml @ 0:1f1214983a1c draft default tip

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planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
author nml
date Mon, 20 Jun 2022 20:05:57 +0000
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0
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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1 <tool id="distance" name="Quasispecies Distance" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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2 <description>Calculate the evolutionary distance between viral quasispecies.</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 <expand macro="requirements"/>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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7 <command detect_errors="exit_code"><![CDATA[
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8
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9 #for $bam_file in $bam_files
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10 ln -s $bam_file '${bam_file.name}' &&
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11 ln -s $bam_file.metadata.bam_index '${bam_file.name}.bai' &&
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12 #end for
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1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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14 quasitools distance $ref_file
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1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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16 #for $bam_file in $bam_files
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17 '${bam_file.name}'
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18 #end for
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19
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20 -o matrix.csv
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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22 $normalize
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24 #if $low_coverage.coverage_selector == 'keep':
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25 -k
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26 #else if $low_coverage.coverage_selector == 'remove':
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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27 -r
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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28 #else if $low_coverage.coverage_selector == 'truncate':
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29 -t
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30 #end if
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31
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32 #if $select_range.manual_input == 'select_range':
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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33 -s $select_range.start
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34 -e $select_range.end
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35 #end if
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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36
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37 $output_similarity
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38
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39 ]]></command>
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40 <inputs>
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41 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
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42 <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."/>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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43 <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."/>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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44 <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." />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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45 <conditional name="low_coverage">
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46 <param name="coverage_selector" type="select" label="Choose how to treat zero coverage positions.">
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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47 <option value="remove" selected = "true">Remove all zero coverage positions.</option>
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48 <option value="keep">Keep all zero coverage positions.</option>
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49 <option value="truncate">Truncate zero coverage positions at start and end of pileup.</option>
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50 </param>
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51 <when value="remove">
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52 </when>
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53 <when value="keep">
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54 </when>
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55 <when value="truncate">
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56 </when>
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57 </conditional>
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58 <conditional name="select_range">
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59 <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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60 <option value="keep_range" selected = "true">Use original pileup for distance calculation.</option>
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61 <option value="select_range">Manually select pileup's start and end position for distance calculation.</option>
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62 </param>
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63 <when value="select_range">
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64 <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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65 <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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66 </when>
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67 <when value="keep_range">
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68 </when>
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69 </conditional>
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70 </inputs>
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71 <outputs>
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72 <data format="csv" name="matrix" from_work_dir="matrix.csv" />
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73 </outputs>
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74 <tests>
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75 <test>
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76 <param name="ref_file" value="hxb2_pol.fas" />
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77 <param name="bam_files" value="quasi1.bam,quasi2.bam" />
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78 <param name="normalize" value="-n" />
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79 <param name="coverage_selector" value="truncate" />
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80 <param name="manual_input" value="keep_range" />
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81 <param name="output_similarity" value="-od" />
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82 <output name="matrix" ftype="csv" >
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83 <assert_contents>
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84 <has_text_matching expression="Quasispecies"/>
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85 </assert_contents>
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86 </output>
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87 </test>
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88 </tests>
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89 <help><![CDATA[
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90
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91 Quasispecies Distance
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92 =====================
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93
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94 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 ------
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97 Inputs
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98 ------
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99
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100 1. A reference FASTA.
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101 2. At least two BAM files generated in coordination with the above reference.
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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
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107 1. Normalize pileup (True or False).
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108 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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109 3. Choose how to treat zero coverage regions (keep, remove all, or truncate).
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110
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111 -------
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112 Outputs
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113 -------
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114
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115 A CSV file containing a matrix of similarities or distances, as requested by the user.
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116
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117 ]]></help>
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118 <expand macro="citations" />
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119 </tool>