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comparison 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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children b69e898b8109
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3:8dacd75ca8f1 4:8cdffc02d2e2
1 <tool id="distance" name="Quasispecies Distance" version="0.1.0">
2 <description>Calculate the evolutionary distance between viral quasispecies.</description>
3 <requirements>
4 <requirement type="package" version="0.3.1">quasitools</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7
8 #for $bam_file in $bam_files
9 ln -s $bam_file '${bam_file.name}' &&
10 ln -s $bam_file.metadata.bam_index '${bam_file.name}.bai' &&
11 #end for
12
13 quasitools distance $ref_file
14
15 #for $bam_file in $bam_files
16 '${bam_file.name}'
17 #end for
18
19 -o matrix.csv
20
21 $normalize
22
23 #if $low_coverage.coverage_selector == 'keep':
24 -k
25 #else if $low_coverage.coverage_selector == 'remove':
26 -r
27 #else if $low_coverage.coverage_selector == 'truncate':
28 -t
29 #end if
30
31 #if $select_range.manual_input == 'select_range':
32 -s $select_range.start
33 -e $select_range.end
34 #end if
35
36 $output_similarity
37
38 ]]></command>
39 <inputs>
40 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
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."/>
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."/>
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." />
44 <conditional name="low_coverage">
45 <param name="coverage_selector" type="select" label="Choose how to treat zero coverage positions.">
46 <option value="remove" selected = "true">Remove all zero coverage positions.</option>
47 <option value="keep">Keep all zero coverage positions.</option>
48 <option value="truncate">Truncate zero coverage positions at start and end of pileup.</option>
49 </param>
50 <when value="remove">
51 </when>
52 <when value="keep">
53 </when>
54 <when value="truncate">
55 </when>
56 </conditional>
57 <conditional name="select_range">
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.">
59 <option value="keep_range" selected = "true">Use original pileup for distance calculation.</option>
60 <option value="select_range">Manually select pileup's start and end position for distance calculation.</option>
61 </param>
62 <when value="select_range">
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." />
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." />
65 </when>
66 <when value="keep_range">
67 </when>
68 </conditional>
69 </inputs>
70 <outputs>
71 <data format="csv" name="matrix" from_work_dir="matrix.csv" />
72 </outputs>
73 <tests>
74 <test>
75 <param name="ref_file" value="hxb2_pol.fas" />
76 <param name="bam_files" value="quasi1.bam,quasi2.bam" />
77 <param name="normalize" value="-n" />
78 <param name="coverage_selector" value="truncate" />
79 <param name="manual_input" value="keep_range" />
80 <param name="output_similarity" value="-od" />
81 <output name="matrix" ftype="csv" >
82 <assert_contents>
83 <has_text_matching expression="Quasispecies"/>
84 </assert_contents>
85 </output>
86 </test>
87 </tests>
88 <help><![CDATA[
89
90 Quasispecies Distance
91 =====================
92
93 Determines the evolutionary distance between viral quasispecies.
94 Uses the angular cosine distance function by default.
95
96 ------
97 Inputs
98 ------
99
100 1. FASTA Consensus file
101 2. Two or more BAM files (otherwise tool will throw an error)
102
103 ----------
104 Parameters
105 ----------
106 1. Normalize pileup (True or False)
107 2. Select custom start and end position. Currently only supports selection of custom start and end position for one single reference.
108 3. Choose how to treat zero coverage regions (keep, remove all, or truncate)
109
110 -------
111 Outputs
112 -------
113
114 CSV containing distance matrix.
115
116 ]]></help>
117 <citations>
118 <citation type="bibtex">
119 @misc{GitHubquasitoolsdistance,
120 title = {quasitools distance},
121 publisher = {phac-nml},
122 journal = {GitHub repository},
123 url = {https://github.com/phac-nml/quasitools},
124 }
125 </citation>
126 </citations>
127 </tool>