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comparison seqtk_nml.xml @ 0:e1867440ed36 draft

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planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 008f4667b70be22e9ddf496738b3f74bb942ed28
author nml
date Tue, 19 Sep 2017 16:37:42 -0400
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1 <tool id="seqtk_nml_sample" name="seqTK Sample NML" version="1.0.0">
2 <description>Runs seqTK sample if raw coverage is above user defined threshold </description>
3 <requirements>
4 <requirement type="package" version="1.2">seqtk</requirement>
5 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
6 </requirements>
7 <stdio>
8 <exit_code range="1:" level="fatal" description="Unknown error has occured"/>
9 </stdio>
10 <command>
11 perl $__tool_directory__/seqtk_nml.pl --ref $fastar
12
13 #if $single_or_paired.type == "single"
14 --type single
15 --forward $input_se
16 --cov $coverage
17 --out_forward $output
18 --log $log
19 #elif $single_or_paired.type == "paired"
20 --type paired
21 --forward $single_or_paired.forward_pe
22 --reverse $single_or_paired.reverse_pe
23 --cov $coverage
24 --out_forward $output
25 --out_reverse $output_rev
26 --log $log
27 #else
28 collection
29 $single_or_paired.fastq_collection.forward $single_or_paired.fastq_collection.reverse
30 $coverage $output_collection.forward $output_collection.reverse
31 #end if
32
33 </command>
34 <inputs>
35 <conditional name="single_or_paired">
36 <param name="type" type="select" label="Read type">
37 <option value="single">Single-end</option>
38 <option value="paired">Paired-end</option>
39 <option value="collection">Collection Paired-end</option>
40 </param>
41 <when value="single">
42 <param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/>
43 </when>
44 <when value="paired">
45 <param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/>
46 <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/>
47 </when>
48 <when value="collection">
49 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="txt" collection_type="paired" />
50 </when>
51 </conditional>
52 <param name="fastar" type="data" label="Fasta Reference File" format="fasta" />
53 <param name="coverage" type="integer" label="Desired Coverage" value="50" />
54 </inputs>
55 <outputs>
56 <data format="fastqsanger" name="output" label="SubSampled Fastq" >
57 <filter>single_or_paired['type']!="collection"</filter>
58 </data>
59 <data format="fastqsanger" name="output_rev" label="SubSampled Fastq Reverse">
60 <filter>single_or_paired['type']=="paired"</filter>
61 </data>
62 <collection name="output_collection" type="paired" label="SubSampled Fastqs">
63 <data name="forward" format="fastqsanger"/>
64 <data name="reverse" format="fastqsanger"/>
65 <filter>single_or_paired['type']=="collection"</filter>
66 </collection>
67 <data format="txt" name="log" label="Log file"/>
68 </outputs>
69
70 <tests>
71 <test>
72 <param name="type" value="paired" />
73 <param name="forward_pe" value="inputforward.fastq" />
74 <param name="reverse_pe" value="inputreverse.fastq" />
75 <param name="fastar" value="testref.fasta"/>
76 <param name="coverage" value="50" />
77 <output name="output" file="outputforward.fastq" />
78 <output name="output_rev" file="outputreverse.fastq" />
79 <output name="log" file="lognosample.log" />
80 </test>
81 <test>
82 <param name="type" value="paired" />
83 <param name="forward_pe" value="inputforward.fastq" />
84 <param name="reverse_pe" value="inputreverse.fastq" />
85 <param name="fastar" value="testref.fasta"/>
86 <param name="coverage" value="25" />
87 <output name="output" file="outputdownsamepleforward.fastq" />
88 <output name="output_rev" file="outputdownsameplereverse.fastq" />
89 <output name="log" file="logdownsample.log" />
90 </test>
91 </tests>
92 <help>
93 What it does
94 ============
95
96 Calculates raw coverage. If the raw coverage is greater than desired coverage, runs seqTK sample to generate downsampled reads.
97
98
99 Usage
100 =====
101
102 **Parameters**
103 - Fastq reads (single end, paired end, or paired end collection)
104 - Fasta reference file
105
106 **Options**
107 - Desired coverage (50)
108 </help>
109 <citations>
110 <citation type="doi">doi.org/10.1371/journal.pone.0163962</citation>
111 </citations>
112 </tool>
113