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planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 969557932bff35913d93068d16facb8da4d64123
author nml
date Thu, 02 Nov 2017 14:09:07 -0400
parents e1867440ed36
children
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0:e1867440ed36 1:f49992c79fe4
1 <tool id="seqtk_nml_sample" name="seqTK Sample NML" version="1.0.0"> 1 <tool id="seqtk_nml_sample" name="seqTK Sample NML" version="1.0.1">
2 <description>Runs seqTK sample if raw coverage is above user defined threshold </description> 2 <description>Runs seqTK sample if raw coverage is above user defined threshold </description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.2">seqtk</requirement> 4 <requirement type="package" version="1.2">seqtk</requirement>
5 <requirement type="package" version="1.6.924">perl-bioperl</requirement> 5 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
6 </requirements> 6 </requirements>
7 <stdio> 7 <command detect_errors="exit_code"><![CDATA[
8 <exit_code range="1:" level="fatal" description="Unknown error has occured"/> 8 perl '$__tool_directory__/seqtk_nml.pl'
9 </stdio>
10 <command>
11 perl $__tool_directory__/seqtk_nml.pl --ref $fastar
12 9
13 #if $single_or_paired.type == "single" 10 --ref '$fastar'
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 11
33 </command> 12 #if $single_or_paired.type == "single"
13 --type single
14 --forward '$input_se'
15 --out_forward '$output'
16
17 #elif $single_or_paired.type == "paired"
18 --type paired
19 --forward '$single_or_paired.forward_pe'
20 --reverse '$single_or_paired.reverse_pe'
21 --out_forward '$output'
22 --out_reverse '$output_rev'
23
24 #else
25 --type paired
26 --forward '$single_or_paired.fastq_collection.forward'
27 --reverse '$single_or_paired.fastq_collection.reverse'
28 --out_forward '$output_collection.forward'
29 --out_reverse '$output_collection.reverse'
30 #end if
31
32 --cov '$coverage'
33 --log '$log'
34
35 ]]></command>
34 <inputs> 36 <inputs>
35 <conditional name="single_or_paired"> 37 <conditional name="single_or_paired">
36 <param name="type" type="select" label="Read type"> 38 <param name="type" type="select" label="Read type">
37 <option value="single">Single-end</option> 39 <option value="single">Single-end</option>
38 <option value="paired">Paired-end</option> 40 <option value="paired">Paired-end</option>
39 <option value="collection">Collection Paired-end</option> 41 <option value="collection">Collection Paired-end</option>
40 </param> 42 </param>
41 <when value="single"> 43 <when value="single">
42 <param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/> 44 <param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/>
43 </when> 45 </when>
44 <when value="paired"> 46 <when value="paired">
45 <param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/> 47 <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"/> 48 <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/>
47 </when> 49 </when>
48 <when value="collection"> 50 <when value="collection">
49 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="txt" collection_type="paired" /> 51 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="txt" collection_type="paired" />
50 </when> 52 </when>
51 </conditional> 53 </conditional>
52 <param name="fastar" type="data" label="Fasta Reference File" format="fasta" /> 54 <param name="fastar" type="data" label="Fasta Reference File" format="fasta" />
53 <param name="coverage" type="integer" label="Desired Coverage" value="50" /> 55 <param name="coverage" type="integer" label="Desired Coverage" value="50" />
54 </inputs> 56 </inputs>
55 <outputs> 57 <outputs>
56 <data format="fastqsanger" name="output" label="SubSampled Fastq" > 58 <data format="fastqsanger" name="output" label="SubSampled Fastq" >
57 <filter>single_or_paired['type']!="collection"</filter> 59 <filter>single_or_paired['type']!="collection"</filter>
58 </data> 60 </data>
59 <data format="fastqsanger" name="output_rev" label="SubSampled Fastq Reverse"> 61 <data format="fastqsanger" name="output_rev" label="SubSampled Fastq Reverse">
60 <filter>single_or_paired['type']=="paired"</filter> 62 <filter>single_or_paired['type']=="paired"</filter>
61 </data> 63 </data>
62 <collection name="output_collection" type="paired" label="SubSampled Fastqs"> 64 <collection name="output_collection" type="paired" label="SubSampled Fastqs">
63 <data name="forward" format="fastqsanger"/> 65 <data name="forward" format="fastqsanger"/>
64 <data name="reverse" format="fastqsanger"/> 66 <data name="reverse" format="fastqsanger"/>
65 <filter>single_or_paired['type']=="collection"</filter> 67 <filter>single_or_paired['type']=="collection"</filter>
66 </collection> 68 </collection>
67 <data format="txt" name="log" label="Log file"/> 69 <data format="txt" name="log" label="Log file"/>
68 </outputs> 70 </outputs>
69 71
70 <tests> 72 <tests>
71 <test> 73 <test>
72 <param name="type" value="paired" /> 74 <param name="type" value="paired" />
73 <param name="forward_pe" value="inputforward.fastq" /> 75 <param name="forward_pe" value="inputforward.fastq" />
74 <param name="reverse_pe" value="inputreverse.fastq" /> 76 <param name="reverse_pe" value="inputreverse.fastq" />
75 <param name="fastar" value="testref.fasta"/> 77 <param name="fastar" value="testref.fasta"/>
76 <param name="coverage" value="50" /> 78 <param name="coverage" value="50" />
77 <output name="output" file="outputforward.fastq" /> 79 <output name="output" file="outputforward.fastq" />
78 <output name="output_rev" file="outputreverse.fastq" /> 80 <output name="output_rev" file="outputreverse.fastq" />
79 <output name="log" file="lognosample.log" /> 81 <output name="log" file="lognosample.log" />
80 </test> 82 </test>
81 <test> 83 <test>
82 <param name="type" value="paired" /> 84 <param name="type" value="paired" />
83 <param name="forward_pe" value="inputforward.fastq" /> 85 <param name="forward_pe" value="inputforward.fastq" />
84 <param name="reverse_pe" value="inputreverse.fastq" /> 86 <param name="reverse_pe" value="inputreverse.fastq" />
85 <param name="fastar" value="testref.fasta"/> 87 <param name="fastar" value="testref.fasta"/>
86 <param name="coverage" value="25" /> 88 <param name="coverage" value="25" />
87 <output name="output" file="outputdownsamepleforward.fastq" /> 89 <output name="output" file="outputdownsamepleforward.fastq" />
88 <output name="output_rev" file="outputdownsameplereverse.fastq" /> 90 <output name="output_rev" file="outputdownsameplereverse.fastq" />
89 <output name="log" file="logdownsample.log" /> 91 <output name="log" file="logdownsample.log" />
90 </test> 92 </test>
91 </tests> 93 </tests>
92 <help> 94 <help><![CDATA[
95 ============
93 What it does 96 What it does
94 ============ 97 ============
95
96 Calculates raw coverage. If the raw coverage is greater than desired coverage, runs seqTK sample to generate downsampled reads. 98 Calculates raw coverage. If the raw coverage is greater than desired coverage, runs seqTK sample to generate downsampled reads.
97 99
98 100 =====
99 Usage 101 Usage
100 ===== 102 =====
101 103
102 **Parameters** 104 **Parameters**
103 - Fastq reads (single end, paired end, or paired end collection) 105 - Fastq reads (single end, paired end, or paired end collection)
104 - Fasta reference file 106 - Fasta reference file
105 107
106 **Options** 108 **Options**
107 - Desired coverage (50) 109 - Desired coverage (50)
108 </help> 110 ]]></help>
109 <citations> 111 <citations>
110 <citation type="doi">doi.org/10.1371/journal.pone.0163962</citation> 112 <citation type="doi">10.1371/journal.pone.0163962</citation>
111 </citations> 113 </citations>
112 </tool> 114 </tool>
113