Mercurial > repos > nml > seqtk_nml
comparison seqtk_nml.xml @ 1:f49992c79fe4 draft default tip
planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 969557932bff35913d93068d16facb8da4d64123
author | nml |
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date | Thu, 02 Nov 2017 14:09:07 -0400 |
parents | e1867440ed36 |
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0:e1867440ed36 | 1:f49992c79fe4 |
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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 |