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comparison poretools_extract.xml @ 0:f97175ea170d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
author iuc
date Tue, 19 Dec 2017 14:15:31 -0500
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children 263124f77b6f
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-1:000000000000 0:f97175ea170d
1 <?xml version="1.0"?>
2 <tool id="poretools_extract" name="Extract reads" version="@VERSION@.0">
3 <description>in FASTA or FASTQ format from nanopore files</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="aggressive">
9 <![CDATA[
10 poretools $output_format --type $type --min-length $min_length --max-length $max_length
11 $quality
12 #if $group:
13 --group '$group'
14 #end if
15 #if $start:
16 --start '$start'
17 #end if
18 #if $end:
19 --end '$end'
20 #end if
21 '$input' > '$output'
22 ]]>
23 </command>
24 <inputs>
25 <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" />
26 <param name="output_format" type="select" label="Output format">
27 <option value="fastq">FASTQ</option>
28 <option value="fasta">FASTA</option>
29 </param>
30 <expand macro="length_options" />
31 <param argument="--type" type="select" label="FASTQ Type">
32 <option value="all">All</option>
33 <option value="fwd">Forward</option>
34 <option value="rev">Reverse</option>
35 <option value="2D">2D</option>
36 <option value="fwd,rev">Forward and reverse</option>
37 <option value="best">Best</option>
38 </param>
39 <param name="quality" type="select" label="Filter by complement events">
40 <option value="">Do not filter</option>
41 <option value="--high-quality">Only report reads with more</option>
42 <option value="--normal-quality">Only report reads with fewer</option>
43 </param>
44 <param argument="--group" type="integer" optional="True" label="Base calling group serial number to extract" />
45 <param argument="--start" type="integer" optional="True" label="Start timestamp" />
46 <param argument="--end" type="integer" optional="True" label="End timestamp" />
47 </inputs>
48 <outputs>
49 <data name="output" format="fastq">
50 <change_format>
51 <when input="output_format" value="fasta" format="fasta" />
52 </change_format>
53 </data>
54 </outputs>
55 <tests>
56 <test>
57 <expand macro="test_input" />
58 <param name="output_format" value="fastq" />
59 <output name="output" file="poretools-extract-out1.fastq" ftype="fastq" />
60 </test>
61 <test>
62 <expand macro="test_input" />
63 <param name="output_format" value="fasta" />
64 <output name="output" file="poretools-extract-out1.fasta" ftype="fasta" />
65 </test>
66 </tests>
67 <help>
68 Extract sequences from fast5 files generated by the Oxford Nanopore sequencing technology.
69 </help>
70 <expand macro="citations" />
71 </tool>