Mercurial > repos > iuc > poretools_extract
comparison poretools_extract.xml @ 0:7593f94691fb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
author | iuc |
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date | Tue, 19 Dec 2017 14:46:31 -0500 |
parents | |
children | 08064da7b7fb |
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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> |