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comparison yac.xml @ 0:ad6b978daa2e draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit e9cf2978954c546bb90eb11931f9cfd6562156f3
author artbio
date Wed, 26 Jul 2017 13:35:39 -0400
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1 <tool id="yac" name="Clip adapter" version="2.0.0">
2 <description />
3 <command interpreter="python">yac.py --input $input
4 --output $output
5 --output_format "$out_format"
6 --adapter_to_clip $clip_source.clip_sequence
7 --min $min
8 --max $max
9 --Nmode $Nmode
10 </command>
11 <inputs>
12 <param format="fastq" label="Source file" name="input" type="data" />
13 <param label="min size" name="min" size="4" type="integer" value="15" />
14 <param label="max size" name="max" size="4" type="integer" value="36" />
15 <param label="Select output format" name="out_format" type="select">
16 <option selected="true" value="fasta">Fasta format</option>
17 <option value="fastq">Fastq format</option>
18 </param>
19 <param label="Accept reads containing N?" name="Nmode" type="select">
20 <option selected="True" value="accept">accept</option>
21 <option value="reject">reject</option>
22 </param>
23 <conditional name="clip_source">
24 <param help="Built-in adapters or User-provided" label="Source" name="clip_source_list" type="select">
25 <option selected="True" value="prebuilt">Use a built-in adapter (select from the list below)</option>
26 <option value="user">Use custom sequence</option>
27 </param>
28 <when value="prebuilt">
29 <param help="if your adapter is not listed, input your own sequence" label="Select Adapter to clip" name="clip_sequence" type="select">
30 <option value="TCGTATGCCGTCTTCTGCTTG">Solexa TCGTATGCCGTCTTCTGCTTG</option>
31 <option value="ATCTCGTATGCCGTCTTCTGCTT">Illumina ATCTCGTATGCCGTCTTCTGCTT</option>
32 <option selected="True" value="TGGAATTCTCGGGTGCCAAG">Illumina TruSeq TGGAATTCTCGGGTGCCAAG</option>
33 <option value="CTGTAGGCACCATCAATCGT">IdT CTGTAGGCACCATCAATCGT</option>
34 </param>
35 </when>
36 <when value="user">
37 <param label="Enter your Sequence" name="clip_sequence" size="35" type="text" value="GAATCC" />
38 </when>
39 </conditional>
40 </inputs>
41 <outputs>
42 <data format="fasta" metadata_source="input" name="output" label="Clipping of ${input.name}">
43 <change_format>
44 <when input="out_format" value="fastq" format="fastq" />
45 </change_format>
46 </data>
47 </outputs>
48 <tests>
49 <test>
50 <param ftype="fastqsanger" name="input" value="yac.fastq" />
51 <param name="min" value="18" />
52 <param name="max" value="29" />
53 <param name="clip_source_list" value="prebuilt" />
54 <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" />
55 <param name="Nmode" value="accept" />
56 <output file="yac.out" name="output" />
57 </test>
58 <test>
59 <param ftype="fastqsanger" name="input" value="yac.fastq" />
60 <param name="min" value="18" />
61 <param name="max" value="29" />
62 <param name="clip_source_list" value="prebuilt" />
63 <param name="clip_sequence" value="ATCTCGTATGCCGTCTTCTGCTT" />
64 <param name="Nmode" value="accept" />
65 <param name="out_format" value="fastq" />
66 <output file="yac_fastq.out" name="output" />
67 </test>
68 </tests>
69 <help>
70
71 **What it does**
72
73 + Clips adapter sequences
74 + Renumbers sequence headers
75 + Filters sequences on their size
76 + Filters sequences containing unknown nucleotides (optional)
77
78 -------
79
80 **Inputs**
81
82 1. A fastq file of reads to be clipped
83 2. Select the size of the reads to be kept
84 3. Select an output format when input is a fastq file (this may be fastq or fastq)
85 4. Select whether you wish or do not wish to keep clipped sequences with unknown nucleotides (N)
86 5. Select a pre-built adapter sequence or enter your own sequence (at least 7 nucleotides long)
87
88 -------
89
90 **Output**
91
92 A fastq or fasta file containing clipped sequences satisfying the selected criteria.
93
94 </help>
95 </tool>