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comparison fastq_paired_end_deinterlacer.xml @ 0:f0949bc49926 draft

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author devteam
date Mon, 27 Jan 2014 09:27:16 -0500
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1 <tool id="fastq_paired_end_deinterlacer" name="FASTQ de-interlacer" version="1.1">
2 <description>on paired end reads</description>
3 <requirements>
4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
5 </requirements>
6 <command interpreter="python">fastq_paired_end_deinterlacer.py '$input_file' '${input_file.extension[len( 'fastq' ):]}' '$output1_pairs_file' '$output2_pairs_file' '$output1_singles_file' '$output2_singles_file'</command>
7 <inputs>
8 <param name="input_file" type="data" format="fastqsanger,fastqcssanger" label="FASTQ reads" />
9 </inputs>
10 <outputs>
11 <data name="output1_pairs_file" format="input" label="FASTQ de-interlacer left mates from data ${input_file.hid}" />
12 <data name="output2_pairs_file" format="input" label="FASTQ de-interlacer right mates from data ${input_file.hid}"/>
13 <data name="output1_singles_file" format="input" label="FASTQ de-interlacer left singles from data ${input_file.hid}"/>
14 <data name="output2_singles_file" format="input" label="FASTQ de-interlacer right singles from data ${input_file.hid}"/>
15 </outputs>
16 <tests>
17 <test>
18 <param name="input_file" value="paired_end_merged.fastqsanger" ftype="fastqsanger" />
19 <output name="output1_pairs_file" file="paired_end_1.fastqsanger" />
20 <output name="output2_pairs_file" file="paired_end_2.fastqsanger" />
21 <output name="output1_singles_file" file="paired_end_1_singles.fastqsanger" />
22 <output name="output2_singles_file" file="paired_end_2_singles.fastqsanger" />
23 </test>
24 <test>
25 <param name="input_file" value="paired_end_merged_errors.fastqsanger" ftype="fastqsanger" />
26 <output name="output1_pairs_file" file="paired_end_1_cleaned.fastqsanger" />
27 <output name="output2_pairs_file" file="paired_end_2_cleaned.fastqsanger" />
28 <output name="output1_singles_file" file="paired_end_1_cleaned_singles.fastqsanger" />
29 <output name="output2_singles_file" file="paired_end_2_cleaned_singles.fastqsanger" />
30 </test>
31 </tests>
32 <help>
33 **What it does**
34
35 De-interlaces a single fastq dataset representing paired-end run into two fastq datasets containing only the first or second mate read. Reads without mate are saved in separate output files.
36
37 Sequence identifiers for paired-end reads must follow the /1 and /2 convention.
38
39 -----
40
41 **Input**
42
43 A multiple-fastq file containing paired-end reads, for example::
44
45 @1539:931/1
46 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
47 +1539:931/1
48 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
49 @1539:931/2
50 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
51 +1539:931/2
52 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
53
54 -----
55
56 **Output**
57
58 Multi-fastq file with left-hand mate only::
59
60 @1539:931/1
61 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
62 +1539:931/1
63 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
64
65 Multi-fastq file with right-hand mate only::
66
67 @1539:931/2
68 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
69 +1539:931/2
70 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
71
72 </help>
73 </tool>