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/tools/fastq/fastq_paired_end_deinterlacer.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 70 lines | 57 code | 13 blank | 0 comment | 0 complexity | c0ed3d900ebb16f93c4b6f2c02a19dea MD5 | raw file
 1<tool id="fastq_paired_end_deinterlacer" name="FASTQ de-interlacer" version="1.1">
 2  <description>on paired end reads</description>
 3  <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>
 4  <inputs>
 5    <param name="input_file" type="data" format="fastqsanger,fastqcssanger" label="FASTQ reads" />
 6  </inputs>
 7  <outputs>
 8    <data name="output1_pairs_file" format="input" label="FASTQ de-interlacer left mates from data ${input_file.hid}" />
 9    <data name="output2_pairs_file" format="input" label="FASTQ de-interlacer right mates from data ${input_file.hid}"/>
10    <data name="output1_singles_file" format="input" label="FASTQ de-interlacer left singles from data ${input_file.hid}"/>
11    <data name="output2_singles_file" format="input" label="FASTQ de-interlacer right singles from data ${input_file.hid}"/>
12  </outputs>
13  <tests>
14    <test>
15      <param name="input_file" value="paired_end_merged.fastqsanger" ftype="fastqsanger" />
16      <output name="output1_pairs_file" file="paired_end_1.fastqsanger" />
17      <output name="output2_pairs_file" file="paired_end_2.fastqsanger" />
18      <output name="output1_singles_file" file="paired_end_1_singles.fastqsanger" />
19      <output name="output2_singles_file" file="paired_end_2_singles.fastqsanger" />
20    </test>
21    <test>
22      <param name="input_file" value="paired_end_merged_errors.fastqsanger" ftype="fastqsanger" />
23      <output name="output1_pairs_file" file="paired_end_1_cleaned.fastqsanger" />
24      <output name="output2_pairs_file" file="paired_end_2_cleaned.fastqsanger" />
25      <output name="output1_singles_file" file="paired_end_1_cleaned_singles.fastqsanger" />
26      <output name="output2_singles_file" file="paired_end_2_cleaned_singles.fastqsanger" />
27    </test>
28  </tests>
29  <help>
30**What it does**
31
32De-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.
33
34Sequence identifiers for paired-end reads must follow the /1 and /2 convention.
35
36-----
37
38**Input**
39
40A multiple-fastq file containing paired-end reads, for example::
41
42    @1539:931/1
43    ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
44    +1539:931/1
45    BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
46    @1539:931/2
47    CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
48    +1539:931/2
49    WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
50
51-----
52
53**Output**
54
55Multi-fastq file with left-hand mate only::
56
57    @1539:931/1
58    ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
59    +1539:931/1
60    BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
61
62Multi-fastq file with right-hand mate only::
63
64    @1539:931/2
65    CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
66    +1539:931/2
67    WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
68
69  </help>
70</tool>