Mercurial > repos > peterjc > get_orfs_or_cdss
comparison tools/fastq/fastq_paired_unpaired.xml @ 3:6a14074bc810 draft
Uploaded v0.0.8, automated Biopython dependency handling via ToolShed; MIT license; reST markup for README file.
author | peterjc |
---|---|
date | Mon, 29 Jul 2013 09:28:55 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
2:324775a016ce | 3:6a14074bc810 |
---|---|
1 <tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.0.7"> | |
2 <description>using the read name suffices</description> | |
3 <version_command interpreter="python">fastq_paired_unpaired.py --version</version_command> | |
4 <command interpreter="python"> | |
5 fastq_paired_unpaired.py $input_fastq.extension $input_fastq | |
6 #if $output_choice_cond.output_choice=="separate" | |
7 $output_forward $output_reverse | |
8 #elif $output_choice_cond.output_choice=="interleaved" | |
9 $output_paired | |
10 #end if | |
11 $output_singles | |
12 </command> | |
13 <stdio> | |
14 <!-- Anything other than zero is an error --> | |
15 <exit_code range="1:" /> | |
16 <exit_code range=":-1" /> | |
17 </stdio> | |
18 <inputs> | |
19 <param name="input_fastq" type="data" format="fastq" label="FASTQ file to divide into paired and unpaired reads"/> | |
20 <conditional name="output_choice_cond"> | |
21 <param name="output_choice" type="select" label="How to output paired reads?"> | |
22 <option value="separate">Separate (two FASTQ files, for the forward and reverse reads, in matching order).</option> | |
23 <option value="interleaved">Interleaved (one FASTQ file, alternating forward read then partner reverse read).</option> | |
24 </param> | |
25 <!-- Seems need these dummy entries here, compare this to indels/indel_sam2interval.xml --> | |
26 <when value="separate" /> | |
27 <when value="interleaved" /> | |
28 </conditional> | |
29 </inputs> | |
30 <outputs> | |
31 <data name="output_singles" format="input" label="Orphan or single reads"/> | |
32 <data name="output_forward" format="input" label="Forward paired reads"> | |
33 <filter>output_choice_cond["output_choice"] == "separate"</filter> | |
34 </data> | |
35 <data name="output_reverse" format="input" label="Reverse paired reads"> | |
36 <filter>output_choice_cond["output_choice"] == "separate"</filter> | |
37 </data> | |
38 <data name="output_paired" format="input" label="Interleaved paired reads"> | |
39 <filter>output_choice_cond["output_choice"] == "interleaved"</filter> | |
40 </data> | |
41 </outputs> | |
42 <tests> | |
43 <test> | |
44 <param name="input_fastq" value="sanger-pairs-mixed.fastq" ftype="fastq"/> | |
45 <param name="output_choice" value="separate"/> | |
46 <output name="output_singles" file="sanger-pairs-singles.fastq" ftype="fastq"/> | |
47 <output name="output_forward" file="sanger-pairs-forward.fastq" ftype="fastq"/> | |
48 <output name="output_reverse" file="sanger-pairs-reverse.fastq" ftype="fastq"/> | |
49 </test> | |
50 <test> | |
51 <param name="input_fastq" value="sanger-pairs-mixed.fastq" ftype="fastq"/> | |
52 <param name="output_choice" value="interleaved"/> | |
53 <output name="output_singles" file="sanger-pairs-singles.fastq" ftype="fastq"/> | |
54 <output name="output_paired" file="sanger-pairs-interleaved.fastq" ftype="fastq"/> | |
55 </test> | |
56 </tests> | |
57 <help> | |
58 | |
59 **What it does** | |
60 | |
61 Using the common read name suffix conventions, it divides a FASTQ file into | |
62 paired reads, and orphan or single reads. | |
63 | |
64 The input file should be a valid FASTQ file which has been sorted so that | |
65 any partner forward+reverse reads are consecutive. The output files all | |
66 preserve this sort order. Pairing are recognised based on standard name | |
67 suffices. See below or run the tool with no arguments for more details. | |
68 | |
69 Any reads where the forward/reverse naming suffix used is not recognised | |
70 are treated as orphan reads. The tool supports the /1 and /2 convention | |
71 originally used by Illumina, .f and .r convention, the Sanger convention | |
72 (see http://staden.sourceforge.net/manual/pregap4_unix_50.html for details), | |
73 and the current Illumina convention where the reads get the same identifier | |
74 with the fragment number in the description, for example: | |
75 | |
76 * @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 1:N:0:TGNCCA | |
77 * @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 2:N:0:TGNCCA | |
78 | |
79 Note that this does support multiple forward and reverse reads per template | |
80 (which is quite common with Sanger sequencing), e.g. this which is sorted | |
81 alphabetically: | |
82 | |
83 * WTSI_1055_4p17.p1kapIBF | |
84 * WTSI_1055_4p17.p1kpIBF | |
85 * WTSI_1055_4p17.q1kapIBR | |
86 * WTSI_1055_4p17.q1kpIBR | |
87 | |
88 or this where the reads already come in pairs: | |
89 | |
90 * WTSI_1055_4p17.p1kapIBF | |
91 * WTSI_1055_4p17.q1kapIBR | |
92 * WTSI_1055_4p17.p1kpIBF | |
93 * WTSI_1055_4p17.q1kpIBR | |
94 | |
95 both become: | |
96 | |
97 * WTSI_1055_4p17.p1kapIBF paired with WTSI_1055_4p17.q1kapIBR | |
98 * WTSI_1055_4p17.p1kpIBF paired with WTSI_1055_4p17.q1kpIBR | |
99 | |
100 **Citation** | |
101 | |
102 This tool is available to install into other Galaxy Instances via the Galaxy | |
103 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired | |
104 </help> | |
105 </tool> |