Mercurial > repos > devteam > fastq_quality_converter

comparison fastq_quality_converter.xml @ 1:253c7f4976e3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:39:43 -0400
parents ee975578075f
children 0b7eccecaa34
comparison
equal deleted inserted replaced
0:ee975578075f 1:253c7f4976e3
1 <tool id="cshl_fastq_quality_converter" name="Quality format converter" version="1.0.0"> 1 <tool id="cshl_fastq_quality_converter" name="Quality format converter" version="1.0.0">
2 <description>(ASCII-Numeric)</description> 2 <description>(ASCII-Numeric)</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> 4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
5 </requirements> 5 </requirements>
6 <command>zcat -f $input | fastq_quality_converter $QUAL_FORMAT -o $output -Q $offset</command> 6 <command>
7 <inputs> 7 <![CDATA[
8 <param format="fastq" name="input" type="data" label="Library to convert" /> 8 zcat -f < '$input' | fastq_quality_converter $QUAL_FORMAT -o '$output' -Q $offset
9 ]]>
10 </command>
11 <inputs>
12 <param format="fastq" name="input" type="data" label="Library to convert" />
9 13
10 <param name="QUAL_FORMAT" type="select" label="Desired output format"> 14 <param name="QUAL_FORMAT" type="select" label="Desired output format">
11 <option value="-a">ASCII (letters) quality scores</option> 15 <option value="-a">ASCII (letters) quality scores</option>
12 <option value="-n">Numeric quality scores</option> 16 <option value="-n">Numeric quality scores</option>
13 </param> 17 </param>
14 18
15 <param name="offset" type="select" label="FASTQ ASCII offset"> 19 <param name="offset" type="select" label="FASTQ ASCII offset">
16 <option value="33">33</option> 20 <option value="33">33</option>
17 <option selected="true" value="64">64</option> 21 <option selected="true" value="64">64</option>
18 </param> 22 </param>
19 </inputs> 23 </inputs>
20 24 <outputs>
21 <tests> 25 <data format="fastq" name="output" metadata_source="input" />
22 <test> 26 </outputs>
23 <!-- ASCII to NUMERIC --> 27 <tests>
24 <param name="input" value="fastq_qual_conv1.fastq" /> 28 <test>
25 <param name="QUAL_FORMAT" value="Numeric quality scores" /> 29 <!-- ASCII to NUMERIC -->
26 <param name="offset" value="64" /> 30 <param name="input" value="fastq_qual_conv1.fastq" />
27 <output name="output" file="fastq_qual_conv1.out" /> 31 <param name="QUAL_FORMAT" value="Numeric quality scores" />
28 </test> 32 <param name="offset" value="64" />
29 <test> 33 <output name="output" file="fastq_qual_conv1.out" />
30 <!-- ASCII to ASCII (basically, a no-op, but it should still produce a valid output --> 34 </test>
31 <param name="input" value="fastq_qual_conv1.fastq" /> 35 <test>
32 <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" /> 36 <!-- ASCII to ASCII (basically, a no-op, but it should still produce a valid output -->
33 <param name="offset" value="64" /> 37 <param name="input" value="fastq_qual_conv1.fastq" />
34 <output name="output" file="fastq_qual_conv1a.out" /> 38 <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" />
35 </test> 39 <param name="offset" value="64" />
36 <test> 40 <output name="output" file="fastq_qual_conv1a.out" />
37 <!-- NUMERIC to ASCII --> 41 </test>
38 <param name="input" value="fastq_qual_conv2.fastq" /> 42 <test>
39 <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" /> 43 <!-- NUMERIC to ASCII -->
40 <param name="offset" value="64" /> 44 <param name="input" value="fastq_qual_conv2.fastq" />
41 <output name="output" file="fastq_qual_conv2.out" /> 45 <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" />
42 </test> 46 <param name="offset" value="64" />
43 <test> 47 <output name="output" file="fastq_qual_conv2.out" />
44 <!-- NUMERIC to NUMERIC (basically, a no-op, but it should still produce a valid output --> 48 </test>
45 <param name="input" value="fastq_qual_conv2.fastq" /> 49 <test>
46 <param name="QUAL_FORMAT" value="Numeric quality scores" /> 50 <!-- NUMERIC to NUMERIC (basically, a no-op, but it should still produce a valid output -->
47 <param name="offset" value="64" /> 51 <param name="input" value="fastq_qual_conv2.fastq" />
48 <output name="output" file="fastq_qual_conv2n.out" /> 52 <param name="QUAL_FORMAT" value="Numeric quality scores" />
49 </test> 53 <param name="offset" value="64" />
50 </tests> 54 <output name="output" file="fastq_qual_conv2n.out" />
51 55 </test>
52 <outputs> 56 </tests>
53 <data format="fastq" name="output" metadata_source="input" /> 57 <help>
54 </outputs>
55 <help>
56
57 **What it does** 58 **What it does**
58 59
59 Converts a Solexa FASTQ file to/from numeric or ASCII quality format. 60 Converts a Solexa FASTQ file to/from numeric or ASCII quality format.
60 61
61 .. class:: warningmark 62 .. class:: warningmark
62 63
63 Re-scaling is **not** performed. (e.g. conversion from Phred scale to Solexa scale). 64 Re-scaling is **not** performed. (e.g. conversion from Phred scale to Solexa scale).
64
65 65
66 ----- 66 -----
67 67
68 FASTQ with Numeric quality scores:: 68 FASTQ with Numeric quality scores::
69 69
91 ------ 91 ------
92 92
93 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. 93 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
94 94
95 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ 95 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
96 96 </help>
97 </help>
98 <!-- FASTQ-Quality-Converter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> 97 <!-- FASTQ-Quality-Converter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
99 </tool> 98 </tool>