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comparison fastq_quality_converter.xml @ 2:0b7eccecaa34 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 12:49:47 -0400
parents 253c7f4976e3
children ee0f7c04ad36
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1:253c7f4976e3 2:0b7eccecaa34
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="1.0.1">
2 <description>(ASCII-Numeric)</description> 2 <description>(ASCII-Numeric)</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> 4 <import>macros.xml</import>
5 </requirements> 5 </macros>
6 <command> 6 <expand macro="requirements" />
7 <![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 zcat -f < '$input' | fastq_quality_converter $QUAL_FORMAT -o '$output' -Q $offset 8 @CATS@ fastq_quality_converter
9 ]]> 9 $QUAL_FORMAT
10 </command> 10 -o '$output'
11 @FQQUAL@
12 ]]></command>
11 <inputs> 13 <inputs>
12 <param format="fastq" name="input" type="data" label="Library to convert" /> 14 <expand macro="fastq_input" />
13 15
14 <param name="QUAL_FORMAT" type="select" label="Desired output format"> 16 <param name="QUAL_FORMAT" type="select" label="Desired output format">
15 <option value="-a">ASCII (letters) quality scores</option> 17 <option value="-a">ASCII (letters) quality scores</option>
16 <option value="-n">Numeric quality scores</option> 18 <option value="-n">Numeric quality scores</option>
17 </param> 19 </param>
18
19 <param name="offset" type="select" label="FASTQ ASCII offset">
20 <option value="33">33</option>
21 <option selected="true" value="64">64</option>
22 </param>
23 </inputs> 20 </inputs>
24 <outputs> 21 <outputs>
25 <data format="fastq" name="output" metadata_source="input" /> 22 <data name="output" format="fastq" metadata_source="input" />
26 </outputs> 23 </outputs>
27 <tests> 24 <tests>
28 <test> 25 <test>
29 <!-- ASCII to NUMERIC --> 26 <!-- ASCII to NUMERIC -->
30 <param name="input" value="fastq_qual_conv1.fastq" /> 27 <param name="input" ftype="fastqillumina" value="fastq_qual_conv1.fastq" />
31 <param name="QUAL_FORMAT" value="Numeric quality scores" /> 28 <param name="QUAL_FORMAT" value="Numeric quality scores" />
32 <param name="offset" value="64" />
33 <output name="output" file="fastq_qual_conv1.out" /> 29 <output name="output" file="fastq_qual_conv1.out" />
34 </test> 30 </test>
35 <test> 31 <test>
36 <!-- ASCII to ASCII (basically, a no-op, but it should still produce a valid output --> 32 <!-- ASCII to ASCII (should basically copy the input to the output unchanged) -->
37 <param name="input" value="fastq_qual_conv1.fastq" /> 33 <param name="input" ftype="fastqillumina" value="fastq_qual_conv1.fastq" />
38 <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" /> 34 <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" />
39 <param name="offset" value="64" />
40 <output name="output" file="fastq_qual_conv1a.out" /> 35 <output name="output" file="fastq_qual_conv1a.out" />
41 </test> 36 </test>
42 <test> 37 <test>
43 <!-- NUMERIC to ASCII --> 38 <!-- NUMERIC to ASCII -->
44 <param name="input" value="fastq_qual_conv2.fastq" /> 39 <param name="input" ftype="fastqillumina" value="fastq_qual_conv2.fastq" />
45 <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" /> 40 <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" />
46 <param name="offset" value="64" />
47 <output name="output" file="fastq_qual_conv2.out" /> 41 <output name="output" file="fastq_qual_conv2.out" />
48 </test> 42 </test>
49 <test> 43 <test>
50 <!-- NUMERIC to NUMERIC (basically, a no-op, but it should still produce a valid output --> 44 <!-- NUMERIC to NUMERIC (should basically copy the input to the output unchanged) -->
51 <param name="input" value="fastq_qual_conv2.fastq" /> 45 <param name="input" ftype="fastqillumina" value="fastq_qual_conv2.fastq" />
52 <param name="QUAL_FORMAT" value="Numeric quality scores" /> 46 <param name="QUAL_FORMAT" value="Numeric quality scores" />
53 <param name="offset" value="64" />
54 <output name="output" file="fastq_qual_conv2n.out" /> 47 <output name="output" file="fastq_qual_conv2n.out" />
55 </test> 48 </test>
49 <test>
50 <!-- ASCII to NUMERIC -->
51 <param name="input" ftype="fastqsanger" value="fastq_quality_converter-in5.fastq" />
52 <param name="QUAL_FORMAT" value="Numeric quality scores" />
53 <output name="output" file="fastq_quality_converter-out5.fastq" />
54 </test>
55 <test>
56 <!-- ASCII to ASCII (should basically copy the input to the output unchanged) -->
57 <param name="input" ftype="fastqsanger" value="fastq_quality_converter-in6.fastq" />
58 <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" />
59 <output name="output" file="fastq_quality_converter-out6.fastq" />
60 </test>
56 </tests> 61 </tests>
57 <help> 62 <help><![CDATA[
58 **What it does** 63 **What it does**
59 64
60 Converts a Solexa FASTQ file to/from numeric or ASCII quality format. 65 Converts a Solexa FASTQ file to/from numeric or ASCII quality format.
61 66
62 .. class:: warningmark 67 .. class:: warningmark
91 ------ 96 ------
92 97
93 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. 98 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
94 99
95 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ 100 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
96 </help> 101 ]]></help>
102 <expand macro="citations" />
97 <!-- FASTQ-Quality-Converter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> 103 <!-- FASTQ-Quality-Converter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
98 </tool> 104 </tool>