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comparison fastq_to_fasta.xml @ 2:ce309f4ff17f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 13:26:51 -0400
parents 186b8d913e6c
children 02a5f43cd5d1
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1:186b8d913e6c 2:ce309f4ff17f
1 <tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA" version="1.0.0"> 1 <tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA" version="1.0.1">
2 <description>converter</description> 2 <description>converter from FASTX-toolkit</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>gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v 6 <expand macro="requirements" />
7 #if $input.ext == "fastqsanger": 7 <command detect_errors="exit_code"><![CDATA[
8 -Q 33 8 @CATS@ fastq_to_fasta
9 #end if 9 $SKIPN
10 </command> 10 $RENAMESEQ
11 11 -o '$output'
12 <inputs> 12 -v @FQQUAL@
13 <param format="fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="FASTQ Library to convert" /> 13 ]]></command>
14 14 <inputs>
15 <param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases "> 15 <expand macro="fastq_input" />
16 <option value="">yes</option> 16 <param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases ">
17 <option value="-n">no</option> 17 <option value="">yes</option>
18 </param> 18 <option value="-n">no</option>
19 19 </param>
20 <param name="RENAMESEQ" type="select" label="Rename sequence names in output file (reduces file size)"> 20 <param name="RENAMESEQ" type="select" label="Rename sequence names in output file (reduces file size)">
21 <option value="-r">yes</option> 21 <option value="-r">yes</option>
22 <option value="">no</option> 22 <option value="">no</option>
23 </param> 23 </param>
24 24 </inputs>
25 </inputs> 25 <outputs>
26 26 <data name="output" format="fasta" metadata_source="input" />
27 <tests> 27 </outputs>
28 <test> 28 <tests>
29 <!-- FASTQ-To-FASTA, keep N, don't rename --> 29 <test>
30 <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" /> 30 <!-- FASTQ-To-FASTA, keep N, don't rename -->
31 <param name="SKIPN" value=""/> 31 <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
32 <param name="RENAMESEQ" value=""/> 32 <param name="SKIPN" value=""/>
33 <output name="output" file="fastq_to_fasta1a.out" /> 33 <param name="RENAMESEQ" value=""/>
34 </test> 34 <output name="output" file="fastq_to_fasta1a.out" />
35 <test> 35 </test>
36 <!-- FASTQ-To-FASTA, discard N, rename --> 36 <test>
37 <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" /> 37 <!-- FASTQ-To-FASTA, discard N, rename -->
38 <param name="SKIPN" value="no"/> 38 <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
39 <param name="RENAMESEQ" value="yes"/> 39 <param name="SKIPN" value="no"/>
40 <output name="output" file="fastq_to_fasta1b.out" /> 40 <param name="RENAMESEQ" value="yes"/>
41 </test> 41 <output name="output" file="fastq_to_fasta1b.out" />
42 </tests> 42 </test>
43 43 <test>
44 <outputs> 44 <!-- FASTQ-To-FASTA, discard N, rename -->
45 <data format="fasta" name="output" metadata_source="input" /> 45 <param name="input" value="fastq_to_fasta-in2.fastq" ftype="fastqsanger" />
46 </outputs> 46 <param name="SKIPN" value="no"/>
47 47 <param name="RENAMESEQ" value="yes"/>
48 <help> 48 <output name="output" file="fastq_to_fasta-out2.out" />
49 49 </test>
50 </tests>
51 <help><![CDATA[
50 **What it does** 52 **What it does**
51 53
52 This tool converts data from Solexa format to FASTA format (scroll down for format description). 54 This tool converts data from Solexa format to FASTA format (scroll down for format description).
53 55
54 -------- 56 --------
75 ------ 77 ------
76 78
77 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. 79 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
78 80
79 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ 81 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
80 </help> 82 ]]></help>
83 <expand macro="citations" />
81 <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> 84 <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
82 </tool> 85 </tool>