Mercurial > repos > devteam > fastx_quality_statistics

comparison macros.xml @ 3:29924496aeb0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 12:52:11 -0400
parents
children 0674d92802bf
comparison
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2:76cefe061c3d 3:29924496aeb0
1 <?xml version="1.0"?>
2 <macros>
3 <token name="@CATS@">
4 #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
5 zcat -f '$input' |
6 #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'):
7 bzcat -f '$input' |
8 #else:
9 cat '$input' |
10 #end if
11 </token>
12 <token name="@FQQUAL@">
13 <![CDATA[
14 #if $input.is_of_type('fastqsanger', 'fastqsanger.gz', 'fastqsanger.bz2'):
15 -Q 33
16 #elif $input.is_of_type('fastqsolexa', 'fastqsolexa.gz', 'fastqsolexa.bz2', 'fastqillumina', 'fastqillumina.gz', 'fastqillumina.bz2'):
17 -Q 64
18 #end if
19 ]]>
20 </token>
21 <xml name="requirements">
22 <requirements>
23 <requirement type="package" version="@VERSION@">fastx_toolkit</requirement>
24 <yield />
25 </requirements>
26 </xml>
27 <token name="@VERSION@">0.0.14</token>
28 <token name="@SANGER@">fastqsanger,fastqsanger.gz,fastqsanger.bz2</token>
29 <token name="@SOLEXA@">fastqsolexa,fastqsolexa.gz,fastqsolexa.bz2</token>
30 <token name="@ILLUMINA@">fastqillumina,fastqillumina.gz,fastqillumina.bz2</token>
31 <token name="@FASTQS@">@SANGER@,@SOLEXA@,@ILLUMINA@</token>
32 <token name="@FASTAS@">fasta,fasta.gz</token>
33 <xml name="citations">
34 <citations>
35 <citation type="bibtex">
36 @UNPUBLISHED{agordon,
37 author = "Assaf Gordon",
38 title = "FASTQ/A short-reads pre-processing tools",
39 year = "2010",
40 note = "http://hannonlab.cshl.edu/fastx_toolkit/",
41 url = "http://hannonlab.cshl.edu/fastx_toolkit/"}
42 </citation>
43 </citations>
44 </xml>
45 <xml name="fasta_input">
46 <param name="input" type="data" format="@FASTAS@" label="Input FASTA file" />
47 </xml>
48 <xml name="fastq_input">
49 <param name="input" type="data" format="@FASTQS@" label="Input FASTQ file" />
50 </xml>
51 <xml name="fastx_input">
52 <param name="input" type="data" format="@FASTAS@,@FASTQS@" label="Input file in FASTA or FASTQ format" />
53 </xml>
54 </macros>