Mercurial > repos > devteam > fastq_quality_boxplot

comparison macros.xml @ 3:7cf5b1d072b5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
author iuc
date Thu, 30 Jan 2020 13:29:05 -0500
parents 3987db70a4b0
children 867ab348287d
comparison
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2:3987db70a4b0 3:7cf5b1d072b5
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@CATS@"> 3 <token name="@CATS@">
4 #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'): 4 #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
5 zcat -f '$input' | 5 gunzip -c -f '$input' |
6 #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'): 6 #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'):
7 bzcat -f '$input' | 7 bzcat -f '$input' |
8 #else: 8 #else:
9 cat '$input' | 9 cat '$input' |
10 #end if 10 #end if
13 <![CDATA[ 13 <![CDATA[
14 #if $input.is_of_type('fastqsanger', 'fastqsanger.gz', 'fastqsanger.bz2'): 14 #if $input.is_of_type('fastqsanger', 'fastqsanger.gz', 'fastqsanger.bz2'):
15 -Q 33 15 -Q 33
16 #elif $input.is_of_type('fastqsolexa', 'fastqsolexa.gz', 'fastqsolexa.bz2', 'fastqillumina', 'fastqillumina.gz', 'fastqillumina.bz2'): 16 #elif $input.is_of_type('fastqsolexa', 'fastqsolexa.gz', 'fastqsolexa.bz2', 'fastqillumina', 'fastqillumina.gz', 'fastqillumina.bz2'):
17 -Q 64 17 -Q 64
18 #end if
19 ]]>
20 </token>
21 <token name="@GZIP@">
22 <![CDATA[
23 #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
24 | gzip -c
25 #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'):
26 | bzip2 -c
18 #end if 27 #end if
19 ]]> 28 ]]>
20 </token> 29 </token>
21 <xml name="requirements"> 30 <xml name="requirements">
22 <requirements> 31 <requirements>