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comparison macros.xml @ 4:cc0fd298cc17 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics commit fd099d17eceaa319fbfe429f4725328d88b18c9f
author iuc
date Thu, 10 Aug 2023 06:54:10 +0000
parents 59003d0543cd
children
comparison
equal deleted inserted replaced
3:59003d0543cd 4:cc0fd298cc17
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
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 18 #end if
19 ]]> 19 ]]>
20 </token> 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
27 #end if
28 ]]>
29 </token>
21 <xml name="requirements"> 30 <xml name="requirements">
22 <requirements> 31 <requirements>
23 <requirement type="package" version="@VERSION@">fastx_toolkit</requirement> 32 <requirement type="package" version="@VERSION@">fastx_toolkit</requirement>
24 <yield /> 33 <yield />
25 </requirements> 34 </requirements>
26 </xml> 35 </xml>
27 <token name="@VERSION@">0.0.14</token> 36 <token name="@VERSION@">0.0.14</token>
37 <token name="@VERSION_SUFFIX@">2</token>
28 <token name="@SANGER@">fastqsanger,fastqsanger.gz,fastqsanger.bz2</token> 38 <token name="@SANGER@">fastqsanger,fastqsanger.gz,fastqsanger.bz2</token>
29 <token name="@SOLEXA@">fastqsolexa,fastqsolexa.gz,fastqsolexa.bz2</token> 39 <token name="@SOLEXA@">fastqsolexa,fastqsolexa.gz,fastqsolexa.bz2</token>
30 <token name="@ILLUMINA@">fastqillumina,fastqillumina.gz,fastqillumina.bz2</token> 40 <token name="@ILLUMINA@">fastqillumina,fastqillumina.gz,fastqillumina.bz2</token>
31 <token name="@FASTQS@">@SANGER@,@SOLEXA@,@ILLUMINA@</token> 41 <token name="@FASTQS@">@SANGER@,@SOLEXA@,@ILLUMINA@</token>
32 <token name="@FASTAS@">fasta,fasta.gz</token> 42 <token name="@FASTAS@">fasta,fasta.gz</token>