Mercurial > repos > devteam > fastq_to_fasta
comparison macros.xml @ 3:02a5f43cd5d1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
author | iuc |
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date | Wed, 22 Aug 2018 11:04:47 -0400 |
parents | ce309f4ff17f |
children | e282bc27be9a |
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2:ce309f4ff17f | 3:02a5f43cd5d1 |
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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 -z | |
18 #end if | 25 #end if |
19 ]]> | 26 ]]> |
20 </token> | 27 </token> |
21 <xml name="requirements"> | 28 <xml name="requirements"> |
22 <requirements> | 29 <requirements> |