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comparison macros.xml @ 5:8979c288aefb 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 415a5c5de30530910f3039e5fc66aa15103c6f20
author iuc
date Tue, 27 Jun 2023 17:37:28 +0000
parents e282bc27be9a
children 77b41c89d856
comparison
equal deleted inserted replaced
4:e282bc27be9a 5:8979c288aefb
9 cat '$input' | 9 cat '$input' |
10 #end if 10 #end if
11 </token> 11 </token>
12 <token name="@FQQUAL@"> 12 <token name="@FQQUAL@">
13 <![CDATA[ 13 <![CDATA[
14 #if $input.is_of_type('fastqsanger', 'fastqsanger.gz', 'fastqsanger.bz2'): 14 #if 'fastqsanger' in $input.ext:
15 -Q 33 15 -Q 33
16 #elif $input.is_of_type('fastqsolexa', 'fastqsolexa.gz', 'fastqsolexa.bz2', 'fastqillumina', 'fastqillumina.gz', 'fastqillumina.bz2'): 16 #elif 'fastqsolexa' in $input.ext or 'fastqillumina' in $input.ext:
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
27 #end if 18 #end if
28 ]]> 19 ]]>
29 </token> 20 </token>
30 <xml name="requirements"> 21 <xml name="requirements">
31 <requirements> 22 <requirements>
49 note = "http://hannonlab.cshl.edu/fastx_toolkit/", 40 note = "http://hannonlab.cshl.edu/fastx_toolkit/",
50 url = "http://hannonlab.cshl.edu/fastx_toolkit/"} 41 url = "http://hannonlab.cshl.edu/fastx_toolkit/"}
51 </citation> 42 </citation>
52 </citations> 43 </citations>
53 </xml> 44 </xml>
54 <xml name="fasta_input">
55 <param name="input" type="data" format="@FASTAS@" label="Input FASTA file" />
56 </xml>
57 <xml name="fastq_input"> 45 <xml name="fastq_input">
58 <param name="input" type="data" format="@FASTQS@" label="Input FASTQ file" /> 46 <param name="input" type="data" format="@FASTQS@" label="Input FASTQ file" />
59 </xml> 47 </xml>
60 <xml name="fastx_input">
61 <param name="input" type="data" format="@FASTAS@,@FASTQS@" label="Input file in FASTA or FASTQ format" />
62 </xml>
63 </macros> 48 </macros>