Mercurial > repos > devteam > fastq_to_fasta

annotate macros.xml @ 5:b8e3c0a52f33 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 17:37:16 +0000
parents 5dbca5fbdc45
children 0a759fe3fd43
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
2 <macros>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
3 <token name="@CATS@">
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
4 #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
3
4498e994e31b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
iuc
parents: 2
diff changeset
5 gunzip -c -f '$input' |
2
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
6 #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'):
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
7 bzcat -f '$input' |
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
8 #else:
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
9 cat '$input' |
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
10 #end if
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
11 </token>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
12 <token name="@FQQUAL@">
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
13 <![CDATA[
5
b8e3c0a52f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit 415a5c5de30530910f3039e5fc66aa15103c6f20
iuc
parents: 4
diff changeset
14 #if 'fastqsanger' in $input.ext:
2
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
15 -Q 33
5
b8e3c0a52f33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit 415a5c5de30530910f3039e5fc66aa15103c6f20
iuc
parents: 4
diff changeset
16 #elif 'fastqsolexa' in $input.ext or 'fastqillumina' in $input.ext:
2
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
17 -Q 64
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
18 #end if
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
19 ]]>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
20 </token>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
21 <xml name="requirements">
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
22 <requirements>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
23 <requirement type="package" version="@VERSION@">fastx_toolkit</requirement>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
24 <yield />
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
25 </requirements>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
26 </xml>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
27 <token name="@VERSION@">0.0.14</token>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
28 <token name="@SANGER@">fastqsanger,fastqsanger.gz,fastqsanger.bz2</token>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
29 <token name="@SOLEXA@">fastqsolexa,fastqsolexa.gz,fastqsolexa.bz2</token>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
30 <token name="@ILLUMINA@">fastqillumina,fastqillumina.gz,fastqillumina.bz2</token>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
31 <token name="@FASTQS@">@SANGER@,@SOLEXA@,@ILLUMINA@</token>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
32 <token name="@FASTAS@">fasta,fasta.gz</token>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
33 <xml name="citations">
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
34 <citations>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
35 <citation type="bibtex">
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
36 @UNPUBLISHED{agordon,
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
37 author = "Assaf Gordon",
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
38 title = "FASTQ/A short-reads pre-processing tools",
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
39 year = "2010",
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
40 note = "http://hannonlab.cshl.edu/fastx_toolkit/",
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
41 url = "http://hannonlab.cshl.edu/fastx_toolkit/"}
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
42 </citation>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
43 </citations>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
44 </xml>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
45 <xml name="fastq_input">
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
46 <param name="input" type="data" format="@FASTQS@" label="Input FASTQ file" />
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
47 </xml>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
48 </macros>