Mercurial > repos > devteam > fastx_reverse_complement

annotate macros.xml @ 5:a4167b7c73cb 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/fastx_reverse_complement commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
author iuc
date Thu, 30 Jan 2020 18:28:08 +0000
parents 64203edc4ec1
children 80aff5c453b0
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
2 <macros>
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
3 <token name="@CATS@">
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
4 #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
4
64203edc4ec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
iuc
parents: 3
diff changeset
5 gunzip -c -f '$input' |
3
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
6 #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'):
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
7 bzcat -f '$input' |
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
8 #else:
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
9 cat '$input' |
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
10 #end if
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
11 </token>
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
12 <token name="@FQQUAL@">
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
13 <![CDATA[
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
14 #if $input.is_of_type('fastqsanger', 'fastqsanger.gz', 'fastqsanger.bz2'):
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
15 -Q 33
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
16 #elif $input.is_of_type('fastqsolexa', 'fastqsolexa.gz', 'fastqsolexa.bz2', 'fastqillumina', 'fastqillumina.gz', 'fastqillumina.bz2'):
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
17 -Q 64
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
18 #end if
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
19 ]]>
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
20 </token>
4
64203edc4ec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
iuc
parents: 3
diff changeset
21 <token name="@GZIP@">
64203edc4ec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
iuc
parents: 3
diff changeset
22 <![CDATA[
64203edc4ec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
iuc
parents: 3
diff changeset
23 #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
5
a4167b7c73cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
parents: 4
diff changeset
24 | gzip -c
a4167b7c73cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
parents: 4
diff changeset
25 #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'):
a4167b7c73cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
parents: 4
diff changeset
26 | bzip2 -c
4
64203edc4ec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
iuc
parents: 3
diff changeset
27 #end if
64203edc4ec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
iuc
parents: 3
diff changeset
28 ]]>
64203edc4ec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
iuc
parents: 3
diff changeset
29 </token>
3
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
30 <xml name="requirements">
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
31 <requirements>
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
32 <requirement type="package" version="@VERSION@">fastx_toolkit</requirement>
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
33 <yield />
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
34 </requirements>
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
35 </xml>
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
36 <token name="@VERSION@">0.0.14</token>
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
37 <token name="@SANGER@">fastqsanger,fastqsanger.gz,fastqsanger.bz2</token>
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
38 <token name="@SOLEXA@">fastqsolexa,fastqsolexa.gz,fastqsolexa.bz2</token>
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
39 <token name="@ILLUMINA@">fastqillumina,fastqillumina.gz,fastqillumina.bz2</token>
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
40 <token name="@FASTQS@">@SANGER@,@SOLEXA@,@ILLUMINA@</token>
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
41 <token name="@FASTAS@">fasta,fasta.gz</token>
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
42 <xml name="citations">
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
43 <citations>
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
44 <citation type="bibtex">
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
45 @UNPUBLISHED{agordon,
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
46 author = "Assaf Gordon",
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
47 title = "FASTQ/A short-reads pre-processing tools",
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
48 year = "2010",
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
49 note = "http://hannonlab.cshl.edu/fastx_toolkit/",
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
50 url = "http://hannonlab.cshl.edu/fastx_toolkit/"}
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
51 </citation>
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
52 </citations>
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
53 </xml>
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
54 <xml name="fasta_input">
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
55 <param name="input" type="data" format="@FASTAS@" label="Input FASTA file" />
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
56 </xml>
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
57 <xml name="fastq_input">
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
58 <param name="input" type="data" format="@FASTQS@" label="Input FASTQ file" />
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
59 </xml>
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
60 <xml name="fastx_input">
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
61 <param name="input" type="data" format="@FASTAS@,@FASTQS@" label="Input file in FASTA or FASTQ format" />
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
62 </xml>
9d06c848a628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
63 </macros>