Mercurial > repos > devteam > fastx_nucleotides_distribution

annotate macros.xml @ 5:ad116ae3f4d9 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_nucleotides_distribution commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
author iuc
date Thu, 30 Jan 2020 13:30:27 -0500
parents 21796f46e0ba
children b6b54ba71bd8
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
2 <macros>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
3 <token name="@CATS@">
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
4 #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
5
ad116ae3f4d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
parents: 4
diff changeset
5 gunzip -c -f '$input' |
4
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
6 #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'):
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
7 bzcat -f '$input' |
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
8 #else:
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
9 cat '$input' |
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
10 #end if
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
11 </token>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
12 <token name="@FQQUAL@">
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
13 <![CDATA[
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
14 #if $input.is_of_type('fastqsanger', 'fastqsanger.gz', 'fastqsanger.bz2'):
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
15 -Q 33
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
16 #elif $input.is_of_type('fastqsolexa', 'fastqsolexa.gz', 'fastqsolexa.bz2', 'fastqillumina', 'fastqillumina.gz', 'fastqillumina.bz2'):
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
17 -Q 64
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
18 #end if
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
19 ]]>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
20 </token>
5
ad116ae3f4d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
parents: 4
diff changeset
21 <token name="@GZIP@">
ad116ae3f4d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
parents: 4
diff changeset
22 <![CDATA[
ad116ae3f4d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
parents: 4
diff changeset
23 #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
ad116ae3f4d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
parents: 4
diff changeset
24 | gzip -c
ad116ae3f4d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
parents: 4
diff changeset
25 #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'):
ad116ae3f4d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
parents: 4
diff changeset
26 | bzip2 -c
ad116ae3f4d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
parents: 4
diff changeset
27 #end if
ad116ae3f4d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
parents: 4
diff changeset
28 ]]>
ad116ae3f4d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
parents: 4
diff changeset
29 </token>
4
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
30 <xml name="requirements">
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
31 <requirements>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
32 <requirement type="package" version="@VERSION@">fastx_toolkit</requirement>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
33 <yield />
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
34 </requirements>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
35 </xml>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
36 <token name="@VERSION@">0.0.14</token>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
37 <token name="@SANGER@">fastqsanger,fastqsanger.gz,fastqsanger.bz2</token>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
38 <token name="@SOLEXA@">fastqsolexa,fastqsolexa.gz,fastqsolexa.bz2</token>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
39 <token name="@ILLUMINA@">fastqillumina,fastqillumina.gz,fastqillumina.bz2</token>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
40 <token name="@FASTQS@">@SANGER@,@SOLEXA@,@ILLUMINA@</token>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
41 <token name="@FASTAS@">fasta,fasta.gz</token>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
42 <xml name="citations">
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
43 <citations>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
44 <citation type="bibtex">
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
45 @UNPUBLISHED{agordon,
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
46 author = "Assaf Gordon",
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
47 title = "FASTQ/A short-reads pre-processing tools",
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
48 year = "2010",
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
49 note = "http://hannonlab.cshl.edu/fastx_toolkit/",
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
50 url = "http://hannonlab.cshl.edu/fastx_toolkit/"}
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
51 </citation>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
52 </citations>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
53 </xml>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
54 <xml name="fasta_input">
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
55 <param name="input" type="data" format="@FASTAS@" label="Input FASTA file" />
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
56 </xml>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
57 <xml name="fastq_input">
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
58 <param name="input" type="data" format="@FASTQS@" label="Input FASTQ file" />
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
59 </xml>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
60 <xml name="fastx_input">
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
61 <param name="input" type="data" format="@FASTAS@,@FASTQS@" label="Input file in FASTA or FASTQ format" />
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
62 </xml>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
63 </macros>