annotate macros.xml @ 2:54053ea6c77e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 13:26:24 -0400
parents
children 045f0e1043f7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
2 <macros>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
3 <token name="@CATS@">
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
4 #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
5 zcat -f '$input' |
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
6 #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'):
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
7 bzcat -f '$input' |
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
8 #else:
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
9 cat '$input' |
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
10 #end if
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
11 </token>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
12 <token name="@FQQUAL@">
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
13 <![CDATA[
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
14 #if $input.is_of_type('fastqsanger', 'fastqsanger.gz', 'fastqsanger.bz2'):
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
15 -Q 33
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
16 #elif $input.is_of_type('fastqsolexa', 'fastqsolexa.gz', 'fastqsolexa.bz2', 'fastqillumina', 'fastqillumina.gz', 'fastqillumina.bz2'):
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
17 -Q 64
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
18 #end if
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
19 ]]>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
20 </token>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
21 <xml name="requirements">
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
22 <requirements>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
23 <requirement type="package" version="@VERSION@">fastx_toolkit</requirement>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
24 <yield />
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
25 </requirements>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
26 </xml>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
27 <token name="@VERSION@">0.0.14</token>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
28 <token name="@SANGER@">fastqsanger,fastqsanger.gz,fastqsanger.bz2</token>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
29 <token name="@SOLEXA@">fastqsolexa,fastqsolexa.gz,fastqsolexa.bz2</token>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
30 <token name="@ILLUMINA@">fastqillumina,fastqillumina.gz,fastqillumina.bz2</token>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
31 <token name="@FASTQS@">@SANGER@,@SOLEXA@,@ILLUMINA@</token>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
32 <token name="@FASTAS@">fasta,fasta.gz</token>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
33 <xml name="citations">
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
34 <citations>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
35 <citation type="bibtex">
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
36 @UNPUBLISHED{agordon,
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
37 author = "Assaf Gordon",
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
38 title = "FASTQ/A short-reads pre-processing tools",
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
39 year = "2010",
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
40 note = "http://hannonlab.cshl.edu/fastx_toolkit/",
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
41 url = "http://hannonlab.cshl.edu/fastx_toolkit/"}
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
42 </citation>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
43 </citations>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
44 </xml>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
45 <xml name="fasta_input">
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
46 <param name="input" type="data" format="@FASTAS@" label="Input FASTA file" />
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
47 </xml>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
48 <xml name="fastq_input">
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
49 <param name="input" type="data" format="@FASTQS@" label="Input FASTQ file" />
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
50 </xml>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
51 <xml name="fastx_input">
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
52 <param name="input" type="data" format="@FASTAS@,@FASTQS@" label="Input file in FASTA or FASTQ format" />
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
53 </xml>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
54 </macros>