Mercurial > repos > devteam > fastq_to_fasta

annotate fastq_to_fasta.xml @ 2:44ed3f74ea7a 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 bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 12:50:22 -0400
parents 3f358f73d45e
children 4498e994e31b
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: 1
diff changeset
1 <tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA" version="1.0.1">
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
2 <description>converter from FASTX-toolkit</description>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
3 <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: 1
diff changeset
4 <import>macros.xml</import>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
5 </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: 1
diff changeset
6 <expand macro="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: 1
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
8 @CATS@ fastq_to_fasta
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
9 $SKIPN
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
10 $RENAMESEQ
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
11 -o '$output'
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
12 -v @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: 1
diff changeset
13 ]]></command>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
14 <inputs>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
15 <expand macro="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: 1
diff changeset
16 <param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases ">
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
17 <option value="">yes</option>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
18 <option value="-n">no</option>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
19 </param>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
20 <param name="RENAMESEQ" type="select" label="Rename sequence names in output file (reduces file size)">
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
21 <option value="-r">yes</option>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
22 <option value="">no</option>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
23 </param>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
24 </inputs>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
25 <outputs>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
26 <data name="output" format="fasta" metadata_source="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: 1
diff changeset
27 </outputs>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
28 <tests>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
29 <test>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
30 <!-- FASTQ-To-FASTA, keep N, don't rename -->
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
31 <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
32 <param name="SKIPN" value=""/>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
33 <param name="RENAMESEQ" value=""/>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
34 <output name="output" file="fastq_to_fasta1a.out" />
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
35 </test>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
36 <test>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
37 <!-- FASTQ-To-FASTA, discard N, rename -->
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
38 <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
39 <param name="SKIPN" value="no"/>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
40 <param name="RENAMESEQ" value="yes"/>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
41 <output name="output" file="fastq_to_fasta1b.out" />
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
42 </test>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
43 <test>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
44 <!-- FASTQ-To-FASTA, discard N, rename -->
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
45 <param name="input" value="fastq_to_fasta-in2.fastq" ftype="fastqsanger" />
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
46 <param name="SKIPN" value="no"/>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
47 <param name="RENAMESEQ" value="yes"/>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
48 <output name="output" file="fastq_to_fasta-out2.out" />
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
49 </test>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
50 </tests>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
51 <help><![CDATA[
0
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
52 **What it does**
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
53
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
54 This tool converts data from Solexa format to FASTA format (scroll down for format description).
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
55
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
56 --------
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
57
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
58 **Example**
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
59
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
60 The following data in Solexa-FASTQ format::
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
61
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
62 @CSHL_4_FC042GAMMII_2_1_517_596
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
63 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
64 +CSHL_4_FC042GAMMII_2_1_517_596
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
65 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
1
3f358f73d45e planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
66
0
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
67 Will be converted to FASTA (with 'rename sequence names' = NO)::
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
68
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
69 >CSHL_4_FC042GAMMII_2_1_517_596
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
70 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
1
3f358f73d45e planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
71
0
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
72 Will be converted to FASTA (with 'rename sequence names' = YES)::
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
73
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
74 >1
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
75 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
1
3f358f73d45e planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
76
0
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
77 ------
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
78
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
79 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
80
1
3f358f73d45e planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 0
diff changeset
81 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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: 1
diff changeset
82 ]]></help>
44ed3f74ea7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 1
diff changeset
83 <expand macro="citations" />
0
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
84 <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
9d253ab73d8b Uploaded tool tarball.
devteam
parents:
diff changeset
85 </tool>