Mercurial > repos > devteam > fastx_trimmer

annotate fastx_trimmer.xml @ 5:b962b4efec19 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_trimmer commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
author iuc
date Wed, 22 Aug 2018 11:04:02 -0400
parents 748363ac106b
children 2ff4f91ff564
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
748363ac106b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit f3f313cb59922b945ac9587ff718b231d0f8db5c
iuc
parents: 3
diff changeset
1 <tool id="cshl_fastx_trimmer" version="1.0.2" name="Trim sequences">
2
97f0b63ae7cf planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
2 <description></description>
3
9081fe62bd56 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
3 <macros>
9081fe62bd56 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
4 <import>macros.xml</import>
9081fe62bd56 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
5 </macros>
9081fe62bd56 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
6 <expand macro="requirements" />
9081fe62bd56 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
9081fe62bd56 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
8 @CATS@ fastx_trimmer -v
9081fe62bd56 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
9 -f $first
9081fe62bd56 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
10 -l $last
9081fe62bd56 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
11 -o '$output'
9081fe62bd56 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
12 @FQQUAL@
5
b962b4efec19 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
iuc
parents: 4
diff changeset
13 @GZIP@
3
9081fe62bd56 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
14 ]]></command>
2
97f0b63ae7cf planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
15 <inputs>
3
9081fe62bd56 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
16 <expand macro="fastx_input" />
9081fe62bd56 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
17 <param name="first" type="integer" value="1" label="First base to keep" />
9081fe62bd56 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
18 <param name="last" type="integer" value="21" label="Last base to keep" />
2
97f0b63ae7cf planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
19 </inputs>
97f0b63ae7cf planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
20 <outputs>
3
9081fe62bd56 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
21 <data name="output" format_source="input" metadata_source="input" />
2
97f0b63ae7cf planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
22 </outputs>
97f0b63ae7cf planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
23 <tests>
97f0b63ae7cf planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
24 <test>
97f0b63ae7cf planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
25 <!-- Trim a FASTA file - remove first four bases (e.g. a barcode) -->
97f0b63ae7cf planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
26 <param name="input" value="fastx_trimmer1.fasta" />
97f0b63ae7cf planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
27 <param name="first" value="5"/>
97f0b63ae7cf planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
28 <param name="last" value="36"/>
97f0b63ae7cf planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
29 <output name="output" ftype="fasta" file="fastx_trimmer1.out" />
97f0b63ae7cf planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
30 </test>
97f0b63ae7cf planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
31 <test>
97f0b63ae7cf planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
32 <!-- Trim a FASTQ file - remove last 9 bases (e.g. keep only miRNA length sequences) -->
97f0b63ae7cf planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
33 <param name="input" value="fastx_trimmer2.fastq" ftype="fastqsolexa"/>
97f0b63ae7cf planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
34 <param name="first" value="1"/>
97f0b63ae7cf planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
35 <param name="last" value="27"/>
97f0b63ae7cf planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
36 <output name="output" ftype="fastqsolexa" file="fastx_trimmer2.out" />
97f0b63ae7cf planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
37 </test>
4
748363ac106b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit f3f313cb59922b945ac9587ff718b231d0f8db5c
iuc
parents: 3
diff changeset
38 <test>
748363ac106b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit f3f313cb59922b945ac9587ff718b231d0f8db5c
iuc
parents: 3
diff changeset
39 <!-- Trim a FASTQ.gz file and output FASTQ.gz -->
748363ac106b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit f3f313cb59922b945ac9587ff718b231d0f8db5c
iuc
parents: 3
diff changeset
40 <param name="input" value="fastx_trimmer2.fastq.gz" ftype="fastqsanger.gz"/>
748363ac106b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit f3f313cb59922b945ac9587ff718b231d0f8db5c
iuc
parents: 3
diff changeset
41 <param name="first" value="1"/>
748363ac106b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit f3f313cb59922b945ac9587ff718b231d0f8db5c
iuc
parents: 3
diff changeset
42 <param name="last" value="27"/>
748363ac106b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit f3f313cb59922b945ac9587ff718b231d0f8db5c
iuc
parents: 3
diff changeset
43 <output name="output" ftype="fastqsanger.gz" decompress="true" file="fastx_trimmer2.out.gz" />
748363ac106b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit f3f313cb59922b945ac9587ff718b231d0f8db5c
iuc
parents: 3
diff changeset
44 </test>
2
97f0b63ae7cf planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
45 </tests>
3
9081fe62bd56 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
46 <help><![CDATA[
0
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
47 **What it does**
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
48
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
49 This tool trims (cut bases from) sequences in a FASTA/Q file.
2
97f0b63ae7cf planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
50
0
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
51 --------
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
52
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
53 **Example**
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
54
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
55 Input Fasta file (with 36 bases in each sequences)::
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
56
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
57 >1-1
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
58 TATGGTCAGAAACCATATGCAGAGCCTGTAGGCACC
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
59 >2-1
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
60 CAGCGAGGCTTTAATGCCATTTGGCTGTAGGCACCA
2
97f0b63ae7cf planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
61
0
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
62 Trimming with First=1 and Last=21, we get a FASTA file with 21 bases in each sequences (starting from the first base)::
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
63
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
64 >1-1
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
65 TATGGTCAGAAACCATATGCA
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
66 >2-1
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
67 CAGCGAGGCTTTAATGCCATT
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
68
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
69 Trimming with First=6 and Last=10, will generate a FASTA file with 5 bases (bases 6,7,8,9,10) in each sequences::
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
70
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
71 >1-1
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
72 TCAGA
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
73 >2-1
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
74 AGGCT
2
97f0b63ae7cf planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
75
0
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
76 ------
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
77
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
78 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
79
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
80 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
3
9081fe62bd56 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
81 ]]></help>
9081fe62bd56 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
82 <expand macro="citations" />
0
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
83 <!-- FASTX-Trimmer is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
a7d22d34ec70 Uploaded tool tarball.
devteam
parents:
diff changeset
84 </tool>