Mercurial > repos > devteam > fastx_artifacts_filter

annotate fastx_artifacts_filter.xml @ 6:902e2ff81393 draft default tip

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_artifacts_filter commit fd099d17eceaa319fbfe429f4725328d88b18c9f
author iuc
date Thu, 10 Aug 2023 06:51:11 +0000
parents 84d56dd32719
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
902e2ff81393 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit fd099d17eceaa319fbfe429f4725328d88b18c9f
iuc
parents: 5
diff changeset
1 <tool id="cshl_fastx_artifacts_filter" version="1.0.1+galaxy@VERSION_SUFFIX@" profile="22.05" name="Remove sequencing artifacts">
2
b664e561b28f planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
2 <description></description>
3
ecfaafccf192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
3 <macros>
ecfaafccf192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
4 <import>macros.xml</import>
ecfaafccf192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
5 </macros>
5
84d56dd32719 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
parents: 4
diff changeset
6 <expand macro="requirements">
84d56dd32719 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
parents: 4
diff changeset
7 <requirement type="package" version="1.0.8">bzip2</requirement>
84d56dd32719 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
parents: 4
diff changeset
8 </expand>
3
ecfaafccf192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
ecfaafccf192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
10 @CATS@ fastx_artifacts_filter
ecfaafccf192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
11 -v
ecfaafccf192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
12 @FQQUAL@
5
84d56dd32719 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
parents: 4
diff changeset
13 @GZIP@ > '$output'
3
ecfaafccf192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
14 ]]></command>
0
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
15
2
b664e561b28f planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
16 <inputs>
3
ecfaafccf192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
17 <expand macro="fastx_input" />
2
b664e561b28f planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
18 </inputs>
b664e561b28f planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
19 <outputs>
3
ecfaafccf192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
20 <data name="output" format_source="input" metadata_source="input" />
2
b664e561b28f planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
21 </outputs>
b664e561b28f planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
22 <tests>
b664e561b28f planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
23 <test>
b664e561b28f planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
24 <!-- Filter FASTA file -->
b664e561b28f planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
25 <param name="input" value="fastx_artifacts1.fasta" />
b664e561b28f planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
26 <output name="output" ftype="fasta" file="fastx_artifacts1.out" />
b664e561b28f planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
27 </test>
b664e561b28f planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
28 <test>
b664e561b28f planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
29 <!-- Filter FASTQ file -->
b664e561b28f planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
30 <param name="input" value="fastx_artifacts2.fastq" ftype="fastqsanger" />
b664e561b28f planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
31 <output name="output" ftype="fastqsanger" file="fastx_artifacts2.out" />
b664e561b28f planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
32 </test>
b664e561b28f planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
33 </tests>
3
ecfaafccf192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
34 <help><![CDATA[
0
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
35 **What it does**
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
36
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
37 This tool filters sequencing artifacts (reads with all but 3 identical bases).
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
38
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
39 --------
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
40
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
41 **The following is an example of sequences which will be filtered out**::
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
42
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
43 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
44 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
45 AAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
46 AAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
47 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
48 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
49 AAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAACACAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
50 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
51 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
52 AAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
53 AAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
54 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
55 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
56 AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
57 AAAAAAAAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
58 AAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
59 AAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
60 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
61 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
62 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
63 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
64 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
65 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
66 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
67 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
68 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
69 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
70 AAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
71 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
72 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
73 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
74 AAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
75 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
76 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
77 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
78 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
79 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
80 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
81 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
82 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
83 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAA
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
84 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAA
2
b664e561b28f planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 1
diff changeset
85
0
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
86 ------
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
87
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
88 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
89
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
90 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
3
ecfaafccf192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
91 ]]></help>
ecfaafccf192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents: 2
diff changeset
92 <expand macro="citations" />
0
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
93 <!-- FASTX-Artifacts-filter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
05c6f70deb92 Uploaded tool tarball.
devteam
parents:
diff changeset
94 </tool>