Mercurial > repos > devteam > fastx_artifacts_filter
annotate fastx_artifacts_filter.xml @ 4:567d5b3c52b1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
author | iuc |
---|---|
date | Wed, 22 Aug 2018 11:05:01 -0400 |
parents | dd3737e40dce |
children | d5e9e83cd3d8 |
rev | line source |
---|---|
3
dd3737e40dce
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
|
1 <tool id="cshl_fastx_artifacts_filter" version="1.0.1" name="Remove sequencing artifacts"> |
2
09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
1
diff
changeset
|
2 <description></description> |
3
dd3737e40dce
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> |
dd3737e40dce
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> |
dd3737e40dce
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> |
dd3737e40dce
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
|
6 <expand macro="requirements" /> |
dd3737e40dce
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
|
7 <command detect_errors="exit_code"><![CDATA[ |
dd3737e40dce
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
|
8 @CATS@ fastx_artifacts_filter |
dd3737e40dce
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 -v |
dd3737e40dce
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 -o '$output' |
dd3737e40dce
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 @FQQUAL@ |
4
567d5b3c52b1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
iuc
parents:
3
diff
changeset
|
12 @GZIP@ |
3
dd3737e40dce
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
|
13 ]]></command> |
0 | 14 |
2
09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
1
diff
changeset
|
15 <inputs> |
3
dd3737e40dce
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
|
16 <expand macro="fastx_input" /> |
2
09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
1
diff
changeset
|
17 </inputs> |
09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
1
diff
changeset
|
18 <outputs> |
3
dd3737e40dce
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
|
19 <data name="output" format_source="input" metadata_source="input" /> |
2
09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
1
diff
changeset
|
20 </outputs> |
09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
1
diff
changeset
|
21 <tests> |
09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
1
diff
changeset
|
22 <test> |
09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
1
diff
changeset
|
23 <!-- Filter FASTA file --> |
09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
1
diff
changeset
|
24 <param name="input" value="fastx_artifacts1.fasta" /> |
09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
1
diff
changeset
|
25 <output name="output" ftype="fasta" file="fastx_artifacts1.out" /> |
09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
1
diff
changeset
|
26 </test> |
09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
1
diff
changeset
|
27 <test> |
09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
1
diff
changeset
|
28 <!-- Filter FASTQ file --> |
09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
1
diff
changeset
|
29 <param name="input" value="fastx_artifacts2.fastq" ftype="fastqsanger" /> |
09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
1
diff
changeset
|
30 <output name="output" ftype="fastqsanger" file="fastx_artifacts2.out" /> |
09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
1
diff
changeset
|
31 </test> |
09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
1
diff
changeset
|
32 </tests> |
3
dd3737e40dce
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
|
33 <help><![CDATA[ |
0 | 34 **What it does** |
35 | |
36 This tool filters sequencing artifacts (reads with all but 3 identical bases). | |
37 | |
38 -------- | |
39 | |
40 **The following is an example of sequences which will be filtered out**:: | |
41 | |
42 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
43 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
44 AAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
45 AAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
46 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
47 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
48 AAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAACACAAAAAA | |
49 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
50 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
51 AAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
52 AAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
53 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
54 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC | |
55 AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
56 AAAAAAAAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
57 AAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAA | |
58 AAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
59 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAA | |
60 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
61 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAA | |
62 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACA | |
63 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAA | |
64 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAA | |
65 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAA | |
66 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAA | |
67 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAA | |
68 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAA | |
69 AAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
70 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAA | |
71 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
72 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAA | |
73 AAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
74 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAA | |
75 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
76 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAA | |
77 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAA | |
78 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAA | |
79 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
80 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
81 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAA | |
82 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAA | |
83 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAA | |
2
09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
1
diff
changeset
|
84 |
0 | 85 ------ |
86 | |
87 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | |
88 | |
89 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ | |
3
dd3737e40dce
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
|
90 ]]></help> |
dd3737e40dce
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 <expand macro="citations" /> |
0 | 92 <!-- FASTX-Artifacts-filter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> |
93 </tool> |