Mercurial > repos > devteam > fastx_artifacts_filter
annotate fastx_artifacts_filter.xml @ 5:d5e9e83cd3d8 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
author | iuc |
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date | Thu, 30 Jan 2020 13:29:54 -0500 |
parents | 567d5b3c52b1 |
children | 529bccd5e4a1 |
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d5e9e83cd3d8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
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1 <tool id="cshl_fastx_artifacts_filter" version="1.0.1+galaxy0" name="Remove sequencing artifacts"> |
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09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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2 <description></description> |
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dd3737e40dce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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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
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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
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5 </macros> |
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d5e9e83cd3d8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
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6 <expand macro="requirements"> |
d5e9e83cd3d8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
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7 <requirement type="package" version="1.0.8">bzip2</requirement> |
d5e9e83cd3d8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
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8 </expand> |
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dd3737e40dce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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9 <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
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10 @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
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11 -v |
dd3737e40dce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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12 @FQQUAL@ |
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d5e9e83cd3d8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
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13 @GZIP@ > '$output' |
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dd3737e40dce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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14 ]]></command> |
0 | 15 |
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09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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16 <inputs> |
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dd3737e40dce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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17 <expand macro="fastx_input" /> |
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09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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18 </inputs> |
09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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19 <outputs> |
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dd3737e40dce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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20 <data name="output" format_source="input" metadata_source="input" /> |
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09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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21 </outputs> |
09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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22 <tests> |
09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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23 <test> |
09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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24 <!-- 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
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25 <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
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26 <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
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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
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changeset
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28 <test> |
09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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29 <!-- 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
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30 <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
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changeset
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31 <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
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32 </test> |
09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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33 </tests> |
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dd3737e40dce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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34 <help><![CDATA[ |
0 | 35 **What it does** |
36 | |
37 This tool filters sequencing artifacts (reads with all but 3 identical bases). | |
38 | |
39 -------- | |
40 | |
41 **The following is an example of sequences which will be filtered out**:: | |
42 | |
43 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
44 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
45 AAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
46 AAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
47 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
48 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
49 AAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAACACAAAAAA | |
50 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
51 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
52 AAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
53 AAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
54 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
55 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC | |
56 AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
57 AAAAAAAAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
58 AAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAA | |
59 AAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
60 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAA | |
61 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
62 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAA | |
63 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACA | |
64 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAA | |
65 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAA | |
66 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAA | |
67 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAA | |
68 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAA | |
69 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAA | |
70 AAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
71 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAA | |
72 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
73 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAA | |
74 AAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
75 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAA | |
76 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
77 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAA | |
78 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAA | |
79 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAA | |
80 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
81 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
82 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAA | |
83 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAA | |
84 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAA | |
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09070cacefd8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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85 |
0 | 86 ------ |
87 | |
88 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | |
89 | |
90 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ | |
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dd3737e40dce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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91 ]]></help> |
dd3737e40dce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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92 <expand macro="citations" /> |
0 | 93 <!-- FASTX-Artifacts-filter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> |
94 </tool> |