Mercurial > repos > devteam > fastq_quality_filter
annotate fastq_quality_filter.xml @ 5:ce9cd02d5b88 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
author | iuc |
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date | Thu, 30 Jan 2020 13:29:21 -0500 |
parents | 7b4468117008 |
children | 64e9a6afdd0c |
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ce9cd02d5b88
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
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1 <tool id="cshl_fastq_quality_filter" version="1.0.2+galaxy0" name="Filter by quality"> |
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e41385662e5e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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2 <description></description> |
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43a7370aa010
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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3 <macros> |
43a7370aa010
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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4 <import>macros.xml</import> |
43a7370aa010
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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5 </macros> |
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ce9cd02d5b88
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
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6 <expand macro="requirements"> |
ce9cd02d5b88
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
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7 <requirement type="package" version="1.0.8">bzip2</requirement> |
ce9cd02d5b88
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
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8 </expand> |
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43a7370aa010
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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9 <command detect_errors="exit_code"><![CDATA[ |
43a7370aa010
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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10 @CATS@ fastq_quality_filter |
43a7370aa010
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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11 -q $quality |
43a7370aa010
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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12 -p $percent |
43a7370aa010
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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13 -v |
43a7370aa010
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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14 @FQQUAL@ |
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ce9cd02d5b88
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
iuc
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15 @GZIP@ > '$output' |
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43a7370aa010
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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16 ]]></command> |
0 | 17 |
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e41385662e5e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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18 <inputs> |
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43a7370aa010
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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19 <expand macro="fastq_input" /> |
0 | 20 |
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43a7370aa010
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
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21 <param name="quality" type="integer" value="20" label="Quality cut-off value"/> |
0 | 22 |
3
43a7370aa010
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
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23 <param name="percent" type="integer" value="90" |
43a7370aa010
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
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24 label="Percent of bases in sequence that must have quality equal to / higher than cut-off value" /> |
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e41385662e5e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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25 </inputs> |
e41385662e5e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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26 <outputs> |
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43a7370aa010
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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27 <data name="output" format_source="input" metadata_source="input" /> |
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e41385662e5e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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28 </outputs> |
e41385662e5e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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29 <tests> |
e41385662e5e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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changeset
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30 <test> |
e41385662e5e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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31 <!-- Test1: 100% of bases with quality 33 or higher (pretty steep requirement...) --> |
e41385662e5e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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32 <param name="input" value="fastq_qual_filter1.fastq" ftype="fastqsolexa" /> |
e41385662e5e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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changeset
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33 <param name="quality" value="33"/> |
e41385662e5e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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changeset
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34 <param name="percent" value="100"/> |
e41385662e5e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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35 <output name="output" ftype="fastqsolexa" file="fastq_qual_filter1a.out" /> |
e41385662e5e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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36 </test> |
e41385662e5e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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37 <test> |
e41385662e5e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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38 <!-- Test2: 80% of bases with quality 20 or higher --> |
e41385662e5e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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39 <param name="input" value="fastq_qual_filter1.fastq" ftype="fastqsolexa"/> |
e41385662e5e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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changeset
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40 <param name="quality" value="20"/> |
e41385662e5e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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diff
changeset
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41 <param name="percent" value="80"/> |
e41385662e5e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
1
diff
changeset
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42 <output name="output" ftype="fastqsolexa" file="fastq_qual_filter1b.out" /> |
e41385662e5e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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43 </test> |
e41385662e5e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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44 </tests> |
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43a7370aa010
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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45 <help><![CDATA[ |
0 | 46 **What it does** |
47 | |
48 This tool filters reads based on quality scores. | |
49 | |
50 .. class:: infomark | |
51 | |
52 Using **percent = 100** requires all cycles of all reads to be at least the quality cut-off value. | |
53 | |
54 .. class:: infomark | |
55 | |
56 Using **percent = 50** requires the median quality of the cycles (in each read) to be at least the quality cut-off value. | |
57 | |
58 -------- | |
59 | |
60 Quality score distribution (of all cycles) is calculated for each read. If it is lower than the quality cut-off value - the read is discarded. | |
61 | |
62 | |
63 **Example**:: | |
64 | |
65 @CSHL_4_FC042AGOOII:1:2:214:584 | |
66 GACAATAAAC | |
67 +CSHL_4_FC042AGOOII:1:2:214:584 | |
68 30 30 30 30 30 30 30 30 20 10 | |
69 | |
70 Using **percent = 50** and **cut-off = 30** - This read will not be discarded (the median quality is higher than 30). | |
71 | |
72 Using **percent = 90** and **cut-off = 30** - This read will be discarded (90% of the cycles do no have quality equal to / higher than 30). | |
73 | |
74 Using **percent = 100** and **cut-off = 20** - This read will be discarded (not all cycles have quality equal to / higher than 20). | |
75 | |
76 ------ | |
77 | |
78 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | |
79 | |
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e41385662e5e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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80 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ |
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43a7370aa010
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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81 ]]></help> |
43a7370aa010
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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82 <expand macro="citations" /> |
0 | 83 <!-- FASTQ-Quality-Filter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> |
84 </tool> |