Mercurial > repos > yqiancolumbia > ctk_test
comparison removeLowQualityBases.xml @ 0:0475e4175855 draft default tip
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
author | yqiancolumbia |
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date | Mon, 30 Apr 2018 05:25:11 -0400 |
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1 <tool id="removeLowQualityBases" name="Remove low quality bases"> | |
2 <description></description> | |
3 | |
4 <command> | |
5 fastq_quality_trimmer -i $input -v -l $MinimumLength $CompressOutput -t $Qualitythreshold -o $output | |
6 </command> | |
7 | |
8 <inputs> | |
9 <param name="input" type="data" format="fastq" label="Input FASTQ file"/> | |
10 <param name="Qualitythreshold" type="integer" value="5" label="Quality threshold - nucleotides with lower quality will be trimmed (from the end of the sequence)"/> | |
11 <param name="MinimumLength" type="integer" value="29" label="Minimum length - sequences shorter than this (after trimming) will be discarded (0 = no minimum length)"/> | |
12 <param name="CompressOutput" type="boolean" truevalue="-z" falsevalue="" checked="no" label="Compress output with GZIP"/> | |
13 </inputs> | |
14 | |
15 <outputs> | |
16 <data name="output" format="fastq" /> | |
17 </outputs> | |
18 <help> | |
19 | |
20 .. class:: infomark | |
21 | |
22 **What this tool does** | |
23 | |
24 This tool (fastq_quality_trimmer) will remove extremely low quality bases (e.g. score less than 5). | |
25 | |
26 It will take as input FASTQ files and output FASTQ files with low quality bases removed. | |
27 | |
28 It is a part of the Fastx Toolkit. | |
29 | |
30 ----- | |
31 | |
32 **Parameter suggestion for minimum length** | |
33 | |
34 * For standard CLIP: discard sequences shorter than 20 nucleotides. | |
35 * For BrdU CLIP: discard sequences shorter than 29 nucleotides. | |
36 | |
37 </help> | |
38 | |
39 </tool> |