Mercurial > repos > yqiancolumbia > ctk_test
comparison trimming3.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="trimming3" name="Trim 3' adapter"> | |
2 <description></description> | |
3 | |
4 <command> | |
5 fastx_clipper -a $Adapter -l $DiscardShort $DiscardNonclipped $DiscardClipped $AdapterOnly $KeepUnknown | |
6 #if $minAdapterAlignment.Mrequired =="yes": | |
7 -M $minAdapterAlignment.Min | |
8 #end if | |
9 -v -i $input 2>/dev/null | fastq_quality_trimmer -v -l $DiscardShort $CompressOutput -t $Qualitythreshold -o $output | |
10 </command> | |
11 | |
12 <inputs> | |
13 <param name="input" type="data" format="fastq" label="Input FASTQ file"/> | |
14 | |
15 <param name="Adapter" type="text" value="" label="Adapter sequence (the 3' adapter will vary for different CLIP protocol variations)"/> | |
16 <param name="DiscardShort" type="integer" value="" label="Discard sequences shorter than N nucleotides (see help below for parameter suggestion)"/> | |
17 <param name="DiscardNonclipped" type="boolean" truevalue="-c" falsevalue="" checked="no" label="Discard non-trimmed sequences (i.e. - keep only sequences which contained the adapter)" /> | |
18 <param name="DiscardClipped" type="boolean" truevalue="-C" falsevalue="" checked="no" label="Discard trimmed sequences (i.e. - keep only sequences which did not contained the adapter)" /> | |
19 <param name="AdapterOnly" type="boolean" truevalue="-k" falsevalue="" checked="no" label="Report Adapter-Only sequences"/> | |
20 <param name="KeepUnknown" type="boolean" truevalue="-n" falsevalue="" checked="yes" label="Keep sequences with unknown nucleotides"/> | |
21 <conditional name="minAdapterAlignment"> | |
22 <param name="Mrequired" type="select" label="Require minimum adapter alignment length of N. If less than N nucleotides aligned with the adapter - don't trim it."> | |
23 <option value="yes">Yes</option> | |
24 <option value="no" selected="True">No</option> | |
25 </param> | |
26 <when value="yes"> | |
27 <param name="Min" type="integer" value="" label="Input the length"/> | |
28 </when> | |
29 <when value="no"> | |
30 </when> | |
31 </conditional> | |
32 <param name="Qualitythreshold" type="integer" value="5" label="Quality threshold - nucleotides with lower quality will be trimmed (from the end of the sequence)"/> | |
33 <param name="CompressOutput" type="boolean" truevalue="-z" falsevalue="" checked="no" label="Compress output with GZIP"/> | |
34 | |
35 </inputs> | |
36 | |
37 <outputs> | |
38 <data name="output" format="fastq" label="Trim 3' adapter on ${on_string} "/> | |
39 </outputs> | |
40 <help> | |
41 | |
42 .. class:: infomark | |
43 | |
44 **What this tool does** | |
45 | |
46 For long reads that are common now, collapsing before trimming is not very helpful. Therefore, trim the 3' adapter first. | |
47 | |
48 This tool (fastx_clipper and fastq_quality_trimmer) will take as input FASTQ files and output FASTQ files with 3' adapters and extremely low quality bases (e.g. score less than 5) removed. | |
49 | |
50 It is a part of FASTX Toolkit. | |
51 | |
52 ----- | |
53 | |
54 **Parameter suggestion for discarding sequences** | |
55 | |
56 * For standard CLIP: discard sequences shorter than 20 nucleotides. | |
57 * For BrdU CLIP: discard sequences shorter than 29 nucleotides. | |
58 | |
59 </help> | |
60 | |
61 </tool> |