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comparison SMART/galaxy/trimSequences.xml @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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children 440ceca58672
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5:ea3082881bf8 6:769e306b7933
1 <tool id="trimSequences" name="trim sequences">
2 <description>Remove the 5' and/or 3' adaptors of a list of reads.</description>
3 <command interpreter="python"> ../Java/Python/trimSequences.py -i $inputFile -f fastq
4 #if $OptionFPADP.FPADP == "Yes":
5 -5 $OptionFPADP.fivePAdaptor
6 #end if
7 #if $OptionTPADP.TPADP == "Yes":
8 -3 $OptionTPADP.threePAdaptor
9 #end if
10 #if $OptionError.Error == "Yes":
11 -e $OptionError.ErrorVal
12 #end if
13
14 $indels
15 $noAdaptor5p $noAdaptorFile5p
16 $noAdaptor3p $noAdaptorFile3p
17 -o $outputFile
18
19 </command>
20
21
22 <inputs>
23 <param name="inputFile" type="data" label="Input fastq File" format="fastq"/>
24
25 <conditional name="OptionFPADP">
26 <param name="FPADP" type="select" label="5'adaptor">
27 <option value="Yes">Yes</option>
28 <option value="No" selected="true">No</option>
29 </param>
30 <when value="Yes">
31 <param name="fivePAdaptor" type="text" value="None" />
32 </when>
33 <when value="No">
34 </when>
35 </conditional>
36
37 <conditional name="OptionTPADP">
38 <param name="TPADP" type="select" label="3'adaptor">
39 <option value="Yes">Yes</option>
40 <option value="No" selected="true">No</option>
41 </param>
42 <when value="Yes">
43 <param name="threePAdaptor" type="text" value="None" />
44 </when>
45 <when value="No">
46 </when>
47 </conditional>
48
49 <conditional name="OptionError">
50 <param name="Error" type="select" label="number of errors in percent">
51 <option value="Yes">Yes</option>
52 <option value="No" selected="true">No</option>
53 </param>
54 <when value="Yes">
55 <param name="ErrorVal" type="integer" value="0" />
56 </when>
57 <when value="No">
58 </when>
59 </conditional>
60
61 <param name="indels" type="boolean" truevalue="-d" falsevalue="" checked="false" label="indels option" help="also accept indels"/>
62 <param name="noAdaptor5p" type="boolean" truevalue="-n" falsevalue="" checked="false" label="noAdaptor 5' option" help="file name where to print sequences with no 5' adaptor "/>
63 <param name="noAdaptor3p" type="boolean" truevalue="-m" falsevalue="" checked="false" label="noAdaptor 3' option" help="file name where to print sequences with no 3' adaptor "/>
64
65
66
67 </inputs>
68
69 <outputs>
70 <data format="fastq" name="outputFile" label="[trimSequences] Output File"/>
71 <data name="noAdaptorFile5p" format="fastq" label="[trimSequences] noAdaptor5p File">
72 <filter>noAdaptor5p</filter>
73 </data>
74 <data name="noAdaptorFile3p" format="fastq" label="[trimSequences] noAdaptor3p File">
75 <filter>noAdaptor3p</filter>
76 </data>
77 </outputs>
78
79 <help>
80 </help>
81 </tool>