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comparison SMART/galaxy/trimSequences.xml @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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30:5677346472b5 31:0ab839023fe4
1 <tool id="trimSequences" name="trim sequences"> 1 <tool id="trimSequences" name="trim sequences">
2 <description>Remove the 5' and/or 3' adapters of a list of reads.</description> 2 <description>Remove the 5' and/or 3' adaptors of a list of reads.</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
6 <command interpreter="python"> ../Java/Python/trimSequences.py -i $inputFile -f fastq 3 <command interpreter="python"> ../Java/Python/trimSequences.py -i $inputFile -f fastq
7 #if $OptionFPADP.FPADP == "Yes": 4 #if $OptionFPADP.FPADP == "Yes":
8 -5 $OptionFPADP.fivePAdaptor 5 -5 $OptionFPADP.fivePAdaptor
9 #end if 6 #end if
10 #if $OptionTPADP.TPADP == "Yes": 7 #if $OptionTPADP.TPADP == "Yes":
11 -3 $OptionTPADP.threePAdaptor 8 -3 $OptionTPADP.threePAdaptor
12 #end if 9 #end if
13 -e $errors 10 #if $OptionError.Error == "Yes":
11 -e $OptionError.ErrorVal
12 #end if
13
14 $indels 14 $indels
15 $noAdaptor5p $noAdaptorFile5p 15 $noAdaptor5p $noAdaptorFile5p
16 $noAdaptor3p $noAdaptorFile3p 16 $noAdaptor3p $noAdaptorFile3p
17 -o $outputFile 17 -o $outputFile
18 18
21 21
22 <inputs> 22 <inputs>
23 <param name="inputFile" type="data" label="Input fastq File" format="fastq"/> 23 <param name="inputFile" type="data" label="Input fastq File" format="fastq"/>
24 24
25 <conditional name="OptionFPADP"> 25 <conditional name="OptionFPADP">
26 <param name="FPADP" type="select" label="5' adapter"> 26 <param name="FPADP" type="select" label="5'adaptor">
27 <option value="Yes">Yes</option> 27 <option value="Yes">Yes</option>
28 <option value="No" selected="true">No</option> 28 <option value="No" selected="true">No</option>
29 </param> 29 </param>
30 <when value="Yes"> 30 <when value="Yes">
31 <param name="fivePAdaptor" type="text" value="None" /> 31 <param name="fivePAdaptor" type="text" value="None" />
33 <when value="No"> 33 <when value="No">
34 </when> 34 </when>
35 </conditional> 35 </conditional>
36 36
37 <conditional name="OptionTPADP"> 37 <conditional name="OptionTPADP">
38 <param name="TPADP" type="select" label="3' adapter"> 38 <param name="TPADP" type="select" label="3'adaptor">
39 <option value="Yes">Yes</option> 39 <option value="Yes">Yes</option>
40 <option value="No" selected="true">No</option> 40 <option value="No" selected="true">No</option>
41 </param> 41 </param>
42 <when value="Yes"> 42 <when value="Yes">
43 <param name="threePAdaptor" type="text" value="None" /> 43 <param name="threePAdaptor" type="text" value="None" />
44 </when> 44 </when>
45 <when value="No"> 45 <when value="No">
46 </when> 46 </when>
47 </conditional> 47 </conditional>
48 48
49 <param name="errors" type="integer" label="number of errors in percent" value="0" /> 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
50 <param name="indels" type="boolean" truevalue="-d" falsevalue="" checked="false" label="indels option" help="also accept indels"/> 61 <param name="indels" type="boolean" truevalue="-d" falsevalue="" checked="false" label="indels option" help="also accept indels"/>
51 <param name="noAdaptor5p" type="boolean" truevalue="-n" falsevalue="" checked="false" label="noAdaptor 5' option" help="file name where to print sequences with no 5' adapter "/> 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 "/>
52 <param name="noAdaptor3p" type="boolean" truevalue="-m" falsevalue="" checked="false" label="noAdaptor 3' option" help="file name where to print sequences with no 3' adapter "/> 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
53 66
54 </inputs> 67 </inputs>
55 68
56 <outputs> 69 <outputs>
57 <data format="fastq" name="outputFile" label="[trim sequences] output file"/> 70 <data format="fastq" name="outputFile" label="[trimSequences] Output File"/>
58 <data name="noAdaptorFile5p" format="fastq" label="[trim sequences] noAdapter5p file"> 71 <data name="noAdaptorFile5p" format="fastq" label="[trimSequences] noAdaptor5p File">
59 <filter>noAdaptor5p</filter> 72 <filter>noAdaptor5p</filter>
60 </data> 73 </data>
61 <data name="noAdaptorFile3p" format="fastq" label="[trim sequences] noAdapter3p file"> 74 <data name="noAdaptorFile3p" format="fastq" label="[trimSequences] noAdaptor3p File">
62 <filter>noAdaptor3p</filter> 75 <filter>noAdaptor3p</filter>
63 </data> 76 </data>
64 </outputs> 77 </outputs>
65 78
66 <help> 79 <help>
67 This function removes the adaptor from the 5' or 3' end of your reads. It can even recognize the adaptators which are partially present. You can specify whether you are ready to accept indels or not.
68 </help> 80 </help>
69 <tests> 81 <tests>
70 <test> 82 <test>
71 <param name="inputFile" value="short_fastq.fastq" /> 83 <param name="inputFile" value="short_fastq.fastq" />
72 <param name="FPADP" value="Yes"/> 84 <param name="FPADP" value="Yes"/>
73 <param name="fivePAdaptor" value="AAAA" /> 85 <param name="fivePAdaptor" value="AAAA" />
74 <param name="TPADP" value="No"/> 86 <param name="TPADP" value="No"/>
75 <param name="errors" value="1"/> 87 <param name ="Error" value="No"/>
76 <param name="indels" value="False"/> 88 <param name="indels" value="False"/>
77 <param name="noAdaptor5p" value="False"/> 89 <param name ="noAdaptor5p" value="False"/>
78 <param name= "noAdaptor3p" value="False"/> 90 <param name= "noAdaptor3p" value="False"/>
79 <output name="outputFile" file="exp_trimsequences_short_fastq.fastq" /> 91 <output name="outputFile" file="exp_trimsequences_short_fastq.fastq" />
80 </test> 92 </test>
81 </tests> 93 </tests>
82 </tool> 94 </tool>