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comparison SMART/galaxy/trimSequences.xml @ 15:440ceca58672

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Uploaded
author m-zytnicki
date Mon, 22 Apr 2013 11:08:07 -0400
parents 769e306b7933
children 94ab73e8a190
comparison
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14:c79b9ae3f65f 15:440ceca58672
1 <tool id="trimSequences" name="trim sequences"> 1 <tool id="trimSequences" name="trim sequences">
2 <description>Remove the 5' and/or 3' adaptors of a list of reads.</description> 2 <description>Remove the 5' and/or 3' adapters of a list of reads.</description>
3 <command interpreter="python"> ../Java/Python/trimSequences.py -i $inputFile -f fastq 3 <command interpreter="python"> ../Java/Python/trimSequences.py -i $inputFile -f fastq
4 #if $OptionFPADP.FPADP == "Yes": 4 #if $OptionFPADP.FPADP == "Yes":
5 -5 $OptionFPADP.fivePAdaptor 5 -5 $OptionFPADP.fivePAdaptor
6 #end if 6 #end if
7 #if $OptionTPADP.TPADP == "Yes": 7 #if $OptionTPADP.TPADP == "Yes":
8 -3 $OptionTPADP.threePAdaptor 8 -3 $OptionTPADP.threePAdaptor
9 #end if 9 #end if
10 #if $OptionError.Error == "Yes": 10 -e $errors
11 -e $OptionError.ErrorVal
12 #end if
13
14 $indels 11 $indels
15 $noAdaptor5p $noAdaptorFile5p 12 $noAdaptor5p $noAdaptorFile5p
16 $noAdaptor3p $noAdaptorFile3p 13 $noAdaptor3p $noAdaptorFile3p
17 -o $outputFile 14 -o $outputFile
18 15
21 18
22 <inputs> 19 <inputs>
23 <param name="inputFile" type="data" label="Input fastq File" format="fastq"/> 20 <param name="inputFile" type="data" label="Input fastq File" format="fastq"/>
24 21
25 <conditional name="OptionFPADP"> 22 <conditional name="OptionFPADP">
26 <param name="FPADP" type="select" label="5'adaptor"> 23 <param name="FPADP" type="select" label="5' adapter">
27 <option value="Yes">Yes</option> 24 <option value="Yes">Yes</option>
28 <option value="No" selected="true">No</option> 25 <option value="No" selected="true">No</option>
29 </param> 26 </param>
30 <when value="Yes"> 27 <when value="Yes">
31 <param name="fivePAdaptor" type="text" value="None" /> 28 <param name="fivePAdaptor" type="text" value="None" />
33 <when value="No"> 30 <when value="No">
34 </when> 31 </when>
35 </conditional> 32 </conditional>
36 33
37 <conditional name="OptionTPADP"> 34 <conditional name="OptionTPADP">
38 <param name="TPADP" type="select" label="3'adaptor"> 35 <param name="TPADP" type="select" label="3' adapter">
39 <option value="Yes">Yes</option> 36 <option value="Yes">Yes</option>
40 <option value="No" selected="true">No</option> 37 <option value="No" selected="true">No</option>
41 </param> 38 </param>
42 <when value="Yes"> 39 <when value="Yes">
43 <param name="threePAdaptor" type="text" value="None" /> 40 <param name="threePAdaptor" type="text" value="None" />
44 </when> 41 </when>
45 <when value="No"> 42 <when value="No">
46 </when> 43 </when>
47 </conditional> 44 </conditional>
48 45
49 <conditional name="OptionError"> 46 <param name="errors" type="integer" label="number of errors in percent" value="0" />
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"/> 47 <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 "/> 48 <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 "/>
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 "/> 49 <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 "/>
64
65
66 50
67 </inputs> 51 </inputs>
68 52
69 <outputs> 53 <outputs>
70 <data format="fastq" name="outputFile" label="[trimSequences] Output File"/> 54 <data format="fastq" name="outputFile" label="[trimSequences] Output File"/>
76 </data> 60 </data>
77 </outputs> 61 </outputs>
78 62
79 <help> 63 <help>
80 </help> 64 </help>
65 <tests>
66 <test>
67 <param name="inputFile" value="short_fastq.fastq" />
68 <param name="FPADP" value="Yes"/>
69 <param name="fivePAdaptor" value="AAAA" />
70 <param name="TPADP" value="No"/>
71 <param name ="Error" value="No"/>
72 <param name="indels" value="False"/>
73 <param name ="noAdaptor5p" value="False"/>
74 <param name= "noAdaptor3p" value="False"/>
75 <output name="outputFile" file="exp_trimsequences_short_fastq.fastq" />
76 </test>
77 </tests>
78
79 <help>
80 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.
81 </help>
81 </tool> 82 </tool>