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comparison SMART/galaxy/trimSequences.xml @ 18:94ab73e8a190

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Uploaded
author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
parents 440ceca58672
children 0ab839023fe4
comparison
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17:b0e8584489e6 18:94ab73e8a190
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' adapters of a list of reads.</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
3 <command interpreter="python"> ../Java/Python/trimSequences.py -i $inputFile -f fastq 6 <command interpreter="python"> ../Java/Python/trimSequences.py -i $inputFile -f fastq
4 #if $OptionFPADP.FPADP == "Yes": 7 #if $OptionFPADP.FPADP == "Yes":
5 -5 $OptionFPADP.fivePAdaptor 8 -5 $OptionFPADP.fivePAdaptor
6 #end if 9 #end if
7 #if $OptionTPADP.TPADP == "Yes": 10 #if $OptionTPADP.TPADP == "Yes":
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 "/> 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 "/>
50 53
51 </inputs> 54 </inputs>
52 55
53 <outputs> 56 <outputs>
54 <data format="fastq" name="outputFile" label="[trimSequences] Output File"/> 57 <data format="fastq" name="outputFile" label="[trim sequences] output file"/>
55 <data name="noAdaptorFile5p" format="fastq" label="[trimSequences] noAdaptor5p File"> 58 <data name="noAdaptorFile5p" format="fastq" label="[trim sequences] noAdapter5p file">
56 <filter>noAdaptor5p</filter> 59 <filter>noAdaptor5p</filter>
57 </data> 60 </data>
58 <data name="noAdaptorFile3p" format="fastq" label="[trimSequences] noAdaptor3p File"> 61 <data name="noAdaptorFile3p" format="fastq" label="[trim sequences] noAdapter3p file">
59 <filter>noAdaptor3p</filter> 62 <filter>noAdaptor3p</filter>
60 </data> 63 </data>
61 </outputs> 64 </outputs>
62 65
63 <help> 66 <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.
64 </help> 68 </help>
65 <tests> 69 <tests>
66 <test> 70 <test>
67 <param name="inputFile" value="short_fastq.fastq" /> 71 <param name="inputFile" value="short_fastq.fastq" />
68 <param name="FPADP" value="Yes"/> 72 <param name="FPADP" value="Yes"/>
69 <param name="fivePAdaptor" value="AAAA" /> 73 <param name="fivePAdaptor" value="AAAA" />
70 <param name="TPADP" value="No"/> 74 <param name="TPADP" value="No"/>
71 <param name ="Error" value="No"/> 75 <param name="errors" value="1"/>
72 <param name="indels" value="False"/> 76 <param name="indels" value="False"/>
73 <param name ="noAdaptor5p" value="False"/> 77 <param name="noAdaptor5p" value="False"/>
74 <param name= "noAdaptor3p" value="False"/> 78 <param name= "noAdaptor3p" value="False"/>
75 <output name="outputFile" file="exp_trimsequences_short_fastq.fastq" /> 79 <output name="outputFile" file="exp_trimsequences_short_fastq.fastq" />
76 </test> 80 </test>
77 </tests> 81 </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>
82 </tool> 82 </tool>