Mercurial > repos > serranop > usearch
comparison usearch_fastq_mergepairs.xml @ 8:2ef1c29e783d draft
Updated the XML
| author | serranop |
|---|---|
| date | Fri, 13 Sep 2013 14:56:58 -0400 |
| parents | 94cda55f1bbb |
| children | 5b3a8f988b81 |
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| 7:94cda55f1bbb | 8:2ef1c29e783d |
|---|---|
| 1 <tool id="usearch_fastq_mergepairs" name="usearch fastq_mergepairs" version="0.0.1"> | 1 <tool id="usearch_fastq_mergepairs" name="usearch fastq_mergepairs" version="0.0.1"> |
| 2 <description>merging of paired reads</description> | 2 <description>merging of paired reads</description> |
| 3 <version_command>usearch -version</version_command> | 3 <version_command>usearch -version</version_command> |
| 4 <command>usearch | 4 <command>usearch |
| 5 -quiet | |
| 6 -fastq_mergepairs '$input_forward' | 5 -fastq_mergepairs '$input_forward' |
| 7 -reverse '$input_reverse' | 6 -reverse '$input_reverse' |
| 8 #if $minovlen != '-1': | 7 #if $minovlen.minovlen_val != '-1': |
| 9 -fastq_minovlen $minovlen | 8 -fastq_minovlen $minovlen |
| 10 #end if | 9 #end if |
| 11 -fastq_qmax $qmax | 10 -fastq_qmax $qmax |
| 12 -fastqout '$output' | 11 -fastqout '$output' |
| 13 </command> | 12 </command> |
| 14 <inputs> | 13 <inputs> |
| 15 <param name="input_forward" type="data" format="fastq,fastqsanger,fastqcssanger" label="File with forward reads" /> | 14 <param name="input_forward" type="data" format="fastq,fastqsanger,fastqcssanger" label="File with forward reads" /> |
| 16 <param name="input_reverse" type="data" format="fastq,fastqsanger,fastqcssanger" label="File with reverse reads" /> | 15 <param name="input_reverse" type="data" format="fastq,fastqsanger,fastqcssanger" label="File with reverse reads" /> |
| 17 <param name="minovlen" type="integer" value="-1" label="Minimum length of the overlap" help="'-1' means no minimum." /> | 16 <conditional name="minovlen"> |
| 17 <param name="minovlen_val" type="integer" value="-1" label="Minimum length of the overlap" help="'-1' means no minimum." /> | |
| 18 <when value="-1"> | |
| 19 </when> | |
| 20 <when value="0"> | |
| 21 </when> | |
| 22 </conditional> | |
| 18 <param name="qmax" type="integer" value="41" label="Maximum Q score (input files)." /> | 23 <param name="qmax" type="integer" value="41" label="Maximum Q score (input files)." /> |
| 19 </inputs> | 24 </inputs> |
| 20 <outputs> | 25 <outputs> |
| 21 <data name='output' format='fastq' label="Merge result" /> | 26 <data name='output' format='fastq' label="Merge result" /> |
| 22 </outputs> | 27 </outputs> |