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61 lines
2.3 KiB
XML
61 lines
2.3 KiB
XML
<tool id="EMBOSS: equicktandem31" name="equicktandem" version="5.0.0">
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<description>Finds tandem repeats</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>equicktandem -sequence $input1 -outfile $out_file1 -origfile $ofile2 -maxrepeat $maxrepeat -threshold $threshold -rformat2 $out_format1 -auto</command>
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<inputs>
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<param format="fasta" name="input1" type="data">
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<label>Sequence</label>
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</param>
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<param name="maxrepeat" size="4" type="text" value="600">
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<label>Maximum repeat size</label>
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</param>
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<param name="threshold" size="4" type="text" value="20">
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<label>Threshold score</label>
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</param>
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<param name="out_format1" type="select">
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<label>Output Report File Format</label>
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<option value="table">Table</option>
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<option value="embl">EMBL</option>
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<option value="genbank">GENBANK</option>
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<option value="gff">GFF</option>
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<option value="pir">PIR</option>
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<option value="swiss">SwissProt</option>
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<option value="dbmotif">DbMotif</option>
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<option value="diffseq">Diffseq</option>
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<option value="excel">Excel (tab delimited)</option>
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<option value="feattable">FeatTable</option>
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<option value="motif">Motif</option>
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<option value="regions">Regions</option>
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<option value="seqtable">SeqTable</option>
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<option value="simple">SRS Simple</option>
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<option value="srs">SRS</option>
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<option value="tagseq">TagSeq</option>
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</param>
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</inputs>
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<outputs>
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<data format="table" name="out_file1" />
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<data format="equicktandem" name="ofile2" />
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</outputs>
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<tests>
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<test>
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<param name="input1" value="1.fasta"/>
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<param name="maxrepeat" value="600"/>
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<param name="threshold" value="20"/>
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<param name="out_format1" value="table"/>
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<output name="ofile2" file="emboss_equicktandem_out.equicktandem"/>
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</test>
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</tests>
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<code file="emboss_format_corrector.py" />
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<help>
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.. class:: warningmark
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The input dataset needs to be sequences.
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-----
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You can view the original documentation here_.
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.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/equicktandem.html
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</help>
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</tool>
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