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50 lines
1.7 KiB
XML
50 lines
1.7 KiB
XML
<tool id="EMBOSS_einverted28" name="einverted">
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<description>Finds DNA inverted repeats</description>
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<command>einverted -sequence $input1 -outfile $out_file1 -gap $gap -threshold $threshold -match $match -mismatch $mismatch -maxrepeat $maxrepeat -auto</command>
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<inputs>
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<param format="fasta" name="input1" type="data">
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<label>On query</label>
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</param>
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<param name="gap" size="4" type="text" value="12">
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<label>Gap penalty</label>
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</param>
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<param name="threshold" size="4" type="text" value="50">
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<label>Minimum score threshold</label>
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</param>
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<param name="match" size="4" type="text" value="3">
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<label>Match score</label>
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</param>
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<param name="mismatch" size="4" type="text" value="-4">
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<label>Mismatch score</label>
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</param>
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<param name="maxrepeat" size="4" type="text" value="2000">
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<label>Maximum separation between the start of repeat and the end of the inverted repeat</label>
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</param>
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</inputs>
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<outputs>
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<data format="einverted" name="out_file1" />
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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="gap" value="12"/>
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<param name="threshold" value="50"/>
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<param name="match" value="3"/>
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<param name="mismatch" value="-4"/>
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<param name="maxrepeat" value="2000"/>
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<output name="out_file1" file="emboss_einverted_out.einverted"/>
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</test>
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</tests>
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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/einverted.html
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</help>
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</tool>
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