[2] | 1 | <tool id="EMBOSS: einverted28" name="einverted" version="5.0.0">
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| 2 | <description>Finds DNA inverted repeats</description>
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| 3 | <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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| 4 | <command>einverted -sequence $input1 -outfile $out_file1 -gap $gap -threshold $threshold -match $match -mismatch $mismatch -maxrepeat $maxrepeat -auto</command>
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| 5 | <inputs>
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| 6 | <param format="fasta" name="input1" type="data">
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| 7 | <label>On query</label>
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| 8 | </param>
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| 9 | <param name="gap" size="4" type="text" value="12">
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| 10 | <label>Gap penalty</label>
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| 11 | </param>
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| 12 | <param name="threshold" size="4" type="text" value="50">
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| 13 | <label>Minimum score threshold</label>
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| 14 | </param>
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| 15 | <param name="match" size="4" type="text" value="3">
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| 16 | <label>Match score</label>
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| 17 | </param>
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| 18 | <param name="mismatch" size="4" type="text" value="-4">
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| 19 | <label>Mismatch score</label>
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| 20 | </param>
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| 21 | <param name="maxrepeat" size="4" type="text" value="2000">
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| 22 | <label>Maximum separation between the start of repeat and the end of the inverted repeat</label>
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| 23 | </param>
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| 24 | </inputs>
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| 25 | <outputs>
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| 26 | <data format="einverted" name="out_file1" />
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| 27 | </outputs> |
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| 28 | <tests> |
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| 29 | <test> |
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| 30 | <param name="input1" value="1.fasta"/> |
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| 31 | <param name="gap" value="12"/> |
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| 32 | <param name="threshold" value="50"/> |
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| 33 | <param name="match" value="3"/> |
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| 34 | <param name="mismatch" value="-4"/> |
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| 35 | <param name="maxrepeat" value="2000"/> |
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| 36 | <output name="out_file1" file="emboss_einverted_out.einverted"/> |
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| 37 | </test> |
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| 38 | </tests>
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| 39 | <help> |
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| 40 | .. class:: warningmark |
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| 41 | |
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| 42 | The input dataset needs to be sequences. |
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| 43 | |
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| 44 | ----- |
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| 45 | |
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| 46 | You can view the original documentation here_. |
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| 47 | |
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| 48 | .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/einverted.html |
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| 49 | </help> |
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| 50 | </tool> |
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