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66 lines
2.3 KiB
XML
66 lines
2.3 KiB
XML
<tool id="EMBOSS_water107" name="water">
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<description>Smith-Waterman local alignment</description>
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<command>water -asequence $input1 -bsequence $input2 -outfile $out_file1 -gapopen "$gapopen" -gapextend "$gapextend" -brief $brief -aformat3 $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 1</label>
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</param>
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<param format="fasta" name="input2" type="data">
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<label>Sequence 2</label>
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</param>
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<param name="gapopen" size="6" type="text" value="10.0">
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<label>Gap open penalty</label>
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</param>
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<param name="gapextend" size="6" type="text" value="0.5">
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<label>Gap extension penalty</label>
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</param>
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<param name="brief" type="select">
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<label>Brief identity and similarity</label>
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<option value="yes">Yes</option>
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<option value="no">No</option>
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</param>
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<param name="out_format1" type="select">
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<label>Output Alignment File Format</label>
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<option value="srs">SRS (m)</option>
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<option value="simple">Simple (m)</option>
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<option value="fasta">FASTA (m)</option>
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<option value="msf">MSF (m)</option>
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<option value="pair">Pair (p)</option>
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<option value="markx0">Markx0 (p)</option>
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<option value="markx1">Markx1 (p)</option>
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<option value="markx2">Markx2 (p)</option>
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<option value="markx3">Markx3 (p)</option>
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<option value="markx10">Markx10 (p)</option>
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<option value="srspair">SRS pair (p)</option>
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<option value="score">Score (p)</option>
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</param>
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</inputs>
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<outputs>
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<data format="srs" 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="2.fasta"/>
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<param name="input2" value="1.fasta"/>
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<param name="gapopen" value="10.0"/>
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<param name="gapextend" value="0.5"/>
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<param name="brief" value="no"/>
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<param name="out_format1" value="score"/>
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<output name="out_file1" file="emboss_water_out.score"/>
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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 datasets need 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/water.html
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</help>
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</tool>
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