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63 lines
2.7 KiB
XML
63 lines
2.7 KiB
XML
<tool id="EMBOSS: dan19" name="dan">
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<description>Calculates DNA RNA/DNA melting temperature</description>
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<command interpreter="perl">emboss_single_outputfile_wrapper.pl dan -sequence $input1 -windowsize $window -goutfile $out_file1 -graph png -plot $plot1 -shiftincrement $shift -dnaconc $dnaconc
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-saltconc $saltconc -product $product -formamide $formamide -mismatch $mismatch -prodlen $prodlen -thermo $thermo -temperature $temperature -rna $rna -outfile $out_file1 -auto</command>
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<inputs>
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<param format="data" name="input1" type="data">
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<label>On query</label>
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</param>
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<param name="window" size="4" type="text" value="20">
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<label>Window Size</label>
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</param>
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<param name="shift" size="4" type="text" value="1">
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<label>Step size (shift increment)</label>
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</param>
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<param name="dnaconc" size="4" type="text" value="50.0">
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<label>DNA Concentration (nM)</label>
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</param>
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<param name="saltconc" size="4" type="text" value="50.0">
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<label>Salt concentration (mM)</label>
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</param>
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<param name="thermo" type="select">
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<label>Output the DeltaG, DeltaH and DeltaS values</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="temperature" size="4" type="text" value="25 ">
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<label>Temperature at which to calculate the DeltaG, DeltaH and DeltaS values</label>
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</param>
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<param name="rna" type="select">
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<label>Sequence is RNA</label>
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<option value="no">No</option>
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<option value="yes">Yes</option>
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</param>
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<param name="product" type="select">
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<label>Include percent formamide, percent of mismatches allowed and product length</label>
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<option value="no">No</option>
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<option value="yes">Yes</option>
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</param>
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<param name="formamide" size="4" type="text" value="0 ">
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<label>Formamide concentration (nM)</label>
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</param>
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<param name="mismatch" size="4" type="text" value="0 ">
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<label>Percent mismatch to be used in calculations</label>
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</param>
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<param name="prodlen" size="4" type="text" value="20">
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<label>Product length to be used in calculations</label>
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</param>
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<param name="plot1" type="select">
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<label>Create a graph</label>
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<option value="no">No</option>
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<option value="yes">Yes</option>
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</param>
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</inputs>
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<outputs>
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<data format="txt" name="out_file1" />
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</outputs>
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<code file="emboss_format_corrector.py" />
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<help>
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You can view the original documentation here_.
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.. _here: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/dan.html
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</help>
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</tool> |