Mercurial > repos > xuebing > sharplabtool
diff tools/emboss_5/emboss_dan.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/emboss_5/emboss_dan.xml Fri Mar 09 19:37:19 2012 -0500 @@ -0,0 +1,84 @@ +<tool id="EMBOSS: dan19" name="dan" version="5.0.0"> + <description>Calculates DNA RNA/DNA melting temperature</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> + <command interpreter="perl">emboss_single_outputfile_wrapper.pl dan -sequence $input1 -windowsize $window -goutfile $out_file1 -graph png -plot $plot1 -shiftincrement $shift -dnaconc $dnaconc + -saltconc $saltconc -product $product -formamide $formamide -mismatch $mismatch -prodlen $prodlen -thermo $thermo -temperature $temperature -rna $rna -outfile $out_file1 -auto</command> + <inputs> + <param format="data" name="input1" type="data"> + <label>On query</label> + </param> + <param name="window" size="4" type="text" value="20"> + <label>Window Size</label> + </param> + <param name="shift" size="4" type="text" value="1"> + <label>Step size (shift increment)</label> + </param> + <param name="dnaconc" size="4" type="text" value="50.0"> + <label>DNA Concentration (nM)</label> + </param> + <param name="saltconc" size="4" type="text" value="50.0"> + <label>Salt concentration (mM)</label> + </param> + <param name="thermo" type="select"> + <label>Output the DeltaG, DeltaH and DeltaS values</label> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="temperature" size="4" type="text" value="25 "> + <label>Temperature at which to calculate the DeltaG, DeltaH and DeltaS values</label> + </param> + <param name="rna" type="select"> + <label>Sequence is RNA</label> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="product" type="select"> + <label>Include percent formamide, percent of mismatches allowed and product length</label> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="formamide" size="4" type="text" value="0 "> + <label>Formamide concentration (nM)</label> + </param> + <param name="mismatch" size="4" type="text" value="0 "> + <label>Percent mismatch to be used in calculations</label> + </param> + <param name="prodlen" size="4" type="text" value="20"> + <label>Product length to be used in calculations</label> + </param> + <param name="plot1" type="select"> + <label>Create a graph</label> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + </inputs> + <outputs> + <data format="dan" name="out_file1" /> + </outputs> + <!-- + <tests> + <test> + <param name="input1" value="2.fasta"/> + <param name="window" value="20"/> + <param name="shift" value="1"/> + <param name="dnaconc" value="50"/> + <param name="saltconc" value="50"/> + <param name="thermo" value="yes"/> + <param name="temperature" value="25"/> + <param name="rna" value="no"/> + <param name="product" value="no"/> + <param name="formamide" value="0"/> + <param name="mismatch" value="0"/> + <param name="prodlen" value="20"/> + <param name="plot1" value="yes"/> + <output name="out_file1" file="emboss_dan_out.png"/> + </test> + </tests> + --> + <code file="emboss_format_corrector.py" /> + <help> + You can view the original documentation here_. + + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dan.html + </help> +</tool> \ No newline at end of file