Mercurial > repos > devteam > emboss_5
diff emboss_dan.xml @ 10:d49956b87f7e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author | iuc |
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date | Wed, 08 Feb 2017 12:42:22 -0500 |
parents | |
children | 8992d258e42f |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/emboss_dan.xml Wed Feb 08 12:42:22 2017 -0500 @@ -0,0 +1,66 @@ +<tool id="EMBOSS: dan19" name="dan" version="5.0.0.1"> + <description>Calculates DNA RNA/DNA melting temperature</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <code file="emboss_format_corrector.py" /> + <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' dan -sequence '$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 name="input1" type="data" format="data" label="On query" /> + <param name="window" type="integer" value="20" label="Window size" /> + <param name="shift" type="integer" value="1" label="Step size (shift increment)" /> + <param name="dnaconc" type="float" value="50.0" label="DNA Concentration (nM)" /> + <param name="saltconc" type="float" value="50.0" label="Salt concentration (mM)" /> + <param name="thermo" type="select" label="Output the DeltaG, DeltaH and DeltaS values"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="temperature" type="float" value="25.0" label="Temperature at which to calculate the DeltaG, DeltaH and DeltaS values" /> + <param name="rna" type="select" label="Sequence is RNA"> + <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"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="formamide" type="float" value="0.0" label="Formamide concentration (nM)" /> + <param name="mismatch" type="float" value="0.0" label="Percent mismatch to be used in calculations" /> + <param name="prodlen" type="integer" value="20" label="Product length to be used in calculations" /> + <param name="plot1" type="select" label="Create a graph"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + </inputs> + <outputs> + <data name="out_file1" format="dan" /> + </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> + --> + <help> + You can view the original documentation here_. + + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/dan.html + </help> + <expand macro="citations" /> +</tool>