Mercurial > repos > devteam > emboss_5
diff emboss_dan.xml @ 11:0e2484b6829b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
| author | iuc |
|---|---|
| date | Mon, 30 Jan 2017 13:27:40 -0500 |
| parents | 9b98d3d903c6 |
| children | 27c43fb015f0 |
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--- a/emboss_dan.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_dan.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,60 +1,42 @@ -<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" type="text" value="20"> - <label>Window Size</label> - </param> - <param name="shift" type="text" value="1"> - <label>Step size (shift increment)</label> - </param> - <param name="dnaconc" type="text" value="50.0"> - <label>DNA Concentration (nM)</label> - </param> - <param name="saltconc" 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" 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" type="text" value="0 "> - <label>Formamide concentration (nM)</label> - </param> - <param name="mismatch" type="text" value="0 "> - <label>Percent mismatch to be used in calculations</label> - </param> - <param name="prodlen" 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> +<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> @@ -73,20 +55,12 @@ <param name="plot1" value="yes"/> <output name="out_file1" file="emboss_dan_out.png"/> </test> - </tests> - --> - <code file="emboss_format_corrector.py" /> + </tests> + --> <help> You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dan.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/dan.html </help> -</tool> \ No newline at end of file + <expand macro="citations" /> +</tool>