Mercurial > repos > devteam > emboss_5
diff emboss_prettyplot.xml @ 10:9b98d3d903c6 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
| author | devteam |
|---|---|
| date | Fri, 12 Aug 2016 19:17:10 -0400 |
| parents | |
| children | 0e2484b6829b |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/emboss_prettyplot.xml Fri Aug 12 19:17:10 2016 -0400 @@ -0,0 +1,121 @@ +<tool id="EMBOSS: prettyplot79" name="prettyplot" version="5.0.0"> + <!-- produces png output with file name --> + <description>Displays aligned sequences, with colouring and boxing</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> + <command>prettyplot -sequences $input1 -graph png -goutfile $out_file1 -residuesperline $residuesperline -resbreak $resbreak -ccolours $ccolours -cidentity $cidentity -csimilarity $csimilarity + -cother $cother -docolour $docolour -gtitle $title -pair $pair -identity $identity -box $box -boxcol $boxcol -boxcolval $boxcolval -name $name -maxnamelen $maxnamelen -number $number -listoptions + $listoptions -consensus $consensus -collision $collision -alternative $alternative -showscore $showscore -portrait $portrait -auto</command> + <inputs> + <param format="data" name="input1" type="data"> + <label>Sequence</label> + </param> + <param name="residuesperline" type="text" value="50"> + <label>The number of residues to be displayed on each line</label> + </param> + <param name="resbreak" type="text" value="50"> + <label>Residues before a space</label> + </param> + <param name="ccolours" type="select"> + <label>Colour residues by their consensus value</label> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="cidentity" type="text" value="RED"> + <label>Colour to display identical residues</label> + </param> + <param name="csimilarity" type="text" value="GREEN"> + <label>Colour to display similar residues</label> + </param> + <param name="cother" type="text" value="BLACK"> + <label>Colour to display other residues</label> + </param> + <param name="docolour" type="select"> + <label>Colour residues by table oily, amide etc.</label> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="title" type="select"> + <label>Display the title</label> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="pair" type="text" value="1.5,1.0,0.5"> + <label>Values to represent identical similar related</label> + </param> + <param name="identity" type="text" value="0"> + <label>Only match those which are identical in all sequences</label> + </param> + <param name="box" type="select"> + <label>Display prettyboxes</label> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="boxcol" type="select"> + <label>Colour the background in the boxes</label> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="boxcolval" type="text" value="GREY"> + <label>Colour to be used for background</label> + </param> + <param name="name" type="select"> + <label>Display the sequence names</label> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="maxnamelen" type="text" value="10"> + <label>Margin size for the sequence name</label> + </param> + <param name="number" type="select"> + <label>Display the residue number</label> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="listoptions" type="select"> + <label>Display the date and options used</label> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="consensus" type="select"> + <label>Display the consensus</label> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="collision" type="select"> + <label>Allow collisions in calculating consensus</label> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="alternative" type="select"> + <label>Use alternative collisions routine</label> + <option value="0">Normal collision check</option> + <option value="1">Checks identical scores with the max score found. So if any other residue matches the identical score then a collision has occurred</option> + <option value="2">If another residue has a greater than or equal to matching score and these do not match then a collision has occurred</option> + <option value="3">Checks all those not in the current consensus.If any of these give a top score for matching or identical scores then a collision has occured</option> + </param> + <param name="showscore" type="text" value="-1"> + <label>Print residue scores</label> + </param> + <param name="portrait" type="select"> + <label>Set page to Portrait</label> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + </inputs> + <outputs> + <data format="png" name="out_file1" /> + </outputs> + <help> + You can view the original documentation here_. + + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/prettyplot.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>`_ + </help> +</tool> \ No newline at end of file