Mercurial > repos > devteam > emboss_5
diff emboss_prettyplot.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_prettyplot.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_prettyplot.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,121 +1,83 @@ -<tool id="EMBOSS: prettyplot79" name="prettyplot" version="5.0.0"> +<tool id="EMBOSS: prettyplot79" name="prettyplot" version="5.0.0.1"> <!-- 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> + <description>Displays aligned sequences, with colouring and boxing</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="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 name="input1" type="data" format="data" label="Sequence" /> + <param name="residuesperline" type="integer" value="50" label="The number of residues to be displayed on each line" /> + <param name="resbreak" type="integer" value="50" label="Residues before a space" /> + <param name="ccolours" type="select" label="Colour residues by their consensus value"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="cidentity" type="text" value="RED" label="Colour to display identical residues" /> + <param name="csimilarity" type="text" value="GREEN" label="Colour to display similar residues" /> + <param name="cother" type="text" value="BLACK" label="Colour to display other residues" /> + <param name="docolour" type="select" label="Colour residues by table oily, amide etc."> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="title" type="select" label="Display the title"> + <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" /> + <param name="identity" type="integer" value="0" label="Only match those which are identical in all sequences" /> + <param name="box" type="select" label="Display prettyboxes"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="boxcol" type="select" label="Colour the background in the boxes"> + <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" /> + <param name="name" type="select" label="Display the sequence names"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="maxnamelen" type="integer" value="10" label="Margin size for the sequence name" /> + <param name="number" type="select" label="Display the residue number"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="listoptions" type="select" label="Display the date and options used"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="consensus" type="select" label="Display the consensus"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="collision" type="select" label="Allow collisions in calculating consensus"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="alternative" type="select" label="Use alternative collisions routine"> + <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="integer" value="-1" label="Print residue scores" /> + <param name="portrait" type="select" label="Set page to Portrait"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + </inputs> + <outputs> + <data name="out_file1" format="png" /> + </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>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/prettyplot.html </help> -</tool> \ No newline at end of file + <expand macro="citations" /> +</tool>