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/tools/emboss_5/emboss_prettyplot.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 119 lines | 114 code | 4 blank | 1 comment | 0 complexity | 4b8543d5e7f4ce080db2dab6c2ba4b51 MD5 | raw file
  1<tool id="EMBOSS: prettyplot79" name="prettyplot" version="5.0.0">
  2  <!-- produces png output with file name -->
  3  <description>Displays aligned sequences, with colouring and boxing</description>
  4  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  5  <command>prettyplot -sequences $input1 -graph png -goutfile $out_file1 -residuesperline $residuesperline -resbreak $resbreak -ccolours $ccolours -cidentity $cidentity -csimilarity $csimilarity
  6  -cother $cother -docolour $docolour -gtitle $title -pair $pair -identity $identity -box $box -boxcol $boxcol -boxcolval $boxcolval -name $name -maxnamelen $maxnamelen -number $number -listoptions
  7  $listoptions -consensus $consensus -collision $collision -alternative $alternative -showscore $showscore -portrait $portrait -auto</command>
  8  <inputs>
  9    <param format="data" name="input1" type="data">
 10      <label>Sequence</label>
 11    </param>
 12    <param name="residuesperline" size="10" type="text" value="50">
 13      <label>The number of residues to be displayed on each line</label>
 14    </param>
 15    <param name="resbreak" size="10" type="text" value="50">
 16      <label>Residues before a space</label>
 17    </param>
 18    <param name="ccolours" type="select">
 19      <label>Colour residues by their consensus value</label>
 20      <option value="yes">Yes</option>
 21      <option value="no">No</option>
 22    </param>
 23    <param name="cidentity" size="10" type="text" value="RED">
 24      <label>Colour to display identical residues</label>
 25    </param>
 26    <param name="csimilarity" size="10" type="text" value="GREEN">
 27      <label>Colour to display similar residues</label>
 28    </param>
 29    <param name="cother" size="10" type="text" value="BLACK">
 30      <label>Colour to display other residues</label>
 31    </param>
 32    <param name="docolour" type="select">
 33      <label>Colour residues by table oily, amide etc.</label>
 34      <option value="no">No</option>
 35      <option value="yes">Yes</option>
 36    </param>
 37    <param name="title" type="select">
 38      <label>Display the title</label>
 39      <option value="yes">Yes</option>
 40      <option value="no">No</option>
 41    </param>
 42    <param name="pair" size="10" type="text" value="1.5,1.0,0.5">
 43      <label>Values to represent identical similar related</label>
 44    </param>
 45    <param name="identity" size="10" type="text" value="0">
 46      <label>Only match those which are identical in all sequences</label>
 47    </param>
 48    <param name="box" type="select">
 49      <label>Display prettyboxes</label>
 50      <option value="yes">Yes</option>
 51      <option value="no">No</option>
 52    </param>
 53    <param name="boxcol" type="select">
 54      <label>Colour the background in the boxes</label>
 55      <option value="no">No</option>
 56      <option value="yes">Yes</option>
 57    </param>
 58    <param name="boxcolval" size="10" type="text" value="GREY">
 59      <label>Colour to be used for background</label>
 60    </param>
 61    <param name="name" type="select">
 62      <label>Display the sequence names</label>
 63      <option value="yes">Yes</option>
 64      <option value="no">No</option>
 65    </param>
 66    <param name="maxnamelen" size="10" type="text" value="10">
 67      <label>Margin size for the sequence name</label>
 68    </param>
 69    <param name="number" type="select">
 70      <label>Display the residue number</label>
 71      <option value="yes">Yes</option>
 72      <option value="no">No</option>
 73    </param>
 74    <param name="listoptions" type="select">
 75      <label>Display the date and options used</label>
 76      <option value="yes">Yes</option>
 77      <option value="no">No</option>
 78    </param>
 79    <param name="consensus" type="select">
 80      <label>Display the consensus</label>
 81      <option value="no">No</option>
 82      <option value="yes">Yes</option>
 83    </param>
 84    <param name="collision" type="select">
 85      <label>Allow collisions in calculating consensus</label>
 86      <option value="yes">Yes</option>
 87      <option value="no">No</option>
 88    </param>
 89    <param name="alternative" type="select">
 90      <label>Use alternative collisions routine</label>
 91      <option value="0">Normal collision check</option>
 92      <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>
 93      <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>
 94      <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>
 95    </param>
 96    <param name="showscore" size="10" type="text" value="-1">
 97      <label>Print residue scores</label>
 98    </param>
 99    <param name="portrait" type="select">
100      <label>Set page to Portrait</label>
101      <option value="no">No</option>
102      <option value="yes">Yes</option>
103    </param>
104  </inputs>
105  <outputs>
106    <data format="png" name="out_file1" />
107  </outputs>
108  <help>
109    You can view the original documentation here_.
110    
111    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/prettyplot.html
112
113------
114
115**Citation**
116
117If 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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
118  </help>
119</tool>