Mercurial > repos > devteam > emboss_5
diff emboss_lindna.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_lindna.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_lindna.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,107 +1,72 @@ -<tool id="EMBOSS: lindna48" name="lindna" version="5.0.0"> +<tool id="EMBOSS: lindna48" name="lindna" version="5.0.0.1"> <!-- tool produces memory error in ajmem.c --> - <description>Draws linear maps of DNA constructs</description> - <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>lindna -infile $input1 -graphout png -goutfile $out_file1 -ruler $ruler -blocktype $blocktype -maxgroups $maxgroups -maxlabels $maxlabels -intersymbol $intersymbol -intercolour $intercolour - -interticks $interticks -gapsize $gapsize -ticklines $ticklines -textheight $textheight -textlength $textlength -margin $margin -tickheight $tickheight -blockheight $blockheight -rangeheight - $rangeheight -gapgroup $gapgroup -postext $postext -auto</command> - <inputs> - <param format="data" name="input1" type="data"> - <label>Sequences</label> - </param> - <param name="ruler" type="select"> - <label>Draw a ruler</label> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> - <param name="blocktype" type="select"> - <label>Type of blocks</label> - <option value="Filled">Filled blocks</option> - <option value="Open">Open blocks</option> - <option value="Outline">Black border</option> - </param> - <param name="maxgroups" type="text" value="20"> - <label>Maximum number of groups</label> - </param> - <param name="maxlabels" type="text" value="10000"> - <label>Maximum number of labels</label> - </param> - <param name="intersymbol" type="select"> - <label>Type of blocks</label> - <option value="Straight">Straight</option> - </param> - <param name="intercolour" type="select"> - <label>Colour of junctions between blocks</label> - <option value="1">Red</option> - <option value="0">Black</option> - <option value="2">Yellow</option> - <option value="3">Green</option> - <option value="4">Aquamarine</option> - <option value="5">Pink</option> - <option value="6">Wheat</option> - <option value="7">Grey</option> - <option value="8">Brown</option> - <option value="9">Blue</option> - <option value="10">Blue-violet</option> - <option value="11">Cyan</option> - <option value="12">Turquoise</option> - <option value="13">Magenta</option> - <option value="14">Salmon</option> - <option value="15">White</option> - </param> - <param name="interticks" type="select"> - <label>Horizontal junctions between ticks</label> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <param name="gapsize" type="text" value="500"> - <label>Interval between ticks in the ruler</label> - </param> - <param name="ticklines" type="select"> - <label>Vertical lines at the ruler's ticks</label> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <param name="textheight" type="text" value="1.0"> - <label>Height of text. Enter a number <1.0 or >1.0 to decrease or increase the size, respectively</label> - </param> - <param name="textlength" type="text" value="1.0"> - <label>Length of text. Enter a number <1.0 or >1.0 to decrease or increase the size, respectively</label> - </param> - <param name="margin" type="text" value="1.0"> - <label>Width of left margin. This is the region left to the groups where the names of the groups are displayed. Enter a number <1.0 or >1.0 to decrease or increase the size, - respectively</label> - </param> - <param name="tickheight" type="text" value="1.0"> - <label>Height of ticks. Enter a number <1.0 or >1.0 to decrease or increase the size, respectively</label> - </param> - <param name="blockheight" type="text" value="1.0"> - <label>Height of blocks. Enter a number <1.0 or >1.0 to decrease or increase the size, respectively</label> - </param> - <param name="rangeheight" type="text" value="1.0"> - <label>Height of range ends. Enter a number <1.0 or >1.0 to decrease or increase the size, respectively</label> - </param> - <param name="gapgroup" type="text" value="1.0"> - <label>Space between groups. Enter a number <1.0 or >1.0 to decrease or increase the size, respectively</label> - </param> - <param name="postext" type="text" value="1.0"> - <label>Space between text and ticks, blocks, and ranges. Enter a number <1.0 or >1.0 to decrease or increase the size, respectively</label> - </param> - </inputs> - <outputs> - <data format="png" name="out_file1" /> - </outputs> + <description>Draws linear maps of DNA constructs</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command>lindna -infile '$input1' -graphout png -goutfile '$out_file1' -ruler $ruler -blocktype $blocktype -maxgroups $maxgroups -maxlabels $maxlabels -intersymbol $intersymbol -intercolour $intercolour + -interticks $interticks -gapsize $gapsize -ticklines $ticklines -textheight $textheight -textlength $textlength -margin $margin -tickheight $tickheight -blockheight $blockheight -rangeheight + $rangeheight -gapgroup $gapgroup -postext $postext -auto</command> + <inputs> + <param name="input1" type="data" format="data" label="Sequences" /> + <param name="ruler" type="select" label="Draw a ruler"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <param name="blocktype" type="select" label="Type of blocks"> + <option value="Filled">Filled blocks</option> + <option value="Open">Open blocks</option> + <option value="Outline">Black border</option> + </param> + <param name="maxgroups" type="integer" value="20" label="Maximum number of groups" /> + <param name="maxlabels" type="integer" value="10000" label="Maximum number of labels" /> + <param name="intersymbol" type="select" label="Type of blocks"> + <option value="Straight">Straight</option> + </param> + <param name="intercolour" type="select" label="Colour of junctions between blocks"> + <option value="1">Red</option> + <option value="0">Black</option> + <option value="2">Yellow</option> + <option value="3">Green</option> + <option value="4">Aquamarine</option> + <option value="5">Pink</option> + <option value="6">Wheat</option> + <option value="7">Grey</option> + <option value="8">Brown</option> + <option value="9">Blue</option> + <option value="10">Blue-violet</option> + <option value="11">Cyan</option> + <option value="12">Turquoise</option> + <option value="13">Magenta</option> + <option value="14">Salmon</option> + <option value="15">White</option> + </param> + <param name="interticks" type="select" label="Horizontal junctions between ticks"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="gapsize" type="integer" value="500" label="Interval between ticks in the ruler" /> + <param name="ticklines" type="select" label="Vertical lines at the ruler's ticks"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="textheight" type="float" value="1.0" label="Height of text" help="Enter a number <1.0 or >1.0 to decrease or increase the size, respectively" /> + <param name="textlength" type="float" value="1.0" label="Length of text" help="Enter a number <1.0 or >1.0 to decrease or increase the size, respectively" /> + <param name="margin" type="float" value="1.0" label="Width of left margin" help="This is the region left to the groups where the names of the groups are displayed. Enter a number <1.0 or >1.0 to decrease or increase the size, respectively" /> + <param name="tickheight" type="float" value="1.0" label="Height of ticks" help="Enter a number <1.0 or >1.0 to decrease or increase the size, respectively" /> + <param name="blockheight" type="float" value="1.0" label="Height of blocks" help="Enter a number <1.0 or >1.0 to decrease or increase the size, respectively" /> + <param name="rangeheight" type="float" value="1.0" label="Height of range ends" help="Enter a number <1.0 or >1.0 to decrease or increase the size, respectively" /> + <param name="gapgroup" type="float" value="1.0" label="Space between groups" help="Enter a number <1.0 or >1.0 to decrease or increase the size, respectively" /> + <param name="postext" type="float" value="1.0" label="Space between text and ticks, blocks, and ranges" help="Enter a number <1.0 or >1.0 to decrease or increase the size, respectively" /> + </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/lindna.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/lindna.html </help> -</tool> \ No newline at end of file + <expand macro="citations" /> +</tool>