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comparison emboss_lindna.xml @ 11:0e2484b6829b draft

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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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10:9b98d3d903c6 11:0e2484b6829b
1 <tool id="EMBOSS: lindna48" name="lindna" version="5.0.0"> 1 <tool id="EMBOSS: lindna48" name="lindna" version="5.0.0.1">
2 <!-- tool produces memory error in ajmem.c --> 2 <!-- tool produces memory error in ajmem.c -->
3 <description>Draws linear maps of DNA constructs</description> 3 <description>Draws linear maps of DNA constructs</description>
4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 4 <macros>
5 <command>lindna -infile $input1 -graphout png -goutfile $out_file1 -ruler $ruler -blocktype $blocktype -maxgroups $maxgroups -maxlabels $maxlabels -intersymbol $intersymbol -intercolour $intercolour 5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command>lindna -infile '$input1' -graphout png -goutfile '$out_file1' -ruler $ruler -blocktype $blocktype -maxgroups $maxgroups -maxlabels $maxlabels -intersymbol $intersymbol -intercolour $intercolour
6 -interticks $interticks -gapsize $gapsize -ticklines $ticklines -textheight $textheight -textlength $textlength -margin $margin -tickheight $tickheight -blockheight $blockheight -rangeheight 9 -interticks $interticks -gapsize $gapsize -ticklines $ticklines -textheight $textheight -textlength $textlength -margin $margin -tickheight $tickheight -blockheight $blockheight -rangeheight
7 $rangeheight -gapgroup $gapgroup -postext $postext -auto</command> 10 $rangeheight -gapgroup $gapgroup -postext $postext -auto</command>
8 <inputs> 11 <inputs>
9 <param format="data" name="input1" type="data"> 12 <param name="input1" type="data" format="data" label="Sequences" />
10 <label>Sequences</label> 13 <param name="ruler" type="select" label="Draw a ruler">
11 </param>
12 <param name="ruler" type="select">
13 <label>Draw a ruler</label>
14 <option value="yes">Yes</option> 14 <option value="yes">Yes</option>
15 <option value="no">No</option> 15 <option value="no">No</option>
16 </param> 16 </param>
17 <param name="blocktype" type="select"> 17 <param name="blocktype" type="select" label="Type of blocks">
18 <label>Type of blocks</label>
19 <option value="Filled">Filled blocks</option> 18 <option value="Filled">Filled blocks</option>
20 <option value="Open">Open blocks</option> 19 <option value="Open">Open blocks</option>
21 <option value="Outline">Black border</option> 20 <option value="Outline">Black border</option>
22 </param> 21 </param>
23 <param name="maxgroups" type="text" value="20"> 22 <param name="maxgroups" type="integer" value="20" label="Maximum number of groups" />
24 <label>Maximum number of groups</label> 23 <param name="maxlabels" type="integer" value="10000" label="Maximum number of labels" />
25 </param> 24 <param name="intersymbol" type="select" label="Type of blocks">
26 <param name="maxlabels" type="text" value="10000">
27 <label>Maximum number of labels</label>
28 </param>
29 <param name="intersymbol" type="select">
30 <label>Type of blocks</label>
31 <option value="Straight">Straight</option> 25 <option value="Straight">Straight</option>
32 </param> 26 </param>
33 <param name="intercolour" type="select"> 27 <param name="intercolour" type="select" label="Colour of junctions between blocks">
34 <label>Colour of junctions between blocks</label>
35 <option value="1">Red</option> 28 <option value="1">Red</option>
36 <option value="0">Black</option> 29 <option value="0">Black</option>
37 <option value="2">Yellow</option> 30 <option value="2">Yellow</option>
38 <option value="3">Green</option> 31 <option value="3">Green</option>
39 <option value="4">Aquamarine</option> 32 <option value="4">Aquamarine</option>
47 <option value="12">Turquoise</option> 40 <option value="12">Turquoise</option>
48 <option value="13">Magenta</option> 41 <option value="13">Magenta</option>
49 <option value="14">Salmon</option> 42 <option value="14">Salmon</option>
50 <option value="15">White</option> 43 <option value="15">White</option>
51 </param> 44 </param>
52 <param name="interticks" type="select"> 45 <param name="interticks" type="select" label="Horizontal junctions between ticks">
53 <label>Horizontal junctions between ticks</label>
54 <option value="no">No</option> 46 <option value="no">No</option>
55 <option value="yes">Yes</option> 47 <option value="yes">Yes</option>
56 </param> 48 </param>
57 <param name="gapsize" type="text" value="500"> 49 <param name="gapsize" type="integer" value="500" label="Interval between ticks in the ruler" />
58 <label>Interval between ticks in the ruler</label> 50 <param name="ticklines" type="select" label="Vertical lines at the ruler's ticks">
59 </param>
60 <param name="ticklines" type="select">
61 <label>Vertical lines at the ruler's ticks</label>
62 <option value="no">No</option> 51 <option value="no">No</option>
63 <option value="yes">Yes</option> 52 <option value="yes">Yes</option>
64 </param> 53 </param>
65 <param name="textheight" type="text" value="1.0"> 54 <param name="textheight" type="float" value="1.0" label="Height of text" help="Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively" />
66 <label>Height of text. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label> 55 <param name="textlength" type="float" value="1.0" label="Length of text" help="Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively" />
67 </param> 56 <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 &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively" />
68 <param name="textlength" type="text" value="1.0"> 57 <param name="tickheight" type="float" value="1.0" label="Height of ticks" help="Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively" />
69 <label>Length of text. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label> 58 <param name="blockheight" type="float" value="1.0" label="Height of blocks" help="Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively" />
70 </param> 59 <param name="rangeheight" type="float" value="1.0" label="Height of range ends" help="Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively" />
71 <param name="margin" type="text" value="1.0"> 60 <param name="gapgroup" type="float" value="1.0" label="Space between groups" help="Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively" />
72 <label>Width of left margin. This is the region left to the groups where the names of the groups are displayed. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, 61 <param name="postext" type="float" value="1.0" label="Space between text and ticks, blocks, and ranges" help="Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively" />
73 respectively</label>
74 </param>
75 <param name="tickheight" type="text" value="1.0">
76 <label>Height of ticks. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
77 </param>
78 <param name="blockheight" type="text" value="1.0">
79 <label>Height of blocks. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
80 </param>
81 <param name="rangeheight" type="text" value="1.0">
82 <label>Height of range ends. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
83 </param>
84 <param name="gapgroup" type="text" value="1.0">
85 <label>Space between groups. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
86 </param>
87 <param name="postext" type="text" value="1.0">
88 <label>Space between text and ticks, blocks, and ranges. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
89 </param>
90 </inputs> 62 </inputs>
91 <outputs> 63 <outputs>
92 <data format="png" name="out_file1" /> 64 <data name="out_file1" format="png" />
93 </outputs> 65 </outputs>
94 <help> 66 <help>
95 You can view the original documentation here_. 67 You can view the original documentation here_.
96
97 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/lindna.html
98 68
99 ------ 69 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/lindna.html
100
101 **Citation**
102
103 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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
104
105 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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
106 </help> 70 </help>
71 <expand macro="citations" />
107 </tool> 72 </tool>