Mercurial > repos > dcorreia > newick_display
comparison nwdisplay.xml @ 1:3200899efad9 draft default tip
Uploaded
| author | dcorreia |
|---|---|
| date | Tue, 12 Dec 2017 12:02:31 -0500 |
| parents | 5c11638687d0 |
| children |
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| 0:5c11638687d0 | 1:3200899efad9 |
|---|---|
| 1 <tool id="nwdisplay" name="Newick Display" version="1"> | 1 <tool id="nwdisplay" name="Newick Display" version="1.6"> |
| 2 <description>Display a phylogenetic tree as SVG</description> | 2 <description>Display a phylogenetic tree as SVG</description> |
| 3 <edam_operations> | |
| 4 <edam_operation>operation_0567</edam_operation> | |
| 5 </edam_operations> | |
| 3 <requirements> | 6 <requirements> |
| 4 <requirement type="package" version="1.6">newick_utilities</requirement> | 7 <requirement type="package" version="1.6">newick_utilities</requirement> |
| 8 <requirement type="package" version="1.6">newick_utils</requirement> | |
| 5 </requirements> | 9 </requirements> |
| 6 <command> | 10 <command> |
| 7 nw_display | 11 nw_display |
| 8 -s | 12 -s |
| 9 $scalebar | 13 $scalebar |
| 24 transform:$condbranchlength.lentransform;" | 28 transform:$condbranchlength.lentransform;" |
| 25 #else: | 29 #else: |
| 26 "visibility:hidden;" | 30 "visibility:hidden;" |
| 27 #end if | 31 #end if |
| 28 | 32 |
| 29 -l "font-family:$leafPolice;font-size:$leafSize;" | 33 -l "font-family:$leafFont;font-size:$leafSize;" |
| 30 -d "stroke:grey;fill:none;stroke-width:2;stoke-linecap:round;" | 34 -d "stroke:grey;fill:none;stroke-width:2;stoke-linecap:round;" |
| 31 -w $width | 35 -w $width |
| 32 $radial | 36 $radial |
| 33 | 37 |
| 34 $fileNewick > $output | 38 $fileNewick > $output |
| 36 </command> | 40 </command> |
| 37 <inputs> | 41 <inputs> |
| 38 <param name="fileNewick" format="txt,nw,nwk,nhx" type="data" label="Newick file" /> | 42 <param name="fileNewick" format="txt,nw,nwk,nhx" type="data" label="Newick file" /> |
| 39 <param name="scalebar" type="boolean" truevalue="" falsevalue="-S" checked="True" label="Display scale bar" /> | 43 <param name="scalebar" type="boolean" truevalue="" falsevalue="-S" checked="True" label="Display scale bar" /> |
| 40 <param name="legend" type="text" value="" label="Unit name scale" /> | 44 <param name="legend" type="text" value="" label="Unit name scale" /> |
| 41 <param name="leafPolice" type="text" value="sans-serif" label="Leaf police" /> | 45 <param name="leafFont" type="text" value="sans-serif" label="Leaf font" /> |
| 42 <param name="leafSize" type="text" value="10px" label="Leaf font-size" /> | 46 <param name="leafSize" type="text" value="10px" label="Leaf font-size" /> |
| 43 <conditional name="condbranchsupport"> | 47 <conditional name="condbranchsupport"> |
| 44 <param name="branchsupport" type="select" label="Branch support"> | 48 <param name="branchsupport" type="select" label="Branch support"> |
| 45 <option value="true">Display branch support</option> | 49 <option value="true">Display branch support</option> |
| 46 <option value="false" selected="true">Hide branch support</option> | 50 <option value="false" selected="true">Hide branch support</option> |
| 47 </param> | 51 </param> |
| 48 <when value="true"> | 52 <when value="true"> |
| 49 <param name="supcolor" type="text" value="red" label="color" /> | 53 <param name="supcolor" type="color" value="red" label="color" /> |
| 50 <param name="supfontsize" type="text" value="10px" label="font-size" /> | 54 <param name="supfontsize" type="text" value="10px" label="font-size" /> |
| 51 <param name="suptransform" type="text" value="translateY(1.5em)" label="move" /> | 55 <param name="suptransform" type="text" value="translateY(1.5em)" label="move" /> |
| 52 </when> | 56 </when> |
| 53 <when value="false" /> | 57 <when value="false" /> |
| 54 </conditional> | 58 </conditional> |
| 56 <param name="branchlength" type="select" label="Branch length"> | 60 <param name="branchlength" type="select" label="Branch length"> |
| 57 <option value="true">Display branch length</option> | 61 <option value="true">Display branch length</option> |
| 58 <option value="false" selected="true">Hide branch length</option> | 62 <option value="false" selected="true">Hide branch length</option> |
| 59 </param> | 63 </param> |
| 60 <when value="true"> | 64 <when value="true"> |
| 61 <param name="lencolor" type="text" value="blue" label="color" /> | 65 <param name="lencolor" type="color" value="blue" label="color" /> |
| 62 <param name="lenfontsize" type="text" value="10px" label="font-size" /> | 66 <param name="lenfontsize" type="text" value="10px" label="font-size" /> |
| 63 <param name="lentransform" type="text" value="translate(-1.5em,0em)" label="move" /> | 67 <param name="lentransform" type="text" value="translate(-1.5em,0em)" label="move" /> |
| 64 </when> | 68 </when> |
| 65 <when value="false" /> | 69 <when value="false" /> |
| 66 </conditional> | 70 </conditional> |
| 72 </outputs> | 76 </outputs> |
| 73 <tests> | 77 <tests> |
| 74 <test> | 78 <test> |
| 75 <param name="fileNewick" value="tree.nwk"/> | 79 <param name="fileNewick" value="tree.nwk"/> |
| 76 <param name="width" value="400"/> | 80 <param name="width" value="400"/> |
| 77 <param name="leafPolice" value="courier"/> | 81 <param name="leafFont" value="courier"/> |
| 78 <output name="output" file="tree.svg" lines_diff="2"/> | 82 <output name="output" file="tree.svg" lines_diff="2"/> |
| 79 </test> | 83 </test> |
| 80 <test> | 84 <test> |
| 81 <param name="fileNewick" value="tree.nwk"/> | 85 <param name="fileNewick" value="tree.nwk"/> |
| 82 <param name="radial" value="-r"/> | 86 <param name="radial" value="-r"/> |