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comparison newick_display.xml @ 1:b4163d2f64ab draft default tip

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"planemo upload for repository https://github.com/tjunier/newick_utils commit 352b2b1efa8400e145f02adb34e36c4af4524e54"
author iuc
date Sun, 01 Dec 2019 17:33:02 -0500
parents fe4235285ee8
children
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0:fe4235285ee8 1:b4163d2f64ab
1 <tool id="newick_display" name="Newick Display" version="1.6"> 1 <tool id="newick_display" name="Newick Display" version="1.6+galaxy1">
2 <description>visualize a phylogenetic tree</description> 2 <description>visualize a phylogenetic tree</description>
3 <edam_operations> 3 <edam_operations>
4 <edam_operation>operation_0567</edam_operation> 4 <edam_operation>operation_0567</edam_operation>
5 </edam_operations> 5 </edam_operations>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="1.6">newick_utils</requirement> 7 <requirement type="package" version="1.6">newick_utils</requirement>
8 <requirement type="package" version="7.0.9_6">imagemagick</requirement>
8 </requirements> 9 </requirements>
9 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
10 nw_display 11 nw_display
11 #if $outformat != 'txt': 12 #if $outformat != 'txt':
12 -s 13 -s
34 -l 'font-family:$leafFont;font-size:$leafSize;' 35 -l 'font-family:$leafFont;font-size:$leafSize;'
35 -d "stroke:grey;fill:none;stroke-width:2;stoke-linecap:round;" 36 -d "stroke:grey;fill:none;stroke-width:2;stoke-linecap:round;"
36 -w $width 37 -w $width
37 $radial 38 $radial
38 39
39 '$fileNewick' > output.svg 40 '$fileNewick'
40 41
41 #if $outformat == 'png': 42 #if $outformat == 'png':
42 && convert output.svg output.png 43 | convert - 'png:$output'
43 && mv output.png '$output' 44 #else:
44 #else: 45 > '$output'
45 && mv output.svg '$output' 46 #end if
46 #end if
47
48 ]]></command> 47 ]]></command>
49 <inputs> 48 <inputs>
50 <param name="fileNewick" format="txt,newick,nw,nwk,nhx,mothur.tre" type="data" label="Newick file"/> 49 <param name="fileNewick" format="txt,newick,nw,nwk,nhx,mothur.tre" type="data" label="Newick file"/>
51 <param name="scalebar" type="boolean" truevalue="" falsevalue="-S" checked="True" label="Display scale bar" /> 50 <param name="scalebar" type="boolean" truevalue="" falsevalue="-S" checked="True" label="Display scale bar" />
52 <param name="legend" type="text" value="" label="Unit name for the scale bar" /> 51 <param name="legend" type="text" value="" label="Unit name for the scale bar" />
110 <param name="radial" value="-r"/> 109 <param name="radial" value="-r"/>
111 <param name="branchlength" value="true"/> 110 <param name="branchlength" value="true"/>
112 <param name="outformat" value="png"/> 111 <param name="outformat" value="png"/>
113 <output name="output" file="tree.png" ftype="png" compare="sim_size" delta="15000"/> 112 <output name="output" file="tree.png" ftype="png" compare="sim_size" delta="15000"/>
114 </test> 113 </test>
115 <test><!-- test with txt output format --> 114 <test><!-- test with txt output format -->
116 <param name="fileNewick" value="tree.nwk"/> 115 <param name="fileNewick" value="tree.nwk"/>
117 <param name="outformat" value="txt"/> 116 <param name="outformat" value="txt"/>
118 <output name="output" file="tree.txt" ftype="txt"/> 117 <output name="output" file="tree.txt" ftype="txt"/>
119 </test> 118 </test>
120 </tests> 119 </tests>