Mercurial > repos > iuc > odgi_viz

comparison vis.xml @ 0:1b69beb7fb85 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
author iuc
date Wed, 08 Apr 2020 16:11:29 +0000
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children b1319597ce74
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-1:000000000000 0:1b69beb7fb85
1 <tool id="odgi_viz" name="odgi viz" version="@TOOL_VERSION@">
2 <description>variation graph visualizations</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 odgi viz
9 -i '$input'
10 --out='$output'
11 -x $width
12 -y $height
13 #if str($path_height)
14 --path-height=$path_height
15 #end if
16 #if str($path_x_padding)
17 --path-x-padding=$path_x_padding
18 #end if
19 $path_per_row
20 #if str($link_path_pieces):
21 --link-path-pieces=$link_path_pieces
22 #end if
23 --threads=\${GALAXY_SLOTS:-1}
24 ]]></command>
25 <inputs>
26 <param name="input" type="data" format="odgi" label="odgi input file" />
27
28 <param argument="--width" type="integer" min="0" value="4000" label="Width in pixels of output image" />
29 <param argument="--height" type="integer" min="0" value="500" label="Height in pixels of output image" />
30
31 <param argument="--path-height" type="integer" min="0" optional="true" label="Path display height" />
32 <param argument="--path-x-padding" type="integer" min="0" optional="true" label="Path x padding" />
33 <param argument="--path-per-row" type="boolean" truevalue="--path-per-row" falsevalue=""
34 label="Display a single path per row rather than packing them" />
35
36 <param argument="--link-path-pieces" type="float" optional="true"
37 label="Show thin links of this relative width to connect path pieces" />
38 </inputs>
39 <outputs>
40 <data name="output" format="png" />
41 </outputs>
42 <tests>
43 <test>
44 <param name="input" value="note5_out.og" />
45 <param name="width" value="4000" />
46 <param name="height" value="500" />
47 <output name="output" file="note5.png" ftype="png" />
48 </test>
49 </tests>
50 <help><![CDATA[
51 optimized dynamic genome/graph implementation (odgi)
52 ----------------------------------------------------
53
54 variation graph visualizations (viz)
55 ]]></help>
56 <expand macro="citations" />
57 </tool>