Mercurial > repos > iuc > odgi_viz
diff vis.xml @ 0:eeea2b5a81dd draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
author | iuc |
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date | Wed, 08 Apr 2020 12:12:55 -0400 |
parents | |
children | 536768de4748 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vis.xml Wed Apr 08 12:12:55 2020 -0400 @@ -0,0 +1,57 @@ +<tool id="odgi_viz" name="odgi viz" version="@TOOL_VERSION@"> + <description>variation graph visualizations</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +odgi viz +-i '$input' +--out='$output' +-x $width +-y $height +#if str($path_height) + --path-height=$path_height +#end if +#if str($path_x_padding) + --path-x-padding=$path_x_padding +#end if +$path_per_row +#if str($link_path_pieces): + --link-path-pieces=$link_path_pieces +#end if +--threads=\${GALAXY_SLOTS:-1} + ]]></command> + <inputs> + <param name="input" type="data" format="odgi" label="odgi input file" /> + + <param argument="--width" type="integer" min="0" value="4000" label="Width in pixels of output image" /> + <param argument="--height" type="integer" min="0" value="500" label="Height in pixels of output image" /> + + <param argument="--path-height" type="integer" min="0" optional="true" label="Path display height" /> + <param argument="--path-x-padding" type="integer" min="0" optional="true" label="Path x padding" /> + <param argument="--path-per-row" type="boolean" truevalue="--path-per-row" falsevalue="" + label="Display a single path per row rather than packing them" /> + + <param argument="--link-path-pieces" type="float" optional="true" + label="Show thin links of this relative width to connect path pieces" /> + </inputs> + <outputs> + <data name="output" format="png" /> + </outputs> + <tests> + <test> + <param name="input" value="note5_out.og" /> + <param name="width" value="4000" /> + <param name="height" value="500" /> + <output name="output" file="note5.png" ftype="png" /> + </test> + </tests> + <help><![CDATA[ +optimized dynamic genome/graph implementation (odgi) +---------------------------------------------------- + +variation graph visualizations (viz) + ]]></help> + <expand macro="citations" /> +</tool>