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Add cooler zoomify #15

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Apr 2, 2024
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41 changes: 41 additions & 0 deletions tools/cooler/cooler_zoomify.xml
Original file line number Diff line number Diff line change
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<tool id="cooler_zoomify" name="Cooler zoomify" version="@VERSION@+galaxy0" profile="18.01">
<description>Generate a multi-resolution cooler file by coarsening</description>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements" />
<expand macro="stdio" />
<command detect_errors="exit_code"><![CDATA[
cooler zoomify -p \${GALAXY_SLOTS:-4}
-c $c
-r $r
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-o '$output'
'$input'
]]>
</command>
<inputs>
<param name="input" multiple="false" type="data" format="cool" label="Select the input cool file to zoomify"/>
<param argument="-c" type="integer" value="10000000" label="Number of pixels dedicated to each process"/>
<param argument="-r" type="text" value="B" label="Resultion" help="Comma-separated list of target resolutions. Use suffixes B or N to specify a progression: B for binary (geometric steps of factor 2), N for nice (geometric steps of factor 10 interleaved with steps of 2 and 5). Examples: 1000B=1000,2000,4000,8000,... 1000N=1000,2000,5000,10000,... 5000N=5000,10000,25000,50000,... 4DN is an alias for 1000,2000,5000N">
<validator type="regex">[BDN0-9,]+</validator>
</param>
</inputs>

<outputs>
<data format="mcool" name="output" label="Multi-resolution mcool file from $input.name"/>
</outputs>

<tests>
<test>
<param name="input" value="input.cool" ftype="cool"/>
<output name="output" file="output.mcool" ftype="mcool" compare="sim_size"/>
</test>
</tests>

<help>
**cooler zoomify**
Generate a multi-resolution cooler file by coarsening
Given a set of resolutions, generate a multi-cooler file from a cooler for visualisation with higlass.
</help>
<expand macro="citation_cooler" />
</tool>
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