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Enis Afgan
40 lines
1.4 KiB
XML
40 lines
1.4 KiB
XML
<tool id="interactive_tool_phinch" tool_type="interactive" name="Phinch Visualisation" version="0.1">
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<icon src="phinch.png" />
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<requirements>
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<container type="docker">shiltemann/docker-phinch-galaxy:16.04</container>
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</requirements>
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<entry_points>
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<entry_point name="Phinch Visualisation of $infile.display_name" requires_domain="True">
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<port>80</port>
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</entry_point>
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</entry_points>
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<command><![CDATA[
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## ToDo nginx, proxy.conf etc can be removed from the container
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#import os
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#set $name = os.path.splitext(str($infile.display_name).replace(' ', '_'))[0]
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## in case someone names the data testdata.
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rm /home/Phinch/data/testdata.biom | true &&
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ln -s '$infile' '/home/Phinch/data/${name}.biom' &&
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cd /home/Phinch/data &&
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sed -i "s/'REPLACE_ME'/'${name}.biom'/g" /home/Phinch/scripts/readFile.js &&
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sed -i "s/http/https/g" /home/Phinch/scripts/readFile.js &&
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## keep it running
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cd /home/Phinch &&
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php -S 0.0.0.0:80 2>&1 > /var/log/phinch.log
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]]>
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</command>
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<inputs>
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<param name="infile" type="data" format="biom1" label="Biom1 dataset"/>
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</inputs>
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<outputs>
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<data name="outfile" format="txt" />
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</outputs>
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<tests>
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</tests>
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<help>
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Interactive tool for visualising Biom data.
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</help>
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</tool>
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