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Alexander OSTROVSKY
2641c692e2
accidental files more files migrate ITs from EU accidental files more files migrate ITs from EU accidental files more files migrate ITs from EU accidental files more files
51 lines
2.1 KiB
XML
51 lines
2.1 KiB
XML
<tool id="interactive_tool_vcf_iobio" tool_type="interactive" name="VCF (iobio) Visualisation" version="0.1">
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<requirements>
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<container type="docker">qiaoy/iobio-bundle.vcf-iobio:dev-ondemand</container>
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</requirements>
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<entry_points>
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<entry_point name="VCF io.bio visualisation of $infile.display_name" requires_domain="True">
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<port>80</port>
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<url><![CDATA[/?vcf=http://localhost/tmp/vcffile.vcf.gz]]></url>
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</entry_point>
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</entry_points>
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<command><![CDATA[
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#set $PUB_HOSTNAME = 'localhost'
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#set $PUB_HTTP_PORT = '80'
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cd /var/www/html &&
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sed -i "s@\"wss://services.iobio.io/vcfdepther/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/vcfdepther/\"@" app/vcf.iobio.js &&
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sed -i "s@\"wss://services.iobio.io/vcfstatsalive/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/vcfstatsalive/\"@" app/vcf.iobio.js &&
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sed -i "s@\"wss://services.iobio.io/tabix/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/tabix/\"@" app/vcf.iobio.js &&
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sed -i 's/deny all;//g' /etc/nginx/nginx.conf &&
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ln -s '$infile' /input/vcffile.vcf.gz &&
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#if $infile.metadata.tabix_index:
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ln -s '${infile.metadata.tabix_index}' /input/vcffile.vcf.gz.tbi &&
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#end if
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head -n -2 /etc/supervisor.d/app.conf > /tmp/app.conf &&
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mv /tmp/app.conf /etc/supervisor.d/app.conf &&
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/usr/bin/supervisord -c /etc/supervisord.conf
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]]>
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</command>
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<inputs>
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<param name="infile" type="data" format="vcf_bgzip" label="Compressed VCF file"/>
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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><![CDATA[
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Examine your variant file in seconds with the VCF `iobio visualisation <https://vcf.iobio.io>`_.
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This visualization is using Galaxy Interactive Tool and utilizes an all-in-one Docker container from http://iobio.io.
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Make sure your VCF file is compressed to the vcf_bgzip datatype to load it into the Visualization.
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]]>
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</help>
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</tool>
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