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43 lines
1.8 KiB
XML
43 lines
1.8 KiB
XML
<tool id="interactive_tool_bam_iobio" tool_type="interactive" name="bam.iobio visualisation" version="0.4.0">
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<requirements>
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<container type="docker">quay.io/iobio/bam.iobio.io:0.4.0</container>
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</requirements>
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<entry_points>
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<entry_point name="BAM io.bio visualisation of $baminfile.element_identifier" requires_domain="True">
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<port>9001</port>
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<url>/</url>
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</entry_point>
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</entry_points>
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<command><![CDATA[
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#import re
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mkdir -p /bam/input_files;
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#set $bam_cleaned_name = re.sub('[^\w\-\.]', '_', str($baminfile.element_identifier))
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ln -sf '$baminfile' '/bam/input_files/${bam_cleaned_name}' &&
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ln -sf '$baminfile.metadata.bam_index' '/bam/input_files/${bam_cleaned_name}.bai' &&
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echo '{ "bam": "http://localhost:9999/${bam_cleaned_name}", "bai":"http://localhost:9999/${bam_cleaned_name}.bai"}' >> /bam/config/config.json &&
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cd /bam/input_files &&
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node /iobio-gru-backend/src/static_server.js 9999 > /dev/null 2>&1 &
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node /iobio-gru-backend/src/index.js --tools-dir=/iobio-gru-backend/tool_bin --app-dir=/bam > /dev/null 2>&1;
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]]>
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</command>
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<inputs>
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<param name="baminfile" type="data" format="bam" label="BAM 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>
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Required inputs:
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1. BAM file: binary alignment map file
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The `iobio project`_ is developed by the `Marth lab`_ at the `University of Utah Center for Genetic Discovery`_.
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.. _iobio project: https://iobio.io
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.. _Marth lab: https://marthlab.org/
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.. _University of Utah Center for Genetic Discovery: https://ucgd.genetics.utah.edu/
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</help>
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</tool>
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