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55 lines
2.3 KiB
XML
55 lines
2.3 KiB
XML
<tool id="interactive_tool_blobtoolkit" tool_type="interactive" name="Interactive BlobToolKit" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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<icon src="blobtoolkit.png" />
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<description>genome assembly QC viewer</description>
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<macros>
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<token name="@TOOL_VERSION@">4.1.0</token>
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<token name="@VERSION_SUFFIX@">0</token>
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</macros>
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<requirements>
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<container type="docker">quay.io/galaxy/blobtoolkit-server:@TOOL_VERSION@</container>
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</requirements>
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<entry_points>
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<entry_point name="Blobtoolkit View" requires_domain="True">
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<port>80</port>
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<url>view/all</url>
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</entry_point>
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</entry_points>
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<command detect_errors="exit_code"><![CDATA[
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## The following is a hack. Our embedded pulsar is not respecting the Galaxy jwd-tmp dir.
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export TEMP=\$PWD &&
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export TMP=\$PWD &&
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export TMPDIR=\$PWD &&
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mkdir datasets &&
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cd datasets &&
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mkdir './Blobdir' &&
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#if $blobdir:
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#if $blobdir.is_of_type("tgz")
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tar -zxf '${blobdir}' -C './Blobdir' &&
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#else
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tar -xf '${blobdir}' -C './Blobdir' &&
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#end if
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cd .. &&
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export BTK_FILE_PATH=\$PWD/datasets &&
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startup.sh
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#else:
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cd .. &&
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startup.sh
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#end if
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]]></command>
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<inputs>
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<param name="blobdir" type="data" format="tgz,tar" optional="true" label="Blobdir file" help="This file should be generated by the module create. The collection of JSON files should be packed in the tarbal file without directory structure." />
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</inputs>
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<outputs>
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<data name="Interactive BlobToolKit on data ${on_string}" 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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BlobToolKit is a software suite to aid researchers in identifying and isolating non-target data in draft and publicly available genome assemblies. It can be used to process assembly,
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read and analysis files for fully reproducible interactive exploration in the browser-based Viewer. BlobToolKit can be used during assembly to filter non-target DNA, helping researchers produce assemblies with high biological credibility.
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]]></help>
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<citations>
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<citation type="doi">10.1534/g3.119.400908</citation>
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</citations>
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</tool>
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