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Remove deprecated `interpreter attribute from tools <command>`
This commit is contained in:
Nicola Soranzo
@@ -1,91 +1,95 @@
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<tool id="microbial_import1" name="Get Microbial Data" version="1.0.0">
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<command interpreter="python">microbial_import.py $CDS,$tRNA,$rRNA,$sequence,$GeneMark,$GeneMarkHMM,$Glimmer3 $output ${GALAXY_DATA_INDEX_DIR}/microbial_data.loc</command>
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<inputs>
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<param name="kingdom" type="select" label="Select the Desired Kingdom">
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<options from_file="microbial_data.loc" startswith="ORG">
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<column name="name" index="3"/>
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<column name="value" index="3"/>
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<filter type="unique_value" name="unique" column="3"/>
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</options>
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</param>
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<param name="org" type="select" label="Select the Desired Organism">
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<options from_file="microbial_data.loc" startswith="ORG">
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<column name="name" index="2"/>
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<column name="value" index="1"/>
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<filter type="param_value" ref="kingdom" name="kingdom" column="3"/>
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<filter type="sort_by" column="2"/>
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</options>
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</param>
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<param name="CDS" type="select" label="Select Desired Coding Sequences" display="checkboxes" multiple="True">
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<options from_file="microbial_data.loc" startswith="DATA">
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<column name="name" index="3"/>
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<column name="value" index="1"/>
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<column name="feature" index="4"/>
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<filter type="param_value" ref="org" name="kingdom" column="2"/>
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<filter type="static_value" name="feature" value="CDS" column="4"/>
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</options>
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</param>
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<param name="tRNA" type="select" label="Select Desired tRNA" display="checkboxes" multiple="True">
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<options from_file="microbial_data.loc" startswith="DATA">
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<column name="name" index="3"/>
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<column name="value" index="1"/>
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<column name="feature" index="4"/>
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<filter type="param_value" ref="org" name="kingdom" column="2"/>
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<filter type="static_value" name="feature" value="tRNA" column="4"/>
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</options>
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</param>
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<param name="rRNA" type="select" label="Select Desired rRNA" display="checkboxes" multiple="True">
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<options from_file="microbial_data.loc" startswith="DATA">
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<column name="name" index="3"/>
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<column name="value" index="1"/>
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<column name="feature" index="4"/>
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<filter type="param_value" ref="org" name="kingdom" column="2"/>
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<filter type="static_value" name="feature" value="rRNA" column="4"/>
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</options>
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</param>
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<param name="sequence" type="select" label="Select Desired DNA Sequences" display="checkboxes" multiple="True">
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<options from_file="microbial_data.loc" startswith="DATA">
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<column name="name" index="3"/>
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<column name="value" index="1"/>
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<column name="feature" index="4"/>
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<filter type="param_value" ref="org" name="kingdom" column="2"/>
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<filter type="static_value" name="feature" value="sequence" column="4"/>
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</options>
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</param>
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<param name="GeneMark" type="select" label="Select Desired GeneMark Annotations" display="checkboxes" multiple="True">
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<options from_file="microbial_data.loc" startswith="DATA">
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<column name="name" index="3"/>
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<column name="value" index="1"/>
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<column name="feature" index="4"/>
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<filter type="param_value" ref="org" name="kingdom" column="2"/>
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<filter type="static_value" name="feature" value="GeneMark" column="4"/>
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</options>
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</param>
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<param name="GeneMarkHMM" type="select" label="Select Desired GeneMarkHMM Annotations" display="checkboxes" multiple="True">
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<options from_file="microbial_data.loc" startswith="DATA">
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<column name="name" index="3"/>
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<column name="value" index="1"/>
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<column name="feature" index="4"/>
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<filter type="param_value" ref="org" name="kingdom" column="2"/>
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<filter type="static_value" name="feature" value="GeneMarkHMM" column="4"/>
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</options>
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</param>
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<param name="Glimmer3" type="select" label="Select Desired Glimmer3 Annotations" display="checkboxes" multiple="True">
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<options from_file="microbial_data.loc" startswith="DATA">
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<column name="name" index="3"/>
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<column name="value" index="1"/>
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<column name="feature" index="4"/>
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<filter type="param_value" ref="org" name="kingdom" column="2"/>
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<filter type="static_value" name="feature" value="Glimmer3" column="4"/>
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</options>
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</param>
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</inputs>
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<outputs>
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<data format="bed" name="output"/>
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</outputs>
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<code file="microbial_import_code.py"/>
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<help>
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<command><![CDATA[
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python '$__tool_directory__/microbial_import.py'
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$CDS,$tRNA,$rRNA,$sequence,$GeneMark,$GeneMarkHMM,$Glimmer3
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'$output'
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'${GALAXY_DATA_INDEX_DIR}/microbial_data.loc'
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]]></command>
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<inputs>
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<param name="kingdom" type="select" label="Select the Desired Kingdom">
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<options from_file="microbial_data.loc" startswith="ORG">
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<column name="name" index="3"/>
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<column name="value" index="3"/>
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<filter type="unique_value" name="unique" column="3"/>
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</options>
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</param>
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<param name="org" type="select" label="Select the Desired Organism">
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<options from_file="microbial_data.loc" startswith="ORG">
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<column name="name" index="2"/>
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<column name="value" index="1"/>
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<filter type="param_value" ref="kingdom" name="kingdom" column="3"/>
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<filter type="sort_by" column="2"/>
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</options>
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</param>
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<param name="CDS" type="select" label="Select Desired Coding Sequences" display="checkboxes" multiple="True">
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<options from_file="microbial_data.loc" startswith="DATA">
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<column name="name" index="3"/>
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<column name="value" index="1"/>
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<column name="feature" index="4"/>
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<filter type="param_value" ref="org" name="kingdom" column="2"/>
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<filter type="static_value" name="feature" value="CDS" column="4"/>
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</options>
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</param>
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<param name="tRNA" type="select" label="Select Desired tRNA" display="checkboxes" multiple="True">
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<options from_file="microbial_data.loc" startswith="DATA">
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<column name="name" index="3"/>
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<column name="value" index="1"/>
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<column name="feature" index="4"/>
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<filter type="param_value" ref="org" name="kingdom" column="2"/>
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<filter type="static_value" name="feature" value="tRNA" column="4"/>
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</options>
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</param>
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<param name="rRNA" type="select" label="Select Desired rRNA" display="checkboxes" multiple="True">
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<options from_file="microbial_data.loc" startswith="DATA">
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<column name="name" index="3"/>
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<column name="value" index="1"/>
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<column name="feature" index="4"/>
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<filter type="param_value" ref="org" name="kingdom" column="2"/>
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<filter type="static_value" name="feature" value="rRNA" column="4"/>
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</options>
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</param>
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<param name="sequence" type="select" label="Select Desired DNA Sequences" display="checkboxes" multiple="True">
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<options from_file="microbial_data.loc" startswith="DATA">
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<column name="name" index="3"/>
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<column name="value" index="1"/>
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<column name="feature" index="4"/>
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<filter type="param_value" ref="org" name="kingdom" column="2"/>
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<filter type="static_value" name="feature" value="sequence" column="4"/>
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</options>
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</param>
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<param name="GeneMark" type="select" label="Select Desired GeneMark Annotations" display="checkboxes" multiple="True">
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<options from_file="microbial_data.loc" startswith="DATA">
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<column name="name" index="3"/>
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<column name="value" index="1"/>
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<column name="feature" index="4"/>
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<filter type="param_value" ref="org" name="kingdom" column="2"/>
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<filter type="static_value" name="feature" value="GeneMark" column="4"/>
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</options>
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</param>
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<param name="GeneMarkHMM" type="select" label="Select Desired GeneMarkHMM Annotations" display="checkboxes" multiple="True">
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<options from_file="microbial_data.loc" startswith="DATA">
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<column name="name" index="3"/>
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<column name="value" index="1"/>
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<column name="feature" index="4"/>
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<filter type="param_value" ref="org" name="kingdom" column="2"/>
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<filter type="static_value" name="feature" value="GeneMarkHMM" column="4"/>
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</options>
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</param>
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<param name="Glimmer3" type="select" label="Select Desired Glimmer3 Annotations" display="checkboxes" multiple="True">
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<options from_file="microbial_data.loc" startswith="DATA">
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<column name="name" index="3"/>
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<column name="value" index="1"/>
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<column name="feature" index="4"/>
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<filter type="param_value" ref="org" name="kingdom" column="2"/>
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<filter type="static_value" name="feature" value="Glimmer3" column="4"/>
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</options>
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</param>
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</inputs>
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<outputs>
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<data name="output" format="bed"/>
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</outputs>
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<code file="microbial_import_code.py"/>
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<help><![CDATA[
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This tool will allow you to obtain various genomic datasets for any completed Microbial Genome Project as listed at NCBI_.
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.. _NCBI: http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi?view=1
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@@ -102,5 +106,5 @@ Current datasets available include
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-----
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Organisms in **bold** are available at the UCSC Browser.
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</help>
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]]></help>
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</tool>
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