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69 lines
3.6 KiB
XML
69 lines
3.6 KiB
XML
<tool id="microbial_import1" name="Get Microbial Data">
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<command interpreter="python">microbial_import.py $CDS,$tRNA,$rRNA,$sequence,$GeneMark,$GeneMarkHMM,$Glimmer3 $output</command>
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<inputs>
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<page>
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<display>
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<p><div class="toolFormTitle">Select the Desired Kingdom</div>$kingdom</p>
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</display>
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<param name="kingdom" type="select" display="radio" multiple="False" dynamic_options="get_kingdoms()"/>
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</page>
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<page>
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<display>
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<p><div class="toolFormTitle">Select the Desired Organism</div>$org</p>
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</display>
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<param name="org" type="select" display="radio" multiple="False" dynamic_options="get_orgs_by_kingdom(GALAXY_TOOL_PARAMS.kingdom)"/>
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</page>
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<page>
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<display>
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<p><div class="toolFormTitle">Select Desired Coding Sequences</div>$CDS</p>
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<p><div class="toolFormTitle">Select Desired tRNA</div>$tRNA</p>
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<p><div class="toolFormTitle">Select Desired rRNA</div>$rRNA</p>
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<p><div class="toolFormTitle">Select Desired DNA Sequences</div>$sequence</p>
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<p><div class="toolFormTitle">Select Desired GeneMark Annotations</div>$GeneMark</p>
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<p><div class="toolFormTitle">Select Desired GeneMarkHMM Annotations</div>$GeneMarkHMM</p>
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<p><div class="toolFormTitle">Select Desired Glimmer3 Annotations</div>$Glimmer3</p>
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<p></p>
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</display>
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<param name="CDS" type="select" display="checkboxes" multiple="True" dynamic_options="get_data_by_kingdom_org_feature(GALAXY_TOOL_PARAMS.kingdom,GALAXY_TOOL_PARAMS.org,'CDS')"/>
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<param name="tRNA" type="select" display="checkboxes" multiple="True" dynamic_options="get_data_by_kingdom_org_feature(GALAXY_TOOL_PARAMS.kingdom,GALAXY_TOOL_PARAMS.org,'tRNA')"/>
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<param name="rRNA" type="select" display="checkboxes" multiple="True" dynamic_options="get_data_by_kingdom_org_feature(GALAXY_TOOL_PARAMS.kingdom,GALAXY_TOOL_PARAMS.org,'rRNA')"/>
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<param name="sequence" type="select" display="checkboxes" multiple="True" dynamic_options="get_data_by_kingdom_org_feature(GALAXY_TOOL_PARAMS.kingdom,GALAXY_TOOL_PARAMS.org,'sequence')"/>
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<param name="GeneMark" type="select" display="checkboxes" multiple="True" dynamic_options="get_data_by_kingdom_org_feature(GALAXY_TOOL_PARAMS.kingdom,GALAXY_TOOL_PARAMS.org,'GeneMark')"/>
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<param name="GeneMarkHMM" type="select" display="checkboxes" multiple="True" dynamic_options="get_data_by_kingdom_org_feature(GALAXY_TOOL_PARAMS.kingdom,GALAXY_TOOL_PARAMS.org,'GeneMarkHMM')"/>
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<param name="Glimmer3" type="select" display="checkboxes" multiple="True" dynamic_options="get_data_by_kingdom_org_feature(GALAXY_TOOL_PARAMS.kingdom,GALAXY_TOOL_PARAMS.org,'Glimmer3')"/>
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</page>
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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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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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Current datasets available include
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1. CDS
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2. tRNA
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3. rRNA
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4. FASTA Sequences
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5. GeneMark Annotations
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6. GeneMarkHMM Annotations
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7. Glimmer3 Annotations
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-----
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Organisms in **bold** are available at the UCSC Browser.
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-----
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.. class:: infomark
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**Note:** Having trouble locating your organism? Click here_ for a list of available species and their location.
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.. _here: http://www.bx.psu.edu/cgi-bin/trac.cgi/wiki/Microbes
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</help>
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</tool>
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