[2] | 1 | <tool id="microbial_import1" name="Get Microbial Data">
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| 2 | <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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| 3 | <inputs>
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| 4 | <param name="kingdom" type="select" label="Select the Desired Kingdom">
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| 5 | <options from_file="microbial_data.loc" startswith="ORG">
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| 6 | <column name="name" index="3"/>
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| 7 | <column name="value" index="3"/>
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| 8 | <filter type="unique_value" name="unique" column="3"/>
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| 9 | </options>
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| 10 | </param>
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| 11 | <param name="org" type="select" label="Select the Desired Organism">
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| 12 | <options from_file="microbial_data.loc" startswith="ORG">
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| 13 | <column name="name" index="2"/>
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| 14 | <column name="value" index="1"/>
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| 15 | <filter type="param_value" ref="kingdom" name="kingdom" column="3"/>
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| 16 | <filter type="sort_by" column="2"/>
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| 17 | </options>
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| 18 | </param>
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| 19 | <param name="CDS" type="select" label="Select Desired Coding Sequences" display="checkboxes" multiple="True">
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| 20 | <options from_file="microbial_data.loc" startswith="DATA">
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| 21 | <column name="name" index="3"/>
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| 22 | <column name="value" index="1"/>
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| 23 | <column name="feature" index="4"/>
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| 24 | <filter type="param_value" ref="org" name="kingdom" column="2"/>
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| 25 | <filter type="static_value" name="feature" value="CDS" column="4"/>
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| 26 | </options>
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| 27 | </param>
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| 28 | <param name="tRNA" type="select" label="Select Desired tRNA" display="checkboxes" multiple="True">
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| 29 | <options from_file="microbial_data.loc" startswith="DATA">
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| 30 | <column name="name" index="3"/>
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| 31 | <column name="value" index="1"/>
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| 32 | <column name="feature" index="4"/>
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| 33 | <filter type="param_value" ref="org" name="kingdom" column="2"/>
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| 34 | <filter type="static_value" name="feature" value="tRNA" column="4"/>
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| 35 | </options>
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| 36 | </param>
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| 37 | <param name="rRNA" type="select" label="Select Desired rRNA" display="checkboxes" multiple="True">
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| 38 | <options from_file="microbial_data.loc" startswith="DATA">
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| 39 | <column name="name" index="3"/>
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| 40 | <column name="value" index="1"/>
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| 41 | <column name="feature" index="4"/>
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| 42 | <filter type="param_value" ref="org" name="kingdom" column="2"/>
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| 43 | <filter type="static_value" name="feature" value="rRNA" column="4"/>
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| 44 | </options>
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| 45 | </param>
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| 46 | <param name="sequence" type="select" label="Select Desired DNA Sequences" display="checkboxes" multiple="True">
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| 47 | <options from_file="microbial_data.loc" startswith="DATA">
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| 48 | <column name="name" index="3"/>
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| 49 | <column name="value" index="1"/>
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| 50 | <column name="feature" index="4"/>
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| 51 | <filter type="param_value" ref="org" name="kingdom" column="2"/>
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| 52 | <filter type="static_value" name="feature" value="sequence" column="4"/>
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| 53 | </options>
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| 54 | </param>
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| 55 | <param name="GeneMark" type="select" label="Select Desired GeneMark Annotations" display="checkboxes" multiple="True">
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| 56 | <options from_file="microbial_data.loc" startswith="DATA">
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| 57 | <column name="name" index="3"/>
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| 58 | <column name="value" index="1"/>
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| 59 | <column name="feature" index="4"/>
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| 60 | <filter type="param_value" ref="org" name="kingdom" column="2"/>
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| 61 | <filter type="static_value" name="feature" value="GeneMark" column="4"/>
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| 62 | </options>
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| 63 | </param>
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| 64 | <param name="GeneMarkHMM" type="select" label="Select Desired GeneMarkHMM Annotations" display="checkboxes" multiple="True">
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| 65 | <options from_file="microbial_data.loc" startswith="DATA">
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| 66 | <column name="name" index="3"/>
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| 67 | <column name="value" index="1"/>
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| 68 | <column name="feature" index="4"/>
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| 69 | <filter type="param_value" ref="org" name="kingdom" column="2"/>
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| 70 | <filter type="static_value" name="feature" value="GeneMarkHMM" column="4"/>
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| 71 | </options>
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| 72 | </param>
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| 73 | <param name="Glimmer3" type="select" label="Select Desired Glimmer3 Annotations" display="checkboxes" multiple="True">
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| 74 | <options from_file="microbial_data.loc" startswith="DATA">
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| 75 | <column name="name" index="3"/>
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| 76 | <column name="value" index="1"/>
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| 77 | <column name="feature" index="4"/>
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| 78 | <filter type="param_value" ref="org" name="kingdom" column="2"/>
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| 79 | <filter type="static_value" name="feature" value="Glimmer3" column="4"/>
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| 80 | </options>
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| 81 | </param>
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| 82 | </inputs>
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| 83 | <outputs>
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| 84 | <data format="bed" name="output"/>
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| 85 | </outputs>
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| 86 | <code file="microbial_import_code.py"/>
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| 87 | <help>
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| 88 |
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| 89 | This tool will allow you to obtain various genomic datasets for any completed Microbial Genome Project as listed at NCBI_.
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| 90 |
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| 91 | .. _NCBI: http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi?view=1
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| 92 |
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| 93 | Current datasets available include
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| 94 | 1. CDS
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| 95 | 2. tRNA
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| 96 | 3. rRNA
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| 97 | 4. FASTA Sequences
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| 98 | 5. GeneMark Annotations
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| 99 | 6. GeneMarkHMM Annotations
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| 100 | 7. Glimmer3 Annotations
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| 101 |
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| 102 | -----
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| 103 |
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| 104 | Organisms in **bold** are available at the UCSC Browser.
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| 105 |
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| 106 | -----
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| 107 |
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| 108 | .. class:: infomark
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| 109 |
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| 110 | **Note:** Having trouble locating your organism? Click here_ for a list of available species and their location.
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| 111 |
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| 112 | .. _here: http://bitbucket.org/galaxy/galaxy-central/wiki/Microbes
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| 113 |
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| 114 | </help>
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| 115 | </tool>
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