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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://wiki.g2.bx.psu.edu/Main/Data%20Libraries/Microbes
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113
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114 </help>
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115 </tool>
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