Mercurial > repos > dfornika > blast_report_basic

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author dfornika
date Tue, 03 Mar 2020 10:55:25 +0000
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1 <tool id="blast_report_basic" name="BLAST report" version="0.1.0+galaxy0" >
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2 <description>Produce an HTML table report of BLAST results</description>
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3 <command>
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4 <![CDATA[
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5 python '${__tool_directory__}/blast_report.py'
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6 --min-identity ${min_identity}
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7 --filter-keywords '${filter_keywords}'
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8 $discard_redundant
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9 '${tabular_blast_report_input}'
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10 '${__tool_directory__}/templates/template2.tmpl'
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11 '${out_html}'
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12 '${out_tab}'
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13 #if str($reference_database_bins) != "None"
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14 #for $name, $path in zip(str($reference_database_bins.fields.name).split(','), str($reference_database_bins.fields.path).split(',')):
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15 -b '${name}' '${path}'
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16 #end for
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17 #end if
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18 ]]>
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19 </command>
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20 <inputs>
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21 <param name="tabular_blast_report_input" type="data" format="tabular" label="Tabular BLAST results (extended 25 columns + qcov)"/>
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22 <param name="min_identity" type="integer" min="90" max="100" value="97" label="Minimum percentage identity"/>
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23 <param name="filter_keywords" type="text" size="50" label="Comma-separated list of description keyword filters" value="bovine,clone,environmental,swine,uncultivated,uncultured,unidentified"/>
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24 <param name="reference_database_bins" type="select" label="Reference Database Bins" multiple="true" display="checkboxes">
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25 <options from_data_table="blast_report_reference_database_bins">
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26 <validator type="no_options" message="No BLAST reference bins available" />
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27 </options>
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28 </param>
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29 <param name="discard_redundant" type="boolean" truevalue="-r" falsevalue="" label="Throw out redundant hits?"/>
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30 </inputs>
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31 <outputs>
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32 <data name="out_html" format="html" label="$tool.name on data $tabular_blast_report_input.hid: report"/>
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33 <data name="out_tab" format="tabular" label="$tool.name on data $tabular_blast_report_input.hid: tabular results"/>
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="reference_database_bins" value="test_entry"/>
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38 <param name="tabular_blast_report_input" value="NR_114042.1_vs_NCBI16SMicrobial_top20_standard25col_plus_qcovs.tsv"/>
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39 <output name="out_tab" file="NR_114042.1_vs_NCBI16SMicrobial_output_report_tabular.tsv" ftype="tabular"/>
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40 </test>
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41 </tests>
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42 <help>
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44 .. class:: infomark
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46 **What it does**
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48 This tool produces a HTML report for each query in a tabular BLAST file.
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50 ----
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52 **Tabular BLAST results**
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54 One or more query's BLAST results in extended 26 column tabular format.
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56 ----
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58 **Report template**
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60 The report template dictates the format of the HTML report.
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61 Note that changing the template from the standard "Top 20 hits shown, toggle remainder" to "Euzby results shown first" causes
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62 the order of the results in the HTML report and the tabular BLAST results (if outputted) to be inconsistent with each other.
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64 ----
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66 **Minimum percentage identity**
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68 Filter by percentage identity. This filter is applied before the description keyword filters.
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70 ----
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72 **Comma-separated list of description keyword filters**
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74 Filter by description keywords. Do not include spaces (unless your keyword is two words). These are applied
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75 after the percentage identity filter.
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77 ----
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79 **Database bins**
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81 Bin the results by accession number into "database bins."
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83 ----
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85 **Throw out redundant hits?**
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87 Only the first hit for any accession number will be reported.
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89 </help>
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90 </tool>