Mercurial > repos > dfornika > blast_report_basic
diff blast_report_basic.xml @ 0:5dfd84907521 draft
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
author | dfornika |
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date | Tue, 03 Mar 2020 00:14:34 +0000 |
parents | |
children | a63f676fe808 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/blast_report_basic.xml Tue Mar 03 00:14:34 2020 +0000 @@ -0,0 +1,86 @@ +<tool id="blast_report_basic" name="BLAST report" version="0.1.0+galaxy0" > + <description>Produce an HTML table report of BLAST results</description> + <command detect_errors="error_code"> + <![CDATA[ + '${__tool_directory__}/blast_report.py' + -f ${filter_pident}:$filter_kws + #if str($bins) != "None" + -b "${bins}" + #end if + $discard_redundant + '${tabular_blast_report_input}' + '${__tool_directory__}/templates/template2.tmpl}' + '${out_html}' + '${out_tab}' + ]]> + </command> + <inputs> + <param name="tabular_blast_report_input" type="data" format="tabular" label="Tabular BLAST results (extended 26 columns)"/> + <param name="filter_pident" type="integer" min="90" max="100" value="97" label="Minimum percentage identity"/> + <param name="filter_kws" type="text" size="50" label="Comma-separated list of description keyword filters" value="bovine,clone,environmental,swine,uncultivated,uncultured,unidentified"/> + <param name="bins" type="select" label="Database bins" multiple="true" display="checkboxes"> + <options from_data_table="blast_reference_bins"> + <validator type="no_options" message="No BLAST reference bins available" /> + </options> + </param> + <param name="discard_redundant" type="boolean" truevalue="-r" falsevalue="" label="Throw out redundant hits?"/> + </inputs> + <outputs> + <data name="out_html" format="html" label="$tool.name on data $in_tab.hid: report"/> + <data name="out_tab" format="tabular" label="$tool.name on data $in_tab.hid: tabular results"/> + </outputs> + <help> + +.. class:: infomark + +**What it does** + +This tool produces a HTML report for each query in a tabular BLAST file. + +---- + +**Tabular BLAST results** + +One or more query's BLAST results in extended 26 column tabular format. + +---- + +**Report template** + +The report template dictates the format of the HTML report. +Note that changing the template from the standard "Top 20 hits shown, toggle remainder" to "Euzby results shown first" causes +the order of the results in the HTML report and the tabular BLAST results (if outputted) to be inconsistent with each other. + +---- + +**Minimum percentage identity** + +Filter by percentage identity. This filter is applied before the description keyword filters. + +---- + +**Comma-separated list of description keyword filters** + +Filter by description keywords. Do not include spaces (unless your keyword is two words). These are applied +after the percentage identity filter. + +---- + +**Database bins** + +Bin the results by accession number into "database bins." + +---- + +**Throw out redundant hits?** + +Only the first hit for any accession number will be reported. + +---- + +**Output tabular BLAST results?** + +This option produces a tabular BLAST file with the same results as those shown in the report. + + </help> +</tool>