view blast_report.xml @ 8:71dd0b1d5511 draft

planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/blast_report commit 604191e1284a3d5f8132eec71bb8629901811f8a-dirty

<tool id="blast_report" name="BLAST report" force_history_refresh="true" version="1.1.0">
    <description>Report on BLAST results</description>
    <command >
        <![CDATA[  
          '$__tool_directory__/blast_report.py'
          '${in_tab}'
          '${tmpl.fields.path}'
          '${out_html}'
          '${out_tab}'
          -f '${filter_pident}:$filter_kws'
          #if str($bins) == "None"
            #pass
          #else
          -b "${bins.fields.path}"
          #end if
          #if $hsp_bool
            -r
          #end if
        ]]>
    </command>
    <inputs>
        <param name="in_tab" type="data" format="tabular" label="Tabular BLAST results (extended 26 columns)"/>
        <param name="tmpl" type="select" optional="false" label="Report template">
            <options from_data_table="blast_report_templates">
                <column name="value" index="0"/>
                <column name="name" index="1"/>
		<column name="path" index="2"/>
            </options>
        </param>
        <param name="filter_pident" type="integer" min="90" max="100" value="97" label="Minimum percentage identity"/>
        <param name="filter_kws" type="text" size="50" label="Comma-separated list of description keyword filters" value="bovine,clone,environmental,swine,uncultivated,uncultured,unidentified"/>
        <param name="bins" type="select" label="Database bins" multiple="true" display="checkboxes">
            <options from_data_table="blast_report_bins">
                <column name="value" index="0"/>
                <column name="name" index="1"/>
		<column name="path" index="2"/>
            </options>
        </param>
        <!--<repeat name="hist_bins" title="History database bins">
            <param name="filter" type="data" format="csv" label="History database bin"/>
        </repeat>-->
        <param name="hsp_bool" type="boolean" label="Throw out redundant hits?"/> 
        <param name="tab_bool" type="boolean" label="Output tabular file?"/>
    </inputs>
    <outputs>
        <data name="out_html" format="html" label="$tool.name on data $in_tab.hid: report"/>
        <data name="out_tab" format="tabular" label="$tool.name on data $in_tab.hid: tabular results">
            <filter> tab_bool </filter>
        </data>
    </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>