comparison blast_report_basic.xml @ 21:bb237fe7fb05 draft

Uploaded

20:d8ff114ba12f

    <command>
        <![CDATA[
          python '${__tool_directory__}/blast_report.py' 
            --min-identity ${min_identity}
            --filter-keywords '${filter_keywords}'
            #if str($bins) != "None"
              -b '${bins.fields.path}'
            #end if
            $discard_redundant
            '${tabular_blast_report_input}'
            '${__tool_directory__}/templates/template2.tmpl'
            '${out_html}'

    </command>
    <inputs>
        <param name="tabular_blast_report_input" type="data" format="tabular" label="Tabular BLAST results (extended 25 columns + qcov)"/>
        <param name="min_identity" type="integer" min="90" max="100" value="97" label="Minimum percentage identity"/>
        <param name="filter_keywords" 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="Reference Database Bins" multiple="true" display="checkboxes">
            <options from_data_table="blast_report_reference_database_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?"/> 

    <outputs>
        <data name="out_html" format="html" label="$tool.name on data $tabular_blast_report_input.hid: report"/>
        <data name="out_tab" format="tabular" label="$tool.name on data $tabular_blast_report_input.hid: tabular results"/>
    </outputs>
    <tests>
    </tests>
    <help>

.. class:: infomark

21:bb237fe7fb05

    <command>
        <![CDATA[
          python '${__tool_directory__}/blast_report.py' 
            --min-identity ${min_identity}
            --filter-keywords '${filter_keywords}'
            #if str($reference_database_bins) != "None"
              -b '"${reference_database_bins.fields.name}"=${reference_database_bins.fields.path}'
            #end if
            $discard_redundant
            '${tabular_blast_report_input}'
            '${__tool_directory__}/templates/template2.tmpl'
            '${out_html}'

    </command>
    <inputs>
        <param name="tabular_blast_report_input" type="data" format="tabular" label="Tabular BLAST results (extended 25 columns + qcov)"/>
        <param name="min_identity" type="integer" min="90" max="100" value="97" label="Minimum percentage identity"/>
        <param name="filter_keywords" type="text" size="50" label="Comma-separated list of description keyword filters" value="bovine,clone,environmental,swine,uncultivated,uncultured,unidentified"/>
        <param name="reference_database_bins" type="select" label="Reference Database Bins" multiple="true" display="checkboxes">
            <options from_data_table="blast_report_reference_database_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?"/> 

    <outputs>
        <data name="out_html" format="html" label="$tool.name on data $tabular_blast_report_input.hid: report"/>
        <data name="out_tab" format="tabular" label="$tool.name on data $tabular_blast_report_input.hid: tabular results"/>
    </outputs>
    <tests>
        <test>
	    <param name="reference_database_bins" value="test_entry"/>
	    <param name="tabular_blast_report_input" value="NR_114042.1_vs_NCBI16SMicrobial_top20_standard25col_plus_qcovs.tsv"/>
            <output name="out_tab" file="NR_114042.1_vs_NCBI16SMicrobial_output_report_tabular.tsv" ftype="tabular"/>
        </test>
    </tests>
    <help>

.. class:: infomark