<tool id="edu.tamu.cpt.genbank.shinefind" name="Shine Find" version="21.1.0.0">
    <description>Identify shine-dalgarno sequences</description>
    <macros>
        <import>macros.xml</import>
        <import>cpt-macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive"><![CDATA[
@GENOME_SELECTOR_PRE@

python '$__tool_directory__/shinefind.py'

@GENOME_SELECTOR@
'$gff3_data'

--table_output '$default_output'
--gff3_output '$gff3_output'

--lookahead_min '$lookahead_min'
--lookahead_max '$lookahead_max'
'$add'
'$top_only'


> '$stdout'

]]></command>
    <inputs>
        <expand macro="genome_selector"/>
        <expand macro="gff3_input"/>
        <param label="Minimum number of bases upstream of CDS for gap (--lookahead_min)" name="lookahead_min" type="integer" value="3"/>
        <param label="Maximum number of bases upstream of CDS for gap (--lookahead_max)" name="lookahead_max" type="integer" value="17"/>
        <param checked="true" label="Automatically add RBSs to input GFF3" name="add" type="boolean" truevalue="--add" falsevalue=""/>
        <param checked="true" label="Only report best hits (--top_only)" name="top_only" type="boolean" falsevalue="" truevalue="--top_only"/>
    </inputs>
    <outputs>
        <data format="tabular" name="default_output" label="ShineFind RBS list from $gff3_data.name"/>
        <data format="gff3" name="gff3_output" label="ShineFind GFF3 RBSs from $gff3_data.name"/>
        <data format="gff3" name="stdout" label="$gff3_data.name with RBSs"/>
    </outputs>
    <tests>
        <test>
            <param name="genome_fasta" value="Miro_ShineFindIn.fa"/>
            <param name="reference_genome_source" value="history"/>
            <param name="gff3_data" value="Miro_ShineFindIn.gff3"/>
            <param name="lookahead_max" value="15"/>
            <param name="lookahead_min" value="5"/>
            <param name="add" value="True"/>
            <param name="top_only" value="False"/>
            <output name="default_output" file="Miro_ShineFindOut.tbl"/>
            <output name="gff3_output" file="Miro_ShineFindOut1.gff3"/>
            <output name="stdout" file="Miro_ShineFindOut2.gff3"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

From an input GFF3 and FASTA file, the upstream sequence within user-specified bounds is 
extracted for all CDS features. Input CDS features with an RBS are not re-analyzed. For 
the remaining CDS features, the upstream sequence is searched against the following 
possible Shine-Dalgarno sequences: 
- AGGAGGT
- GGAGGT
- AGGAGG
- AGGAG
- GAGGT
- GGAGG
- AGGT
- GGGT
- GAGG
- GGGG
- AGGA
- GGAG
- GGA
- GAG
- AGG
- GGT

**Gap Min/Max Settings**
 In previous versions of this tool, the min/max was set for the window to find a Shine-Dalgarno sequence, but 
 currently we specify the minimum and maxium GAP between the end of the SD and the start of the closest CDS. 

By default, only the first (closest to consensus) hit to the list is returned to the GFF3. In the case of a tie, it will select the smaller gap.
By selecting ‘No’ for ‘Only report best hits’, **all hits** to the possible SD list will 
be added to the GFF3 file. 

**March 10, 2021 Update**
		Previous to this date, when using "Only report best hits" option the algorithm would pick the "first" one (moving downstream) found in the case of tied sequence length. After this date, it now will report the sequence with the smaller gap between the END of the SD sequence and the START of the CDS.

			]]></help>
    <expand macro="citations">
        <expand macro="sl-citations-clm"/>
    </expand>
</tool>