<tool id="smf_utils_estimate-energy" name="estimate-energy" version="@VERSION@-2">
    <description>Estimates whether a certain Segment(Loop) is present and for which delta-G this transistion takes place</description>
    
    <macros>
        <import>macros.xml</import>
    </macros>
    
    <requirements>
        <requirement type="package" version="2.7.10">python</requirement>
        <requirement type="package" version="1.9">numpy</requirement>
        <requirement type="package" version="0.8.2.1">pysam</requirement>
        <requirement type="package" version="0.6.1">htseq</requirement>
        <requirement type="package" version="2.1.0">segmentation-fold-utils</requirement>

        <requirement type="package" version="1.6.5">segmentation-fold</requirement>
    </requirements>
    <expand macro="stdio" />
    
    <version_command>echo $(@VERSION_COMMAND_SMF@)", "$(@VERSION_COMMAND_UTILS@)</version_command>
    
    <command><![CDATA[
        segmentation-fold-utils
            estimate-energy
                -T \${GALAXY_SLOTS:-2}
                -x
                #if str($parameters.use_custom_xml) == "true"
                    "${parameters.input_xml}"
                #else
                    "\$SEGMENTATION_FOLD_DEFAULT_XML"
                #end if
                
                -p $precision
                -r $randomize
                
                #if $sequences_from_fasta_file:
                    --sequences-from-fasta-file "${sequences_from_fasta_file}"
                #end if
                
                $output_list
    ]]></command>

    <inputs>
        <conditional name="parameters">
            <param name="use_custom_xml"
                type="boolean"
                truevalue="true"
                falsevalue="false"
                selected="false"
                label="Use segment definition from history" />

            <when value="false" />
            <when value="true">
                <param name="input_xml"
                    type="data"
                    format="xml"
                    multiple="false"
                    argument="-x"
                    label="Custom 'segments.xml'-syntaxed file" />
            </when>
        </conditional>
        
        <param name="precision"
               type="float"
               value="0.05"
               min="0"
               argument="--precision"
               label="Precision"
               help="Minimal difference for binary split - the smaller this value the slower. if this value equals 0, the difference is set to infinity (default: 0.05)" />

        <param name="randomize"
               type="integer"
               value="0"
               min="0"
               argument="--randomize"
               label="Shuffle each sequence this many times and predict energy of shuffled sequence(s) (default: 0, 0 means disabled)" />
        
        <param name="sequences_from_fasta_file"
               type="data"
               format="fasta"
               multiple="false"
               optional="true"
               argument="--sequences-from-fasta-file"
               label="Optional sequences to scan for Segment(Loop)s (FASTA)"
               help="Use sequences from a FASTA file instead of the XML file that contains the segments. In XML files you can explicitly link one Segment(Loop) to one particular sequence instead of doing n*n comparisons (default: None)" />
    </inputs>

    <outputs>
        <data format="dbn" name="output_list" label="${tool.name}" />
    </outputs>

    <tests>
        <!-- xml * fasta mode -->
        <test>
            <param name="use_custom_xml" value="false" ftype="fasta" />
            <param name="sequences_from_fasta_file" value="SNORD13-revised.fa" ftype="fasta" />
            
            <output name="output_list" file="SNORD13-revised.scan-for-segments.txt" />
        </test>
        <test>
            <param name="use_custom_xml" value="false" ftype="fasta" />
            <param name="sequences_from_fasta_file" value="SNORD48-revised.fa" ftype="fasta" />
            
            <output name="output_list" file="SNORD48-revised.scan-for-segments.txt" />
        </test>
        <test>
            <param name="use_custom_xml" value="false" ftype="fasta" />
            <param name="sequences_from_fasta_file" value="SNORD114-4-revised.fa" ftype="fasta" />
            
            <output name="output_list" file="SNORD114-4-revised.scan-for-segments.txt" />
        </test>
        <test>
            <param name="use_custom_xml" value="false" ftype="fasta" />
            <param name="sequences_from_fasta_file" value="SNORD118-revised.fa" ftype="fasta" />
            
            <output name="output_list" file="SNORD118-revised.scan-for-segments.txt" />
        </test>
        
        
        <!-- xml * xml mode -->
        <test>
            <param  name="use_custom_xml" value="true" />
            <param  name="input_xml" value="segments_truncated.xml" ftype="xml" />
            <param  name="do_randomization" value="false" />
            <param  name="shuffle_n_times" value="0" />
            
            <output name="output_list" file="segments_truncated.out.txt" lines_diff="2" />
        </test>
        <test>
            <param  name="use_custom_xml" value="true" />
            <param  name="input_xml" value="segments_truncated.xml" ftype="xml" />
            <param  name="do_randomization" value="false" />
            <param  name="shuffle_n_times" value="1" />
            
            <output name="output_list" file="segments_truncated.2.out.txt" lines_diff="10" />
        </test>
    </tests>
    
    <help><![CDATA[
This is an utility of the segmentation-fold package that allows to scan for the presence of certain segments.
If present, it will also scan for the Gibbs free energy necessairy the segment has to provide to contribute to the optimal structure.
    ]]></help>
    
    <expand macro="citations" />
</tool>