comparison parseval.xml @ 1:d6c074a93c51 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit 669dd4d406e86aee7d83e7420dced981c180d805

0:1b52f0c8ad7f

<tool id='aegean_parseval' name='AEGeAn ParsEval' version='@TOOL_VERSION@' profile='20.01'>
    <description> compare two sets of gene annotations for the same sequence.</description>
    <macros>                                                                                           
        <import>macros.xml</import>
    </macros>                                                                                          
    <expand macro='xrefs'/>
    <expand macro='edam_ontology'/>
    <expand macro='requirements'/>
    <version_command>parseval --version</version_command>
    <command detect_errors='exit_code'>
        <![CDATA[
            #if $output_type == 'html'
                mkdir -p '${output_html.extra_files_path}' &&
            #end if
            parseval '$referencegff3' '$predictiongff3' 
            --delta $delta
            --maxtrans $maxtrans
            -w
            #if $refrlabel
                --refrlabel '$refrlabel'
            #end if
            #if $predlabel
                --predlabel '$predlabel'
            #end if
            #if $output_type =='text'
                -f 'text'
                -o '$output_txt'
            #else if $output_type == 'html'
                -f 'html' 
                -o '${output_html.files_path}'  &&
                echo "</div> </body> </html>" >> '${output_html.files_path}'/index.html &&
                cp '${output_html.files_path}'/index.html '$output_html'
            #end if
            ]]>
    </command>
    <inputs>
        <param name='referencegff3' type='data'  format='gff3' label="Reference GFF3 file"/>
        <param name='predictiongff3' type='data'  format='gff3' label="Prediction GFF3 file"/>
        <param argument='--delta' type='integer'
            min='0' max='20' value='0' 
            label='Number of nucleotides to extend gene loci'/>
        <param argument='--maxtrans' type='integer' 
            min='1' max='50' value='32'
            label='Maximum transcript allowed per locus' />
        <param name='output_type' type='select'
            label='Select the output type'>
            <option value='text'>Text</option>
            <option value='html'>HTML</option>
        </param>
        <param argument='--refrlabel' type='text'
            value='' optional='true'
            label='Reference annotations'
            help='Optional label for reference annotations'/>
        <param argument='--predlabel' type='text'
            value='' optional='true'
            label='Prediction annotations'
            help='Optional label for prediction annotations'/>
    </inputs>
    <outputs>
        <data name='output_txt' format='txt'>
            <filter>output_type == 'text'</filter>
        </data>
        <data name='output_html' format='html' from_work_dir="output.html">
            <filter>output_type == 'html'</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name='referencegff3' value='TAIR9_GFF3_genes.gff'/>
            <param name='predictiongff3' value='TAIR10_GFF3_genes.gff'/>
            <param name='delta' value='5'/>
            <param name='maxtrans' value='20'/>
            <output name='output_txt' file='parseval_output_test1.txt' lines_diff='8'/>
        </test>
        <test expect_num_outputs="1">
            <param name='referencegff3' value='TAIR9_GFF3_genes.gff'/>
            <param name='predictiongff3' value='TAIR10_GFF3_genes.gff'/>
            <output name='output_txt' file='parseval_output_test2.txt' lines_diff='8'/>
        </test>
        <test expect_num_outputs="1">
            <param name='referencegff3' value='TAIR9_GFF3_genes.gff'/>
            <param name='predictiongff3' value='TAIR10_GFF3_genes.gff'/>
            <param name='delta' value='10'/>
            <param name='maxtrans' value='10'/>
            <output name='output_txt' file='parseval_output_test3.txt' lines_diff='8'/>
        </test>
        <test expect_num_outputs="1">
            <param name='referencegff3' value='TAIR9_GFF3_genes.gff'/>
            <param name='predictiongff3' value='TAIR10_GFF3_genes.gff'/>
            <param name='output_type' value='html'/>
            <output name='output_html' file='parseval_output_test4.html' lines_diff='8'/>
        </test>
        <test expect_num_outputs="1">
            <param name='referencegff3' value='TAIR9_GFF3_genes.gff'/>
            <param name='predictiongff3' value='TAIR10_GFF3_genes.gff'/>
            <param name='output_type' value='html'/>
            <param name='delta' value='10'/>
            <param name='maxtrans' value='10'/>
            <output name='output_html' file='parseval_output_test5.html' lines_diff='8'/>
        </test>
        <test expect_num_outputs="1">
            <param name='referencegff3' value='TAIR9_GFF3_genes.gff'/>
            <param name='predictiongff3' value='TAIR10_GFF3_genes.gff'/>
            <param name='output_type' value='text'/>
            <param name='refrlabel' value='example_ref_label'/>
            <param name='predlabel' value='example_pred_label'/>
            <output name='output_txt' file='parseval_output_test6.txt' lines_diff='8'/>
        </test>
    </tests>
    <help>
        <![CDATA[
.. class:: infomark

ParsEval output includes a variety of similarity statistics that measure the agreement between the two annotations. Our use of agreement here instead of accuracy is intentional: except in a very few rare cases, you will not be comparing a prediction to a true high-quality “gold standard.” It is much more common to compare two annotation sets whose relative quality is unknown. ParsEval uses the terms reference and prediction only to distinguish the two sets: it makes no assumptions as to their relative quality.
            
            
]]>
    </help>
    <expand macro='citations'/>
</tool>

1:d6c074a93c51

<tool id="aegean_parseval" name="AEGeAn ParsEval" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
    <description> compare two sets of gene annotations for the same sequence.</description>
    <macros>                                                                                           
        <import>macros.xml</import>
    </macros>                                                                                          
    <expand macro="edam_ontology"/>
    <expand macro="xrefs"/>
    <expand macro="requirements"/>
    <version_command>parseval --version</version_command>
    <command detect_errors="exit_code">
        <![CDATA[
            #if $output_type == "html"
                mkdir -p "${output_html.extra_files_path}" &&
            #end if
            parseval "$referencegff3" "$predictiongff3" 
            --delta $delta
            --maxtrans $maxtrans
            -w
            #if $refrlabel
                --refrlabel "$refrlabel"
            #end if
            #if $predlabel
                --predlabel "$predlabel"
            #end if
            #if $output_type =="text"
                -f "text"
                -o "$output_txt"
            #else if $output_type == "html"
                -f "html" 
                -o "${output_html.files_path}"  &&
                echo "</div> </body> </html>" >> "${output_html.files_path}"/index.html &&
                cp "${output_html.files_path}"/index.html "$output_html"
            #end if
            ]]>
    </command>
    <inputs>
        <param name="referencegff3" type="data"  format="gff3" label="Reference GFF3 file"/>
        <param name="predictiongff3" type="data"  format="gff3" label="Prediction GFF3 file"/>
        <param argument="--delta" type="integer"
            min="0" max="20" value="0" 
            label="Number of nucleotides to extend gene loci"/>
        <param argument="--maxtrans" type="integer" 
            min="1" max="50" value="32"
            label="Maximum transcript allowed per locus" />
        <param name="output_type" type="select"
            label="Select the output type">
            <option value="text">Text</option>
            <option value="html">HTML</option>
        </param>
        <param argument="--refrlabel" type="text"
            value="" optional="true"
            label="Reference annotations"
            help="Optional label for reference annotations"/>
        <param argument="--predlabel" type="text"
            value="" optional="true"
            label="Prediction annotations"
            help="Optional label for prediction annotations"/>
    </inputs>
    <outputs>
        <data name="output_txt" format="txt" label="${tool.name} on ${on_string}: text">
            <filter>output_type == "text"</filter>
        </data>
        <data name="output_html" format="html" from_work_dir="output.html" label="${tool.name} on ${on_string}: HTML">
            <filter>output_type == "html"</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>
            <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
            <param name="delta" value="5"/>
            <param name="maxtrans" value="20"/>
            <output name="output_txt" file="parseval_output_test1.txt" lines_diff="8"/>
        </test>
        <test expect_num_outputs="1">
            <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>
            <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
            <output name="output_txt" file="parseval_output_test2.txt" lines_diff="8"/>
        </test>
        <test expect_num_outputs="1">
            <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>
            <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
            <param name="delta" value="10"/>
            <param name="maxtrans" value="10"/>
            <output name="output_txt" file="parseval_output_test3.txt" lines_diff="8"/>
        </test>
        <test expect_num_outputs="1">
            <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>
            <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
            <param name="output_type" value="html"/>
            <output name="output_html" file="parseval_output_test4.html" lines_diff="8"/>
        </test>
        <test expect_num_outputs="1">
            <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>
            <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
            <param name="output_type" value="html"/>
            <param name="delta" value="10"/>
            <param name="maxtrans" value="10"/>
            <output name="output_html" file="parseval_output_test5.html" lines_diff="8"/>
        </test>
        <test expect_num_outputs="1">
            <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>
            <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
            <param name="output_type" value="text"/>
            <param name="refrlabel" value="example_ref_label"/>
            <param name="predlabel" value="example_pred_label"/>
            <output name="output_txt" file="parseval_output_test6.txt" lines_diff="8"/>
        </test>
    </tests>
    <help>
        <![CDATA[
.. class:: infomark

ParsEval output includes a variety of similarity statistics that measure the agreement between the two annotations. Our use of agreement here instead of accuracy is intentional: except in a very few rare cases, you will not be comparing a prediction to a true high-quality “gold standard.” It is much more common to compare two annotation sets whose relative quality is unknown. ParsEval uses the terms reference and prediction only to distinguish the two sets: it makes no assumptions as to their relative quality.
            
            
]]>
    </help>
    <expand macro="citations"/>
</tool>