comparison rnacode.xml @ 3:d49b9759e294 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode commit 3abc213e109bb564de7dee75d71d90eb1bf78c7e

2:434332033e82

<tool id="rbc_rnacode" name="RNAcode" version="0.3.1">
    <description>Analyze the protein coding potential in MSA.</description>
    <requirements>
        <requirement type="package" version="0.3">rnacode</requirement>
    </requirements>
    <version_command>RNAcode --version</version_command>
    <command detect_errors="exit_code">
    <![CDATA[
        #if $cond_breakmaf.select_breakmaf == 'breakmaf'

        #if $outputFormat.value == '--tabular'
            --outfile $outFileDefault
        #elif $outputFormat.value == '--gtf'
            --outfile $outFileGTF
        #end if
        
    ]]>
    </command>
    <inputs>
        <param name="alignment" type="data" format="clustal,maf" label="Multiple Alignment" help="Alignment needs to be formatted in ClustalW or MAF format"/>
        <conditional name="cond_breakmaf">
            <param name="select_breakmaf" type="select" label="Break long alignment blocks" help="If your alignments contain blocks of long genomic regions it is usually not reasonable to score these long regions as a whole.">
                <option value="keepmaf" selected="true">Process original alignment</option>
                <option value="breakmaf">Break long alignment blocks</option>
            </param>

            <when value="custom">
                <param argument="--pars" name="pars" type="text" label="Scoring parameters as comma separated string:'DELTA,OMEGA,omega,stop_penalty'" help="See the appendix of the Paper for an explanation for the meaning of these parameters. Default: '-10.0,-4.0,-2.0,-8.0'"/>
            </when>
        </conditional>
        <conditional name="cond_generateEPS">
            <param name="generateEPS" type="select" label="Create colored plots in EPS format" help="The generated plots are resolution independent vector graphics that can be included in any graphics software. For each high scoring segment below a given cutoff (see --eps-cutoff) a file named hss-N.eps is created (N is the running number of the high scoring segment)">
                <option value="create" selected="true">Create Plots</option>
                <option value="nocreate">Do not generate EPS plots</option>
            </param>
            <when value="create">
                <param argument="--eps_cutoff" name="eps_cutoff" type="float" optional="true" value="0.05" label="Create plots only for high scoring segments with p better than:" help=""/>
            </when>
            <when value="nocreate"/>
        </conditional>

        <param name="outputFormat" type="select" label="Output format">
            <option value="--tabular" selected="true">Default</option>

            <filter>outputFormat == '--tabular'</filter>
        </data>
        <data name="outFileGTF" format="gtf" label="${tool.name} on ${on_string}">
            <filter>outputFormat == '--gtf'</filter>
        </data>
        <collection name="output_eps" type="list" label="Plots for ${tool.name} on ${on_string}">
            <filter>cond_generateEPS['generateEPS'] == "create"</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.eps" directory="eps" ext="eps"/>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="alignment" value="coding.aln"/>
            <param name="generateEPS" value="nocreate"/>
            <param name="outputFormat" value="--tabular"/>
            <output name="outFileDefault" ftype="tabular" file="rnacode_result1.tabular" compare="sim_size"/>
            <!-- sim_size is needed due to rnacode using random sampling: result files differ, better tests should be implemented -->
        </test>
        <test>
            <param name="alignment" value="coding.aln"/>
            <param name="generateEPS" value="nocreate"/>
            <param name="outputFormat" value="--tabular"/>
            <output name="outFileDefault" ftype="tabular" file="rnacode_result1.tabular" compare="sim_size"/>
            <!-- sim_size is needed due to rnacode using random sampling: result files differ, better tests should be implemented -->
        </test>
        <test>
            <param name="alignment" value="coding.maf"/>
            <conditional name="cond_breakmaf">
                <param name="select_breakmaf" value="breakmaf"/>
            </conditional>
            <param name="generateEPS" value="nocreate"/>
            <param name="outputFormat" value="--gtf"/>
            <output name="outFileGTF" ftype="gtf" file="rnacode_result2.gtf" compare="sim_size"/>
            <!-- sim_size is needed due to rnacode using random sampling: result files differ, better tests should be implemented -->
        </test>
        <test>
            <param name="alignment" value="coding.maf"/>
            <conditional name="cond_breakmaf">

3:d49b9759e294

<tool id="rbc_rnacode" name="RNAcode" version="0.3.2">
    <description>Analyze the protein coding potential in MSA.</description>
    <requirements>
        <requirement type="package" version="0.3">rnacode</requirement>
        <requirement type="package" version="9.22">ghostscript</requirement>
    </requirements>
    <version_command>RNAcode --version</version_command>
    <command detect_errors="exit_code">
    <![CDATA[
        #if $cond_breakmaf.select_breakmaf == 'breakmaf'

        #if $outputFormat.value == '--tabular'
            --outfile $outFileDefault
        #elif $outputFormat.value == '--gtf'
            --outfile $outFileGTF
        #end if

        ## add missing header 
        #if $cond_breakmaf.select_breakmaf != 'breakmaf' and $outputFormat.value == '--tabular':
            && sed -i -e "1 i\HSS #\tStrand\tFrame\tLength\tFrom\tTo\tName\tStart\tEnd\tScore\tP" $outFileDefault        #end if

        #if $cond_generateEPS.generateEPS == 'create'
            #if $cond_generateEPS.imgoutfmt == 'zipeps'
                 && tar -czf '$out_eps_zip' eps
            #else if $cond_generateEPS.imgoutfmt == 'eps'
                 && gs -sDEVICE=eps2write -dNOPAUSE -dBATCH -dSAFER -sOutputFile='$out_eps_mp' `ls -v eps/*.eps`
            #end if     
        #end if     
    ]]>
    </command>
    <inputs>
        <param name="alignment" type="data" format="maf" label="Multiple Alignment" help="Alignment needs to be formatted in ClustalW or MAF format"/>
        <conditional name="cond_breakmaf">
            <param name="select_breakmaf" type="select" label="Break long alignment blocks" help="If your alignments contain blocks of long genomic regions it is usually not reasonable to score these long regions as a whole.">
                <option value="keepmaf" selected="true">Process original alignment</option>
                <option value="breakmaf">Break long alignment blocks</option>
            </param>

            <when value="custom">
                <param argument="--pars" name="pars" type="text" label="Scoring parameters as comma separated string:'DELTA,OMEGA,omega,stop_penalty'" help="See the appendix of the Paper for an explanation for the meaning of these parameters. Default: '-10.0,-4.0,-2.0,-8.0'"/>
            </when>
        </conditional>
        <conditional name="cond_generateEPS">
            <param name="generateEPS" type="select" label="Create plots" help="The generated plots are resolution independent vector graphics that can be included in any graphics software. For each high scoring segment below a given cutoff (see --eps-cutoff) a file named hss-N.eps is created (N is the running number of the high scoring segment)">
                <option value="create">Create Plots</option>
                <option value="nocreate" selected="true">Do not generate EPS plots</option>
            </param>
            <when value="create">
                <param argument="--eps_cutoff" name="eps_cutoff" type="float" optional="true" value="0.05" label="Create plots only for high scoring segments with p better than:" help=""/>
                <param name="imgoutfmt" type="select" label="Output format" help="For larger numbers of high scoring segments output to a collection can be slow. Choose zipped or single page eps in this case.">
                    <option value="sepeps" selected="true">separate eps in collection</option>
                    <option value="zipeps">zipped eps</option>
                    <option value="eps">multi page eps</option>
                </param>
	    </when>
            <when value="nocreate"/>
        </conditional>

        <param name="outputFormat" type="select" label="Output format">
            <option value="--tabular" selected="true">Default</option>

            <filter>outputFormat == '--tabular'</filter>
        </data>
        <data name="outFileGTF" format="gtf" label="${tool.name} on ${on_string}">
            <filter>outputFormat == '--gtf'</filter>
        </data>
        <collection name="output_eps" type="list" label="Plots for ${tool.name} on ${on_string} (plots)">
            <filter>cond_generateEPS['generateEPS'] == "create" and cond_generateEPS['imgoutfmt'] == "sepeps"</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.eps" directory="eps" ext="eps"/>
        </collection>
        <data name="out_eps_zip" format="zip" label="${tool.name} on ${on_string} (plots)">
            <filter>cond_generateEPS['generateEPS'] == "create" and cond_generateEPS['imgoutfmt'] == "zipeps"</filter>
        </data>
        <data name="out_eps_mp" format="eps" label="${tool.name} on ${on_string} (plots)">
            <filter>cond_generateEPS['generateEPS'] == "create" and cond_generateEPS['imgoutfmt'] == "eps"</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="alignment" value="coding.aln"/>
            <param name="outputFormat" value="--tabular"/>
            <output name="outFileDefault" ftype="tabular" file="rnacode_result1.tabular" compare="sim_size"/>
            <conditional name="cond_generateEPS">
                <param name="generateEPS" value="create"/>
                <param name="eps_cutoff" value="0.05"/>
                <param name="imgoutfmt" value="sepeps" />
            </conditional>
            <output_collection name="output_eps" type="list" count="2">
                <element name="hss-0" file="hss-0.eps" ftype="eps" compare="sim_size" delta="50000"/>
                <element name="hss-1" file="hss-1.eps" ftype="eps" compare="sim_size" delta="50000"/>
            </output_collection>
            <!-- sim_size is needed due to rnacode using random sampling: result files differ, better tests should be implemented -->
        </test>
        <test>
            <param name="alignment" value="coding.aln"/>
            <conditional name="cond_generateEPS">
                <param name="generateEPS" value="create"/>
                <param name="eps_cutoff" value="0.05"/>
                <param name="imgoutfmt" value="zipeps" />
            </conditional>
            <param name="outputFormat" value="--tabular"/>
            <output name="outFileDefault" ftype="tabular" file="rnacode_result1.tabular" compare="sim_size"/>
            <output name="out_eps_zip" ftype="zip" file="eps.tar.gz" compare="sim_size" delta="50000"/>
            <!-- sim_size is needed due to rnacode using random sampling: result files differ, better tests should be implemented -->
        </test>
        <test>
            <param name="alignment" value="coding.maf"/>
            <conditional name="cond_breakmaf">
                <param name="select_breakmaf" value="breakmaf"/>
            </conditional>
            <conditional name="cond_generateEPS">
                <param name="generateEPS" value="create"/>
                <param name="eps_cutoff" value="0.05"/>
                <param name="imgoutfmt" value="eps" />
            </conditional>
            <param name="outputFormat" value="--gtf"/>
            <output name="outFileGTF" ftype="gtf" file="rnacode_result2.gtf" compare="sim_size"/>
            <output name="out_eps_mp" ftype="eps" file="eps.eps" compare="sim_size" delta="50000"/>
            <!-- sim_size is needed due to rnacode using random sampling: result files differ, better tests should be implemented -->
        </test>
        <test>
            <param name="alignment" value="coding.maf"/>
            <conditional name="cond_breakmaf">