comparison intarna.xml @ 16:f5d850723e63 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c

15:0377acb3f91b

<tool id="intarna" name="IntaRNA" version="3.4.0">
    <description>Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.</description>
    <macros>
        <macro name="query_macro">
            <param argument="--query" format="fasta" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format" label="Query sequence(s)" name="query" type="data" />
            <conditional name="qAcc_cond">
                <param argument="--qAcc" help="" label="Accessibility computation" type="select">
                    <option value="N">No accessibility contributions ('N')</option>
                    <option selected="true" value="C">Computation of accessibilities ('C')</option>
                    <option value="P">Unpaired probabilities in RNAplfold format from --qAccFile</option>
                    <option value="E">ED values in RNAplfold Pu-like format from --qAccFile</option>
                </param>
                <when value="N" />
                <when value="C" />
                <when value="P">
                    <param argument="--qAccFile" format="txt" help="Unpaired probabilities for subsequences as computed and reported by RNAplfold or IntaRNA" label="RNAplfold unpaired probability data" type="data" />
                </when>
                <when value="E">
                    <param argument="--qAccFile" format="txt" help="Accessibility energy penalty terms (ED) for subsequences as computed and reported by IntaRNA" label="IntaRNA accessibility energy penalties (ED terms)" type="data" />
                </when>
            </conditional>
            <param argument="--qAccW" help="... for query accessibility computation. Set to 0 to use full sequence length" label="Max. interaction length" max="99999" min="0" type="integer" value="150" />
            <param argument="--qAccL" help="... for query accessibility computation. 0 defaults to sliding window size 'qAccW'" label="Max. loop length" max="99999" min="0" type="integer" value="100" />
        </macro>
        <macro name="target_macro">
            <param argument="--target" format="fasta" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format" label="Target sequence(s)" name="target" type="data" />
            <conditional name="tAcc_cond">
                <param argument="--tAcc" help="" label="Accessibility computation" type="select">
                    <option value="N">No accessibility contributions ('N')</option>
                    <option selected="true" value="C">Computation of accessibilities ('C')</option>
                    <option value="P">Unpaired probabilities in RNAplfold format from --qAccFile</option>
                    <option value="E">ED values in RNAplfold Pu-like format from --qAccFile</option>
                </param>
                <when value="N" />
                <when value="C" />
                <when value="P">
                    <param argument="--tAccFile" format="txt" help="Unpaired probabilities for subsequences as computed and reported by RNAplfold or IntaRNA" label="RNAplfold unpaired probability data" type="data" />
                </when>
                <when value="E">
                    <param argument="--tAccFile" format="txt" help="Accessibility energy penalty terms (ED) for subsequences as computed and reported by IntaRNA" label="IntaRNA accessibility energy penalties (ED terms)" type="data" />
                </when>
            </conditional>
            <param argument="--tAccW" help="... for target accessibility computation. Set to 0 to use full sequence length" label="Max. interaction length" max="99999" min="0" type="integer" value="150" />
            <param argument="--tAccL" help="... for target accessibility computation. 0 defaults to sliding window size 'tAccW'" label="Max. loop length" max="99999" min="0" type="integer" value="100" />
        </macro>
        <macro name="seed_macro">
            <param argument="--noSeed" checked="false" falsevalue="" help="" label="Disable seed constraint entirely for computation" truevalue="--noSeed" type="boolean" />
            <param argument="--seedBP" help="number of inter-molecular base pairs within the seed region" label="Min. number of basepairs in seed" max="20" min="2" type="integer" value="7" />
            <param argument="--seedMaxUP" help="Maximal number of unpaired seed bases both in query and target" label="Max. overall number of unpaired bases in seed" max="10" min="0" type="integer" value="0" />
        </macro>
        <macro name="interaction_macro">
            <param argument="--mode" help="" label="Prediction mode" type="select">
                <option selected="true" value="H">Heuristic ('H')</option>
                <option value="M">Exact but slow ('M')</option>
            </param>
        </macro>
        <macro name="output_macro">
            <param argument="--outCsvCols" help="An empty argument prints all possible columns from the following available ID list:        [id1], [id2], [seq1], [seq2], [subseq1], [subseq2], [subseqDP], [subseqDB], [start1], [end1], [start2], [end2], [hybridDP], [hybridDB], [hybridDPfull], [hybridDBfull], [E], [ED1], [ED2], [Pu1], [Pu2], [E_init], [E_loops], [E_dangleL], [E_dangleR], [E_endL], [E_endR], [E_hybrid], [E_norm], [E_hybridNorm], [E_add], [seedStart1], [seedEnd1], [seedStart2], [seedEnd2], [seedE], [seedED1], [seedED2], [seedPu1], [seedPu2], [w], [Eall], [Zall], [P_E]" label="Comma separated list of CSV column IDs to print" type="text" value="id1,start1,end1,id2,start2,end2,subseqDP,hybridDP,E" />
            <param argument="--outCsvSort" help="One of the column IDs to be printed that is used to sort the CSV table output" label="Sort CSV output for the given column label from CSV column IDs to print" type="text" value="E" />
            <param argument="--outNumber" help="Number of optimal and suboptimal interaction to predict per query-target pair" label="Max. number of predictions per query/target pair" max="1000" min="0" type="integer" value="1" />
            <param argument="--outOverlap" help="Whether or not interactions can overlap" label="Overlapping of suboptimal predictions" type="select">
                <option value="N">in none of the sequences</option>
                <option value="T">in the target only</option>
                <option selected="true" value="Q">in the query only</option>
                <option value="B">in both sequences</option>
            </param>
            <param argument="--outPairwise" checked="false" falsevalue="" help="" label="Enables pairwise sequence processing, i.e. interactions are only computed for each corresponding query-target pair (same index) instead of all-vs-all" truevalue="--outPairwise" type="boolean" />
        </macro>
    </macros>
    <requirements>
        <requirement type="package" version="3.4.0">intarna</requirement>
    </requirements>
    <version_command>IntaRNA --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
    
        IntaRNA

            #end if
]]>  
    </command>
    <inputs>
        <conditional name="advancedOptions">
            <param label="Options" name="advancedSelector" type="select">
                <option value="basic">Basic Options</option>
                <option value="advanced">Advanced Options</option>
            </param>
            <when value="advanced">
                <section expanded="True" name="query" title="Query Parameters">
                    <expand macro="query_macro" />
                    <param argument="--qIntLoopMax" help="... to be considered in interactions within the query" label="Maximal number of unpaired bases between neighbored interacting bases" max="30" min="0" type="integer" value="16" />
                    <param argument="--qRegion" help="In the format 'from1-to1,from2-to2,..' assuming indexing starts with 1" label="Query regions to be considered for interaction prediction" optional="true" type="text" />
                </section>
                <section expanded="True" name="target" title="Target Parameters">
                    <expand macro="target_macro" />
                    <param argument="--tIntLoopMax" help="... to be considered in interactions within the target" label="Maximal number of unpaired bases between neighbored interacting bases" max="30" min="0" type="integer" value="16" />
                    <param argument="--tRegion" help="In the format 'from1-to1,from2-to2,..' assuming indexing starts with 1" label="Target regions to be considered for interaction prediction" optional="true" type="text" />
                </section>
                <section name="seed" title="Seed Parameters">
                    <expand macro="seed_macro" />
                    <param argument="--seedQMaxUP" help="" label="Max. number of unpaired bases within the query's seed region" max="20" min="-1" type="integer" value="-1" />
                    <param argument="--seedTMaxUP" help="" label="Max. number of unpaired bases within the target's seed region" max="20" min="-1" type="integer" value="-1" />
                    <param argument="--seedMaxE" help="" label="Max. energy a seed region may have" max="999" min="-999" type="integer" value="0" />
                    <param argument="--seedMinPu" help="" label="Min. unpaired probability (per sequence)" max="1" min="0" type="float" value="0" />
                    <param argument="--seedQRange" help="in format 'from1-to1,from2-to2,...' (Note, only for single query)" label="Interval(s) in the query to search for seeds" optional="true" type="text" value="" />
                    <param argument="--seedTRange" help="in format 'from1-to1,from2-to2,...' (Note, only for single query)" label="Interval(s) in the target to search for seeds" optional="true" type="text" value="" />
                </section>
                <section name="shape" title="SHAPE Input Parameters">
                    <param argument="--qShape" format="txt" help="Two column text file with sequence positions (1-based) and normalized reactivity values. Missing values may be left out, or assigned a negative score" label="SHAPE reactivity data to guide the query's accessibility computation" optional="true" type="data" />
                    <param argument="--tShape" format="txt" help="Two column text file with sequence positions (1-based) and normalized reactivity values. Missing values may be left out, or assigned a negative score" label="SHAPE reactivity data to guide the query's accessibility computation" optional="true" type="data" />
                </section>
                <section name="interaction" title="Prediction Parameters">
                    <expand macro="interaction_macro" />
                    <param argument="--model" help="Sets what to optimize for" label="Prediction target" type="select">
                        <option value="S">Single-site minimum-free-energy interaction (IntaRNA v1+2 mode)</option>
                        <option selected="true" value="X">Single-site minimum-free-energy interaction (via seed-extension)</option>
                        <option value="P">Single-site interaction with minimal free ensemble energy per site</option>
                    </param>
                    <param argument="--energyVRNA" help="" label="Energy parameter" type="select">
                        <option value="Turner99">Turner-1999</option>
                        <option selected="true" value="Turner04">Turner-2004</option>
                        <option value="Andronescu07">Andronescu-2007</option>
                    </param>
                    <param argument="--temperature" help="Temperature scaling of ViennaRNA energy parameters" label="Temperature [Celsius]" max="100" min="0" type="integer" value="37" />
                    <param argument="--windowWidth" help="If set, large sequences are decomposed in overlapping windows of the given size to reduce the memory consumption of IntaRNA." label="Window-based computation: window width" max="99999" min="10" optional="True" type="integer" />
                    <param argument="--windowOverlap" help="If window width is set, this specifies the overlap of the windows. Note, it has to exceed the maximal interaction length of both query and target." label="Window-based computation: window overlap" max="99999" min="10" type="integer" value="150" />
                </section>
                <section name="output" title="Output Options">
                    <expand macro="output_macro" />
                    <param argument="--outMaxE" help="Only interactions with E ≤ maxE are reported" label="Max. absolute energy of an interaction" type="float" value="0" />
                    <param argument="--outDeltaE" help="suboptimal output: only interactions with E ≤ (minE+deltaE) are reported" label="Max. delta energy above mfe of an interaction" type="float" value="100" />
                    <conditional name="add_output_cond">
                        <param label="Additional output files" name="selector" type="select">
                            <option value="add">Output additional files</option>
                            <option selected="true" value="none">Don't output additional files</option>
                        </param>
                        <when value="add">
                            <param display="checkboxes" help="Written in a format similar to RNAplfold unpaired probability output." label="Additional output files" multiple="True" name="add_output" type="select">
                                <option value="spotProb">Spot probabilities of all index combinations (spotProb)</option>
                                <option value="qSpotProb">Spot probabilities for all query indices (qSpotProb)</option>
                                <option value="tSpotProb">Spot probabilities for all target indices (tSpotProb)</option>
                                <option value="pMinE">For all index combinations: minimal energy of any interaction covering the index pair (pMinE)</option>
                                <option value="qMinE">For all query indices: minimal energy of any interaction covering the position (qMinE)</option>

                                <option value="tAcc">The target's ED values (tAcc) </option>
                                <option value="qPu">The query's unpaired probabilities used for ED values (qPu) </option>
                                <option value="tPu">The target's unpaired probabilities used for ED values (tPu)</option>
                            </param>
                        </when>
                        <when value="none" />
                    </conditional>
                </section>
            </when>
            <when value="basic">
                <section expanded="True" name="query" title="Query Parameters">
                    <expand macro="query_macro" />
                </section>
                <section expanded="True" name="target" title="Target Parameters">
                    <expand macro="target_macro" />
                </section>
                <section name="seed" title="Seed Parameters">
                    <expand macro="seed_macro" />
                </section>
                <section name="interaction" title="Interaction Parameters">
                    <expand macro="interaction_macro" />
                </section>
                <section name="output" title="Output Options">
                    <expand macro="output_macro" />
                </section>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="tabular" label="IntaRNA on ${on_string}" name="outfile" />
        <collection label="Spot probability of all index combinations, on ${on_string}" name="spotProb_output" type="list">
            <filter>
                ((
                advancedOptions['advancedSelector'] == "advanced" and
                advancedOptions['output']['add_output_cond']['selector'] == "add" and
                'spotProb' in advancedOptions['output']['add_output_cond']['add_output']
                ))
            </filter>
            <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;spotProb.*)\.tabular" visible="true" />
        </collection>
        <collection label="Spot probability for all query indices, on ${on_string}" name="qSpotProb_output" type="list">
            <filter>
                ((
                advancedOptions['advancedSelector'] == "advanced" and
                advancedOptions['output']['add_output_cond']['selector'] == "add" and
                'qSpotProb' in advancedOptions['output']['add_output_cond']['add_output']
                ))
            </filter>
            <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;qSpotProb.*)\.tabular" visible="true" />
        </collection>
        <collection label="Spot probability for all target indices, on ${on_string}" name="tSpotProb_output" type="list">
            <filter>
                ((
                advancedOptions['advancedSelector'] == "advanced" and
                advancedOptions['output']['add_output_cond']['selector'] == "add" and
                'tSpotProb' in advancedOptions['output']['add_output_cond']['add_output']
                ))
            </filter>
            <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;tSpotProb.*)\.tabular" visible="true" />
        </collection>
        <collection label="For all query indices: minimal energy of any interaction covering the position, on ${on_string}" name="qMinE_output" type="list">
            <filter>
                ((
                advancedOptions['advancedSelector'] == "advanced" and
                advancedOptions['output']['add_output_cond']['selector'] == "add" and
                'qMinE' in advancedOptions['output']['add_output_cond']['add_output']
                ))
            </filter>
            <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;qMinE.*)\.tabular" visible="true" />
        </collection>
        <collection label="For all target indices: minimal energy of any interaction covering the position, on ${on_string}" name="tMinE_output" type="list">
            <filter>
                ((
                advancedOptions['advancedSelector'] == "advanced" and
                advancedOptions['output']['add_output_cond']['selector'] == "add" and
                'tMinE' in advancedOptions['output']['add_output_cond']['add_output']
                ))
            </filter>
            <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;tMinE.*)\.tabular" visible="true" />
        </collection>
        <collection label="For all index combinations: minimal energy of any interaction covering the index pair, on ${on_string}" name="pMinE_output" type="list">
            <filter>
                ((
                advancedOptions['advancedSelector'] == "advanced" and
                advancedOptions['output']['add_output_cond']['selector'] == "add" and
                'pMinE' in advancedOptions['output']['add_output_cond']['add_output']
                ))
            </filter>
            <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;pMinE.*)\.tabular" visible="true" />
        </collection>
        <collection label="Query local accessibility penalties (ED values), on ${on_string}" name="qAcc_output" type="list">
            <filter>
                ((
                advancedOptions['advancedSelector'] == "advanced" and
                advancedOptions['output']['add_output_cond']['selector'] == "add" and
                'qAcc' in advancedOptions['output']['add_output_cond']['add_output']
                ))
            </filter>
            <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;qAcc.*)\.led" visible="true" />
        </collection>
        <collection label="Target local accessibility penalties (ED values), on ${on_string}" name="tAcc_output" type="list">
            <filter>
                ((
                advancedOptions['advancedSelector'] == "advanced" and
                advancedOptions['output']['add_output_cond']['selector'] == "add" and
                'tAcc' in advancedOptions['output']['add_output_cond']['add_output']
                ))
            </filter>
            <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;tAcc.*)\.led" visible="true" />
        </collection>
        <collection label="Query local unpaired probabilities, on ${on_string}" name="qPu_output" type="list">
            <filter>
                ((
                advancedOptions['advancedSelector'] == "advanced" and
                advancedOptions['output']['add_output_cond']['selector'] == "add" and
                'qPu' in advancedOptions['output']['add_output_cond']['add_output']
                ))
            </filter>
            <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;qPu.*)\.lpu" visible="true" />
        </collection>
        <collection label="Target local unpaired probabilities, on ${on_string}" name="tPu_output" type="list">
            <filter>
                ((
                advancedOptions['advancedSelector'] == "advanced" and
                advancedOptions['output']['add_output_cond']['selector'] == "add" and
                'tPu' in advancedOptions['output']['add_output_cond']['add_output']
                ))
            </filter>
            <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;tPu.*)\.lpu" visible="true" />
        </collection>
    </outputs>
    <tests>
        <test>
            <conditional name="advancedOptions">
                <param name="advancedSelector" value="basic" />
                <section name="query">
                    <param name="query" value="intarna_query.fa" />
                </section>
                <section name="target">
                    <param name="target" value="intarna_target.fa" />
                </section>
            </conditional>
            <output file="intarna_result.tabular" name="outfile" />
        </test>
        <test>
            <conditional name="advancedOptions">
                <param name="advancedSelector" value="advanced" />
                <section name="query">
                    <param name="query" value="intarna_query.fa" />
                </section>
                <section name="target">
                    <param name="target" value="intarna_target.fa" />
                </section>
                <section name="output">
                    <conditional name="add_output_cond">
                        <param name="selector" value="add" />
                        <param name="add_output" value="spotProb,qMinE,tAcc,qPu" />
                    </conditional>
                </section>
            </conditional>
            <output file="intarna_result.tabular" name="outfile" />
            <output_collection count="4" name="spotProb_output" type="list">
            </output_collection>
            <output_collection count="4" name="qMinE_output" type="list">
            </output_collection>
            <output_collection count="2" name="qPu_output" type="list">

16:f5d850723e63

<tool id="intarna" name="IntaRNA" version="3.4.1" profile="23.0">
    <description>Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.</description>
    <macros>
        <macro name="query_macro">
            <param argument="--query" type="data" format="fasta" label="Query sequence(s)" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format"/>
            <conditional name="qAcc_cond">
                <param argument="--qAcc" type="select" label="Accessibility computation" help="">
                    <option value="N">No accessibility contributions ('N')</option>
                    <option selected="true" value="C">Computation of accessibilities ('C')</option>
                    <option value="P">Unpaired probabilities in RNAplfold format from --qAccFile</option>
                    <option value="E">ED values in RNAplfold Pu-like format from --qAccFile</option>
                </param>
                <when value="N"/>
                <when value="C"/>
                <when value="P">
                    <param argument="--qAccFile" type="data" format="txt" label="RNAplfold unpaired probability data" help="Unpaired probabilities for subsequences as computed and reported by RNAplfold or IntaRNA"/>
                </when>
                <when value="E">
                    <param argument="--qAccFile" type="data" format="txt" label="IntaRNA accessibility energy penalties (ED terms)" help="Accessibility energy penalty terms (ED) for subsequences as computed and reported by IntaRNA"/>
                </when>
            </conditional>
            <param argument="--qAccW" type="integer" min="0" max="99999" value="150" label="Max. interaction length" help="... for query accessibility computation. Set to 0 to use full sequence length"/>
            <param argument="--qAccL" type="integer" min="0" max="99999" value="100" label="Max. loop length" help="... for query accessibility computation. 0 defaults to sliding window size 'qAccW"/>
        </macro>
        <macro name="target_macro">
            <param argument="--target" type="data" format="fasta" label="Target sequence(s)" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format"/>
            <conditional name="tAcc_cond">
                <param argument="--tAcc" type="select" label="Accessibility computation" help="">
                    <option value="N">No accessibility contributions ('N')</option>
                    <option selected="true" value="C">Computation of accessibilities ('C')</option>
                    <option value="P">Unpaired probabilities in RNAplfold format from --qAccFile</option>
                    <option value="E">ED values in RNAplfold Pu-like format from --qAccFile</option>
                </param>
                <when value="N"/>
                <when value="C"/>
                <when value="P">
                    <param argument="--tAccFile" type="data" format="txt" label="RNAplfold unpaired probability data" help="Unpaired probabilities for subsequences as computed and reported by RNAplfold or IntaRNA"/>
                </when>
                <when value="E">
                    <param argument="--tAccFile" type="data" format="txt" label="IntaRNA accessibility energy penalties (ED terms)" help="Accessibility energy penalty terms (ED) for subsequences as computed and reported by IntaRNA"/>
                </when>
            </conditional>
            <param argument="--tAccW" type="integer" min="0" max="99999" value="150" label="Max. interaction length" help="... for target accessibility computation. Set to 0 to use full sequence length"/>
            <param argument="--tAccL" type="integer" min="0" max="99999" value="100" label="Max. loop length" help="... for target accessibility computation. 0 defaults to sliding window size 'tAccW"/>
        </macro>
        <macro name="seed_macro">
            <param argument="--noSeed" type="boolean" truevalue="--noSeed" falsevalue="" checked="false" label="Disable seed constraint entirely for computation" help=""/>
            <param argument="--seedBP" type="integer" min="2" max="20" value="7" label="Min. number of basepairs in seed" help="number of inter-molecular base pairs within the seed region"/>
            <param argument="--seedMaxUP" type="integer" min="0" max="10" value="0" label="Max. overall number of unpaired bases in seed" help="Maximal number of unpaired seed bases both in query and target"/>
        </macro>
        <macro name="interaction_macro">
            <param argument="--mode" type="select" label="Prediction mode" help="">
                <option selected="true" value="H">Heuristic ('H')</option>
                <option value="M">Exact but slow ('M')</option>
            </param>
        </macro>
        <macro name="output_macro">
            <param argument="--outCsvCols" type="text" value="id1,start1,end1,id2,start2,end2,subseqDP,hybridDP,E" label="Comma separated list of CSV column IDs to print" help="An empty argument prints all possible columns from the following available ID list:        [id1], [id2], [seq1], [seq2], [subseq1], [subseq2], [subseqDP], [subseqDB], [start1], [end1], [start2], [end2], [hybridDP], [hybridDB], [hybridDPfull], [hybridDBfull], [E], [ED1], [ED2], [Pu1], [Pu2], [E_init], [E_loops], [E_dangleL], [E_dangleR], [E_endL], [E_endR], [E_hybrid], [E_norm], [E_hybridNorm], [E_add], [seedStart1], [seedEnd1], [seedStart2], [seedEnd2], [seedE], [seedED1], [seedED2], [seedPu1], [seedPu2], [w], [Eall], [Zall], [P_E]"/>
            <param argument="--outCsvSort" type="text" value="E" label="Sort CSV output for the given column label from CSV column IDs to print" help="One of the column IDs to be printed that is used to sort the CSV table output"/>
            <param argument="--outNumber" type="integer" min="0" max="1000" value="1" label="Max. number of predictions per query/target pair" help="Number of optimal and suboptimal interaction to predict per query-target pair"/>
            <param argument="--outOverlap" type="select" label="Overlapping of suboptimal predictions" help="Whether or not interactions can overlap">
                <option value="N">in none of the sequences</option>
                <option value="T">in the target only</option>
                <option selected="true" value="Q">in the query only</option>
                <option value="B">in both sequences</option>
            </param>
            <param argument="--outPairwise" type="boolean" truevalue="--outPairwise" falsevalue="" checked="false" label="Enables pairwise sequence processing, i.e. interactions are only computed for each corresponding query-target pair (same index) instead of all-vs-all" help=""/>
        </macro>
    </macros>
    <requirements>
        <requirement type="package" version="3.4.1">intarna</requirement>
    </requirements>
    <version_command>IntaRNA --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
    
        IntaRNA

            #end if
]]>  
    </command>
    <inputs>
        <conditional name="advancedOptions">
            <param name="advancedSelector" type="select" label="Options">
                <option value="basic">Basic Options</option>
                <option value="advanced">Advanced Options</option>
            </param>
            <when value="advanced">
                <section expanded="True" name="query" title="Query Parameters">
                    <expand macro="query_macro"/>
                    <param argument="--qIntLoopMax" type="integer" min="0" max="30" value="16" label="Maximal number of unpaired bases between neighbored interacting bases" help="... to be considered in interactions within the query"/>
                    <param argument="--qRegion" type="text" optional="true" label="Query regions to be considered for interaction prediction" help="In the format 'from1-to1,from2-to2,..' assuming indexing starts with 1"/>
                </section>
                <section expanded="True" name="target" title="Target Parameters">
                    <expand macro="target_macro"/>
                    <param argument="--tIntLoopMax" type="integer" min="0" max="30" value="16" label="Maximal number of unpaired bases between neighbored interacting bases" help="... to be considered in interactions within the target"/>
                    <param argument="--tRegion" type="text" optional="true" label="Target regions to be considered for interaction prediction" help="In the format 'from1-to1,from2-to2,..' assuming indexing starts with 1"/>
                </section>
                <section name="seed" title="Seed Parameters">
                    <expand macro="seed_macro"/>
                    <param argument="--seedQMaxUP" type="integer" min="-1" max="20" value="-1" label="Max. number of unpaired bases within the query's seed region" help=""/>
                    <param argument="--seedTMaxUP" type="integer" min="-1" max="20" value="-1" label="Max. number of unpaired bases within the target's seed region" help=""/>
                    <param argument="--seedMaxE" type="integer" min="-999" max="999" value="0" label="Max. energy a seed region may have" help=""/>
                    <param argument="--seedMinPu" type="float" min="0" max="1" value="0" label="Min. unpaired probability (per sequence)" help=""/>
                    <param argument="--seedQRange" type="text" value="" optional="true" label="Interval(s) in the query to search for seeds" help="in format 'from1-to1,from2-to2,...' (Note, only for single query)"/>
                    <param argument="--seedTRange" type="text" value="" optional="true" label="Interval(s) in the target to search for seeds" help="in format 'from1-to1,from2-to2,...' (Note, only for single query)"/>
                </section>
                <section name="shape" title="SHAPE Input Parameters">
                    <param argument="--qShape" type="data" format="txt" optional="true" label="SHAPE reactivity data to guide the query's accessibility computation" help="Two column text file with sequence positions (1-based) and normalized reactivity values. Missing values may be left out, or assigned a negative score"/>
                    <param argument="--tShape" type="data" format="txt" optional="true" label="SHAPE reactivity data to guide the query's accessibility computation" help="Two column text file with sequence positions (1-based) and normalized reactivity values. Missing values may be left out, or assigned a negative score"/>
                </section>
                <section name="interaction" title="Prediction Parameters">
                    <expand macro="interaction_macro"/>
                    <param argument="--model" type="select" label="Prediction target" help="Sets what to optimize for">
                        <option value="S">Single-site minimum-free-energy interaction (IntaRNA v1+2 mode)</option>
                        <option selected="true" value="X">Single-site minimum-free-energy interaction (via seed-extension)</option>
                        <option value="P">Single-site interaction with minimal free ensemble energy per site</option>
                    </param>
                    <param argument="--energyVRNA" type="select" label="Energy parameter" help="">
                        <option value="Turner99">Turner-1999</option>
                        <option selected="true" value="Turner04">Turner-2004</option>
                        <option value="Andronescu07">Andronescu-2007</option>
                    </param>
                    <param argument="--temperature" type="integer" min="0" max="100" value="37" label="Temperature [Celsius]" help="Temperature scaling of ViennaRNA energy parameters"/>
                    <param argument="--windowWidth" type="integer" min="10" max="99999" optional="True" label="Window-based computation: window width" help="If set, large sequences are decomposed in overlapping windows of the given size to reduce the memory consumption of IntaRNA."/>
                    <param argument="--windowOverlap" type="integer" min="10" max="99999" value="150" label="Window-based computation: window overlap" help="If window width is set, this specifies the overlap of the windows. Note, it has to exceed the maximal interaction length of both query and target."/>
                </section>
                <section name="output" title="Output Options">
                    <expand macro="output_macro"/>
                    <param argument="--outMaxE" type="float" value="0" label="Max. absolute energy of an interaction" help="Only interactions with E ≤ maxE are reported"/>
                    <param argument="--outDeltaE" type="float" value="100" label="Max. delta energy above mfe of an interaction" help="suboptimal output: only interactions with E ≤ (minE+deltaE) are reported"/>
                    <conditional name="add_output_cond">
                        <param name="selector" type="select" label="Additional output files">
                            <option value="add">Output additional files</option>
                            <option selected="true" value="none">Don't output additional files</option>
                        </param>
                        <when value="add">
                            <param name="add_output" type="select" label="Additional output files" help="Written in a format similar to RNAplfold unpaired probability output." display="checkboxes" multiple="True">
                                <option value="spotProb">Spot probabilities of all index combinations (spotProb)</option>
                                <option value="qSpotProb">Spot probabilities for all query indices (qSpotProb)</option>
                                <option value="tSpotProb">Spot probabilities for all target indices (tSpotProb)</option>
                                <option value="pMinE">For all index combinations: minimal energy of any interaction covering the index pair (pMinE)</option>
                                <option value="qMinE">For all query indices: minimal energy of any interaction covering the position (qMinE)</option>

                                <option value="tAcc">The target's ED values (tAcc) </option>
                                <option value="qPu">The query's unpaired probabilities used for ED values (qPu) </option>
                                <option value="tPu">The target's unpaired probabilities used for ED values (tPu)</option>
                            </param>
                        </when>
                        <when value="none"/>
                    </conditional>
                </section>
            </when>
            <when value="basic">
                <section expanded="True" name="query" title="Query Parameters">
                    <expand macro="query_macro"/>
                </section>
                <section expanded="True" name="target" title="Target Parameters">
                    <expand macro="target_macro"/>
                </section>
                <section name="seed" title="Seed Parameters">
                    <expand macro="seed_macro"/>
                </section>
                <section name="interaction" title="Interaction Parameters">
                    <expand macro="interaction_macro"/>
                </section>
                <section name="output" title="Output Options">
                    <expand macro="output_macro"/>
                </section>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="tabular" label="IntaRNA on ${on_string}" name="outfile"/>
        <collection label="Spot probability of all index combinations, on ${on_string}" name="spotProb_output" type="list">
            <filter>
                ((
                advancedOptions['advancedSelector'] == "advanced" and
                advancedOptions['output']['add_output_cond']['selector'] == "add" and
                'spotProb' in advancedOptions['output']['add_output_cond']['add_output']
                ))
            </filter>
            <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;spotProb.*)\.tabular" visible="true"/>
        </collection>
        <collection label="Spot probability for all query indices, on ${on_string}" name="qSpotProb_output" type="list">
            <filter>
                ((
                advancedOptions['advancedSelector'] == "advanced" and
                advancedOptions['output']['add_output_cond']['selector'] == "add" and
                'qSpotProb' in advancedOptions['output']['add_output_cond']['add_output']
                ))
            </filter>
            <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;qSpotProb.*)\.tabular" visible="true"/>
        </collection>
        <collection label="Spot probability for all target indices, on ${on_string}" name="tSpotProb_output" type="list">
            <filter>
                ((
                advancedOptions['advancedSelector'] == "advanced" and
                advancedOptions['output']['add_output_cond']['selector'] == "add" and
                'tSpotProb' in advancedOptions['output']['add_output_cond']['add_output']
                ))
            </filter>
            <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;tSpotProb.*)\.tabular" visible="true"/>
        </collection>
        <collection label="For all query indices: minimal energy of any interaction covering the position, on ${on_string}" name="qMinE_output" type="list">
            <filter>
                ((
                advancedOptions['advancedSelector'] == "advanced" and
                advancedOptions['output']['add_output_cond']['selector'] == "add" and
                'qMinE' in advancedOptions['output']['add_output_cond']['add_output']
                ))
            </filter>
            <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;qMinE.*)\.tabular" visible="true"/>
        </collection>
        <collection label="For all target indices: minimal energy of any interaction covering the position, on ${on_string}" name="tMinE_output" type="list">
            <filter>
                ((
                advancedOptions['advancedSelector'] == "advanced" and
                advancedOptions['output']['add_output_cond']['selector'] == "add" and
                'tMinE' in advancedOptions['output']['add_output_cond']['add_output']
                ))
            </filter>
            <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;tMinE.*)\.tabular" visible="true"/>
        </collection>
        <collection label="For all index combinations: minimal energy of any interaction covering the index pair, on ${on_string}" name="pMinE_output" type="list">
            <filter>
                ((
                advancedOptions['advancedSelector'] == "advanced" and
                advancedOptions['output']['add_output_cond']['selector'] == "add" and
                'pMinE' in advancedOptions['output']['add_output_cond']['add_output']
                ))
            </filter>
            <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;pMinE.*)\.tabular" visible="true"/>
        </collection>
        <collection label="Query local accessibility penalties (ED values), on ${on_string}" name="qAcc_output" type="list">
            <filter>
                ((
                advancedOptions['advancedSelector'] == "advanced" and
                advancedOptions['output']['add_output_cond']['selector'] == "add" and
                'qAcc' in advancedOptions['output']['add_output_cond']['add_output']
                ))
            </filter>
            <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;qAcc.*)\.led" visible="true"/>
        </collection>
        <collection label="Target local accessibility penalties (ED values), on ${on_string}" name="tAcc_output" type="list">
            <filter>
                ((
                advancedOptions['advancedSelector'] == "advanced" and
                advancedOptions['output']['add_output_cond']['selector'] == "add" and
                'tAcc' in advancedOptions['output']['add_output_cond']['add_output']
                ))
            </filter>
            <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;tAcc.*)\.led" visible="true"/>
        </collection>
        <collection label="Query local unpaired probabilities, on ${on_string}" name="qPu_output" type="list">
            <filter>
                ((
                advancedOptions['advancedSelector'] == "advanced" and
                advancedOptions['output']['add_output_cond']['selector'] == "add" and
                'qPu' in advancedOptions['output']['add_output_cond']['add_output']
                ))
            </filter>
            <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;qPu.*)\.lpu" visible="true"/>
        </collection>
        <collection label="Target local unpaired probabilities, on ${on_string}" name="tPu_output" type="list">
            <filter>
                ((
                advancedOptions['advancedSelector'] == "advanced" and
                advancedOptions['output']['add_output_cond']['selector'] == "add" and
                'tPu' in advancedOptions['output']['add_output_cond']['add_output']
                ))
            </filter>
            <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;tPu.*)\.lpu" visible="true"/>
        </collection>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <conditional name="advancedOptions">
                <param name="advancedSelector" value="basic"/>
                <section name="query">
                    <param name="query" value="intarna_query.fa"/>
                </section>
                <section name="target">
                    <param name="target" value="intarna_target.fa"/>
                </section>
            </conditional>
            <output file="intarna_result.tabular" name="outfile"/>
        </test>
        <test expect_num_outputs="5">
            <conditional name="advancedOptions">
                <param name="advancedSelector" value="advanced"/>
                <section name="query">
                    <param name="query" value="intarna_query.fa"/>
                </section>
                <section name="target">
                    <param name="target" value="intarna_target.fa"/>
                </section>
                <section name="output">
                    <conditional name="add_output_cond">
                        <param name="selector" value="add"/>
                        <param name="add_output" value="spotProb,qMinE,tAcc,qPu"/>
                    </conditional>
                </section>
            </conditional>
            <output file="intarna_result.tabular" name="outfile"/>
            <output_collection count="4" name="spotProb_output" type="list">
            </output_collection>
            <output_collection count="4" name="qMinE_output" type="list">
            </output_collection>
            <output_collection count="2" name="qPu_output" type="list">