Mercurial > repos > rnateam > intarna
diff intarna.xml @ 16:f5d850723e63 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
| author | bgruening |
|---|---|
| date | Wed, 18 Sep 2024 19:42:08 +0000 |
| parents | 0377acb3f91b |
| children |
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--- a/intarna.xml Thu Jan 25 13:12:23 2024 +0000 +++ b/intarna.xml Wed Sep 18 19:42:08 2024 +0000 @@ -1,74 +1,74 @@ -<tool id="intarna" name="IntaRNA" version="3.4.0"> +<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" format="fasta" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format" label="Query sequence(s)" name="query" type="data" /> + <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" help="" label="Accessibility computation" type="select"> + <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="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" /> + <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" 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" /> + <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" 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" /> + <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" format="fasta" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format" label="Target sequence(s)" name="target" type="data" /> + <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" help="" label="Accessibility computation" type="select"> + <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="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" /> + <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" 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" /> + <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" 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" /> + <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" 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" /> + <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" help="" label="Prediction mode" type="select"> + <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" 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"> + <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" 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" /> + <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="3.4.0">intarna</requirement> + <requirement type="package" version="3.4.1">intarna</requirement> </requirements> <version_command>IntaRNA --version</version_command> <command detect_errors="exit_code"><![CDATA[ @@ -182,61 +182,61 @@ </command> <inputs> <conditional name="advancedOptions"> - <param label="Options" name="advancedSelector" type="select"> + <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" 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" /> + <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" 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" /> + <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" 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="" /> + <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" 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" /> + <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" help="Sets what to optimize for" label="Prediction target" type="select"> + <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" help="" label="Energy parameter" type="select"> + <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" 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" /> + <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" 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" /> + <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 label="Additional output files" name="selector" type="select"> + <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 display="checkboxes" help="Written in a format similar to RNAplfold unpaired probability output." label="Additional output files" multiple="True" name="add_output" type="select"> + <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> @@ -249,31 +249,31 @@ <option value="tPu">The target's unpaired probabilities used for ED values (tPu)</option> </param> </when> - <when value="none" /> + <when value="none"/> </conditional> </section> </when> <when value="basic"> <section expanded="True" name="query" title="Query Parameters"> - <expand macro="query_macro" /> + <expand macro="query_macro"/> </section> <section expanded="True" name="target" title="Target Parameters"> - <expand macro="target_macro" /> + <expand macro="target_macro"/> </section> <section name="seed" title="Seed Parameters"> - <expand macro="seed_macro" /> + <expand macro="seed_macro"/> </section> <section name="interaction" title="Interaction Parameters"> - <expand macro="interaction_macro" /> + <expand macro="interaction_macro"/> </section> <section name="output" title="Output Options"> - <expand macro="output_macro" /> + <expand macro="output_macro"/> </section> </when> </conditional> </inputs> <outputs> - <data format="tabular" label="IntaRNA on ${on_string}" name="outfile" /> + <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> (( @@ -282,7 +282,7 @@ 'spotProb' in advancedOptions['output']['add_output_cond']['add_output'] )) </filter> - <discover_datasets format="tabular" pattern="intarna_(?P<designation>spotProb.*)\.tabular" visible="true" /> + <discover_datasets format="tabular" pattern="intarna_(?P<designation>spotProb.*)\.tabular" visible="true"/> </collection> <collection label="Spot probability for all query indices, on ${on_string}" name="qSpotProb_output" type="list"> <filter> @@ -292,7 +292,7 @@ 'qSpotProb' in advancedOptions['output']['add_output_cond']['add_output'] )) </filter> - <discover_datasets format="tabular" pattern="intarna_(?P<designation>qSpotProb.*)\.tabular" visible="true" /> + <discover_datasets format="tabular" pattern="intarna_(?P<designation>qSpotProb.*)\.tabular" visible="true"/> </collection> <collection label="Spot probability for all target indices, on ${on_string}" name="tSpotProb_output" type="list"> <filter> @@ -302,7 +302,7 @@ 'tSpotProb' in advancedOptions['output']['add_output_cond']['add_output'] )) </filter> - <discover_datasets format="tabular" pattern="intarna_(?P<designation>tSpotProb.*)\.tabular" visible="true" /> + <discover_datasets format="tabular" pattern="intarna_(?P<designation>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> @@ -312,7 +312,7 @@ 'qMinE' in advancedOptions['output']['add_output_cond']['add_output'] )) </filter> - <discover_datasets format="tabular" pattern="intarna_(?P<designation>qMinE.*)\.tabular" visible="true" /> + <discover_datasets format="tabular" pattern="intarna_(?P<designation>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> @@ -322,7 +322,7 @@ 'tMinE' in advancedOptions['output']['add_output_cond']['add_output'] )) </filter> - <discover_datasets format="tabular" pattern="intarna_(?P<designation>tMinE.*)\.tabular" visible="true" /> + <discover_datasets format="tabular" pattern="intarna_(?P<designation>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> @@ -332,7 +332,7 @@ 'pMinE' in advancedOptions['output']['add_output_cond']['add_output'] )) </filter> - <discover_datasets format="tabular" pattern="intarna_(?P<designation>pMinE.*)\.tabular" visible="true" /> + <discover_datasets format="tabular" pattern="intarna_(?P<designation>pMinE.*)\.tabular" visible="true"/> </collection> <collection label="Query local accessibility penalties (ED values), on ${on_string}" name="qAcc_output" type="list"> <filter> @@ -342,7 +342,7 @@ 'qAcc' in advancedOptions['output']['add_output_cond']['add_output'] )) </filter> - <discover_datasets format="txt" pattern="intarna_(?P<designation>qAcc.*)\.led" visible="true" /> + <discover_datasets format="txt" pattern="intarna_(?P<designation>qAcc.*)\.led" visible="true"/> </collection> <collection label="Target local accessibility penalties (ED values), on ${on_string}" name="tAcc_output" type="list"> <filter> @@ -352,7 +352,7 @@ 'tAcc' in advancedOptions['output']['add_output_cond']['add_output'] )) </filter> - <discover_datasets format="txt" pattern="intarna_(?P<designation>tAcc.*)\.led" visible="true" /> + <discover_datasets format="txt" pattern="intarna_(?P<designation>tAcc.*)\.led" visible="true"/> </collection> <collection label="Query local unpaired probabilities, on ${on_string}" name="qPu_output" type="list"> <filter> @@ -362,7 +362,7 @@ 'qPu' in advancedOptions['output']['add_output_cond']['add_output'] )) </filter> - <discover_datasets format="txt" pattern="intarna_(?P<designation>qPu.*)\.lpu" visible="true" /> + <discover_datasets format="txt" pattern="intarna_(?P<designation>qPu.*)\.lpu" visible="true"/> </collection> <collection label="Target local unpaired probabilities, on ${on_string}" name="tPu_output" type="list"> <filter> @@ -372,39 +372,39 @@ 'tPu' in advancedOptions['output']['add_output_cond']['add_output'] )) </filter> - <discover_datasets format="txt" pattern="intarna_(?P<designation>tPu.*)\.lpu" visible="true" /> + <discover_datasets format="txt" pattern="intarna_(?P<designation>tPu.*)\.lpu" visible="true"/> </collection> </outputs> <tests> - <test> + <test expect_num_outputs="1"> <conditional name="advancedOptions"> - <param name="advancedSelector" value="basic" /> + <param name="advancedSelector" value="basic"/> <section name="query"> - <param name="query" value="intarna_query.fa" /> + <param name="query" value="intarna_query.fa"/> </section> <section name="target"> - <param name="target" value="intarna_target.fa" /> + <param name="target" value="intarna_target.fa"/> </section> </conditional> - <output file="intarna_result.tabular" name="outfile" /> + <output file="intarna_result.tabular" name="outfile"/> </test> - <test> + <test expect_num_outputs="5"> <conditional name="advancedOptions"> - <param name="advancedSelector" value="advanced" /> + <param name="advancedSelector" value="advanced"/> <section name="query"> - <param name="query" value="intarna_query.fa" /> + <param name="query" value="intarna_query.fa"/> </section> <section name="target"> - <param name="target" value="intarna_target.fa" /> + <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" /> + <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 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">