Mercurial > repos > rnateam > intarna

annotate intarna.xml @ 10:74fe8c4ba017 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit d33429dd2553acf4f2ec5a62fc37dff058d28fb5"
author bgruening
date Sat, 01 Feb 2020 09:18:50 +0000
parents 778e26161bd9
children 80ecf7309850
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10
74fe8c4ba017 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit d33429dd2553acf4f2ec5a62fc37dff058d28fb5"
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1 <tool id="intarna" name="IntaRNA" version="3.1.5">
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f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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2 <description>Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.</description>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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3 <macros>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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4 <macro name="query_macro">
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e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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5 <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" />
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f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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6 <conditional name="qAcc_cond">
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e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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7 <param argument="--qAcc" help="" label="Accessibility computation" type="select">
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f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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8 <option value="N">No accessibility contributions ('N')</option>
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9 <option selected="true" value="C">Computation of accessibilities ('C')</option>
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f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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10 <option value="P">Unpaired probabilities in RNAplfold format from --qAccFile</option>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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11 <option value="E">ED values in RNAplfold Pu-like format from --qAccFile</option>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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12 </param>
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13 <when value="N" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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14 <when value="C" />
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f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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15 <when value="P">
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e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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16 <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" />
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f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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17 </when>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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18 <when value="E">
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19 <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" />
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f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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20 </when>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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21 </conditional>
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e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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22 <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" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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23 <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" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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24 </macro>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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25 <macro name="target_macro">
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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26 <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" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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27 <conditional name="tAcc_cond">
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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28 <param argument="--tAcc" help="" label="Accessibility computation" type="select">
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29 <option value="N">No accessibility contributions ('N')</option>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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30 <option selected="true" value="C">Computation of accessibilities ('C')</option>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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31 <option value="P">Unpaired probabilities in RNAplfold format from --qAccFile</option>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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32 <option value="E">ED values in RNAplfold Pu-like format from --qAccFile</option>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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33 </param>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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34 <when value="N" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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35 <when value="C" />
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36 <when value="P">
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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37 <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" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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38 </when>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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39 <when value="E">
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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40 <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" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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41 </when>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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42 </conditional>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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43 <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" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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44 <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" />
0
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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45 </macro>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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46 <macro name="seed_macro">
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e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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47 <param argument="--noSeed" checked="false" falsevalue="" help="" label="Disable seed constraint entirely for computation" truevalue="--noSeed" type="boolean" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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48 <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" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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49 <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" />
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50 </macro>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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51 <macro name="interaction_macro">
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52 <param argument="--mode" help="" label="Prediction mode" type="select">
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53 <option selected="true" value="H">Heuristic ('H')</option>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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54 <option value="M">Exact but slow ('M')</option>
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55 </param>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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56 </macro>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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57 <macro name="output_macro">
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e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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58 <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" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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59 <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" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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60 <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" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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61 <param argument="--outOverlap" help="Whether or not interactions can overlap" label="Overlapping of suboptimal predictions" type="select">
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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62 <option value="N">in none of the sequences</option>
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63 <option value="T">in the target only</option>
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e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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64 <option selected="true" value="Q">in the query only</option>
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65 <option value="B">in both sequences</option>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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66 </param>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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67 </macro>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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68 </macros>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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69 <requirements>
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74fe8c4ba017 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit d33429dd2553acf4f2ec5a62fc37dff058d28fb5"
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70 <requirement type="package" version="3.1.5">intarna</requirement>
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f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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71 </requirements>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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72 <version_command>IntaRNA --version</version_command>
7
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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73 <command detect_errors="exit_code"><![CDATA[
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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74
0
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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75 IntaRNA
8
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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76 ## Multithreading
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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77 --threads "\${GALAXY_SLOTS:-1}"
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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78 ## basic general parameters
0
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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79 ## Query parameters
7
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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80 --query '$advancedOptions.query.query'
0
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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81 --qAcc $advancedOptions.query.qAcc_cond.qAcc
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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82 #if $advancedOptions.query.qAcc_cond.qAcc == "P" or $advancedOptions.query.qAcc_cond.qAcc == "E"
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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83 --qAccFile '$advancedOptions.query.qAcc_cond.qAccFile'
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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84 #end if
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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85 --qAccW $advancedOptions.query.qAccW
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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86 --qAccL $advancedOptions.query.qAccL
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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87 ## Target param.
7
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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88 --target '$advancedOptions.target.target'
0
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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89 --tAcc $advancedOptions.target.tAcc_cond.tAcc
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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90 #if $advancedOptions.target.tAcc_cond.tAcc == "P" or $advancedOptions.target.tAcc_cond.tAcc == "E"
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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91 --tAccFile '$advancedOptions.target.tAcc_cond.tAccFile'
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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92 #end if
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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diff changeset
93 --tAccW $advancedOptions.target.tAccW
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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94 --tAccL $advancedOptions.target.tAccL
8
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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95 ## Seed param.
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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96 #if $advancedOptions.seed.noSeed
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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97 $advancedOptions.seed.noSeed
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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98 #else
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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99 --seedBP $advancedOptions.seed.seedBP
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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100 #if $advancedOptions.seed.seedMaxUP > 0
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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101 --seedMaxUP $advancedOptions.seed.seedMaxUP
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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102 #end if
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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103 #end if
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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104 ## Prediction param.
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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105 --mode $advancedOptions.interaction.mode
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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106 --energy V
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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107 ## Output param.
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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108 --out $outfile
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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109 --outMode C
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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110 --outSep "`printf "\t"`"
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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111 --outNumber $advancedOptions.output.outNumber
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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112 --outOverlap $advancedOptions.output.outOverlap
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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113 --outCsvCols '$advancedOptions.output.outCsvCols'
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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114 --outCsvSort '$advancedOptions.output.outCsvSort'
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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115 #if $advancedOptions.advancedSelector == "advanced"
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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116 ## Query parameters
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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117 --qIntLoopMax $advancedOptions.query.qIntLoopMax
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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118 #if $advancedOptions.query.qRegion
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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119 --qRegion '$advancedOptions.query.qRegion'
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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120 #end if
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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121 ## Target param.
0
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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122 --tIntLoopMax $advancedOptions.target.tIntLoopMax
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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123 #if $advancedOptions.target.tRegion
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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124 --tRegion '$advancedOptions.target.tRegion'
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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125 #end if
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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126 ## Seed param.
8
690a3d9b1f21 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
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127 #if not $advancedOptions.seed.noSeed
7
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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128 --seedMaxE $advancedOptions.seed.seedMaxE
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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129 --seedMinPu $advancedOptions.seed.seedMinPu
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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130 #if $advancedOptions.seed.seedQMaxUP
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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131 --seedQMaxUP $advancedOptions.seed.seedQMaxUP
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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132 #end if
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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133 #if $advancedOptions.seed.seedTMaxUP
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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134 --seedTMaxUP $advancedOptions.seed.seedTMaxUP
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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135 #end if
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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136 #if $advancedOptions.seed.seedQRange
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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137 --seedQRange '$advancedOptions.seed.seedQRange'
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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138 #end if
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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139 #if $advancedOptions.seed.seedTRange
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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140 --seedTRange '$advancedOptions.seed.seedTRange'
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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141 #end if
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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142 #end if
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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143 ## SHAPE param.
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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144 #if $advancedOptions.shape.qShape
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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145 --qShape '$advancedOptions.shape.qShape'
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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146 #end if
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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147 #if $advancedOptions.shape.tShape
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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148 --tShape '$advancedOptions.shape.tShape'
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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149 #end if
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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150 ## Prediction param.
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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151 --model $advancedOptions.interaction.model
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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152 --energyVRNA '$advancedOptions.interaction.energyVRNA'
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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153 --temperature $advancedOptions.interaction.temperature
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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154 #if $advancedOptions.interaction.windowWidth
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155 --windowWidth $advancedOptions.interaction.windowWidth
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156 --windowOverlap $advancedOptions.interaction.windowOverlap
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157 #end if
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158 ##Output param.
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159 --outMaxE $advancedOptions.output.outMaxE
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160 --outDeltaE $advancedOptions.output.outDeltaE
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161 ## add additional output files
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162 #if $advancedOptions.output.add_output_cond.selector == "add"
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163 #if str($advancedOptions.output.add_output_cond.add_output.value) != 'None'
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164 #for $outFile in $advancedOptions.output.add_output_cond.add_output.value:
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165 #if $outFile == 'qAcc' or $outFile == 'tAcc'
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166 #set curOutFile = str($outFile) + ':intarna_' + str($outFile) + '.led'
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167 #else
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168 #if $outFile == 'qAcc' or $outFile == 'tAcc' or $outFile == 'qPu' or $outFile == 'tPu'
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169 #set curOutFile = str($outFile) + ':intarna_' + str($outFile) + '.lpu'
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170 #else
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171 #set curOutFile = str($outFile) + ':intarna_' + str($outFile) + '.tabular'
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172 #end if
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173 #end if
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174 --out '$curOutFile'
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175 #end for
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176 #end if
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177 #end if
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178 #end if
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179 ]]>
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180 </command>
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181 <inputs>
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182 <conditional name="advancedOptions">
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183 <param label="Options" name="advancedSelector" type="select">
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184 <option value="basic">Basic Options</option>
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185 <option value="advanced">Advanced Options</option>
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186 </param>
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187 <when value="advanced">
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188 <section expanded="True" name="query" title="Query Parameters">
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189 <expand macro="query_macro" />
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190 <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" />
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191 <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" />
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192 </section>
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193 <section expanded="True" name="target" title="Target Parameters">
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194 <expand macro="target_macro" />
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195 <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" />
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196 <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" />
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197 </section>
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198 <section name="seed" title="Seed Parameters">
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199 <expand macro="seed_macro" />
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200 <param argument="--seedQMaxUP" help="" label="Max. number of unpaired bases within the query's seed region" max="20" min="-1" type="integer" value="-1" />
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201 <param argument="--seedTMaxUP" help="" label="Max. number of unpaired bases within the target's seed region" max="20" min="-1" type="integer" value="-1" />
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202 <param argument="--seedMaxE" help="" label="Max. energy a seed region may have" max="999" min="-999" type="integer" value="0" />
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203 <param argument="--seedMinPu" help="" label="Min. unpaired probability (per sequence)" max="1" min="0" type="float" value="0" />
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204 <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="" />
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205 <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="" />
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206 </section>
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207 <section name="shape" title="SHAPE Input Parameters">
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208 <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" />
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209 <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" />
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210 </section>
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211 <section name="interaction" title="Prediction Parameters">
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212 <expand macro="interaction_macro" />
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213 <param argument="--model" help="Sets what to optimize for" label="Prediction target" type="select">
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214 <option value="S">Single-site minimum-free-energy interaction (IntaRNA v1+2 mode)</option>
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215 <option selected="true" value="X">Single-site minimum-free-energy interaction (via seed-extension)</option>
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216 <option value="P">Single-site interaction with minimal free ensemble energy per site</option>
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217 </param>
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218 <param argument="--energyVRNA" help="" label="Energy parameter" type="select">
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219 <option value="Turner99">Turner-1999</option>
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220 <option selected="true" value="Turner04">Turner-2004</option>
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221 <option value="Andronescu07">Andronescu-2007</option>
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222 </param>
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223 <param argument="--temperature" help="Temperature scaling of ViennaRNA energy parameters" label="Temperature [Celsius]" max="100" min="0" type="integer" value="37" />
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224 <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" />
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225 <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" />
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226 </section>
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227 <section name="output" title="Output Options">
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228 <expand macro="output_macro" />
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229 <param argument="--outMaxE" help="Only interactions with E ≤ maxE are reported" label="Max. absolute energy of an interaction" type="float" value="0" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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230 <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" />
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231 <conditional name="add_output_cond">
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232 <param label="Additional output files" name="selector" type="select">
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233 <option value="add">Output additional files</option>
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234 <option selected="true" value="none">Don't output additional files</option>
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235 </param>
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236 <when value="add">
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237 <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">
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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238 <option value="spotProb">Spot probabilities of all index combinations (spotProb)</option>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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239 <option value="qSpotProb">Spot probabilities for all query indices (qSpotProb)</option>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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240 <option value="tSpotProb">Spot probabilities for all target indices (tSpotProb)</option>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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241 <option value="pMinE">For all index combinations: minimal energy of any interaction covering the index pair (pMinE)</option>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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242 <option value="qMinE">For all query indices: minimal energy of any interaction covering the position (qMinE)</option>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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243 <option value="tMinE">For all target indices: minimal energy of any interaction covering the position (tMinE)</option>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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244 <option value="qAcc">The query's ED values (qAcc)</option>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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245 <option value="tAcc">The target's ED values (tAcc) </option>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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246 <option value="qPu">The query's unpaired probabilities used for ED values (qPu) </option>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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247 <option value="tPu">The target's unpaired probabilities used for ED values (tPu)</option>
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f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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248 </param>
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249 </when>
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250 <when value="none" />
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f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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251 </conditional>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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252 </section>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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253 </when>
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254 <when value="basic">
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255 <section expanded="True" name="query" title="Query Parameters">
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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256 <expand macro="query_macro" />
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f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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257 </section>
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258 <section expanded="True" name="target" title="Target Parameters">
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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259 <expand macro="target_macro" />
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f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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260 </section>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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261 <section name="seed" title="Seed Parameters">
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e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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262 <expand macro="seed_macro" />
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f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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263 </section>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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264 <section name="interaction" title="Interaction Parameters">
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e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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265 <expand macro="interaction_macro" />
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f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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266 </section>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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267 <section name="output" title="Output Options">
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268 <expand macro="output_macro" />
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269 </section>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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270 </when>
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271 </conditional>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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272 </inputs>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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273 <outputs>
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274 <data format="tabular" label="IntaRNA on ${on_string}" name="outfile" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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275 <collection label="Spot probability of all index combinations, on ${on_string}" name="spotProb_output" type="list">
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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276 <filter>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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277 ((
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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278 advancedOptions['advancedSelector'] == "advanced" and
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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279 advancedOptions['output']['add_output_cond']['selector'] == "add" and
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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280 'spotProb' in advancedOptions['output']['add_output_cond']['add_output']
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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281 ))
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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282 </filter>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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283 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;spotProb.*)\.tabular" visible="true" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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284 </collection>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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285 <collection label="Spot probability for all query indices, on ${on_string}" name="qSpotProb_output" type="list">
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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286 <filter>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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287 ((
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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288 advancedOptions['advancedSelector'] == "advanced" and
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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289 advancedOptions['output']['add_output_cond']['selector'] == "add" and
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290 'qSpotProb' in advancedOptions['output']['add_output_cond']['add_output']
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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291 ))
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292 </filter>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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293 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;qSpotProb.*)\.tabular" visible="true" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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294 </collection>
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295 <collection label="Spot probability for all target indices, on ${on_string}" name="tSpotProb_output" type="list">
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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296 <filter>
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297 ((
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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298 advancedOptions['advancedSelector'] == "advanced" and
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299 advancedOptions['output']['add_output_cond']['selector'] == "add" and
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300 'tSpotProb' in advancedOptions['output']['add_output_cond']['add_output']
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301 ))
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302 </filter>
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303 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;tSpotProb.*)\.tabular" visible="true" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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304 </collection>
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305 <collection label="For all query indices: minimal energy of any interaction covering the position, on ${on_string}" name="qMinE_output" type="list">
0
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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306 <filter>
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307 ((
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
308 advancedOptions['advancedSelector'] == "advanced" and
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
309 advancedOptions['output']['add_output_cond']['selector'] == "add" and
7
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
310 'qMinE' in advancedOptions['output']['add_output_cond']['add_output']
0
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
311 ))
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
312 </filter>
7
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
313 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;qMinE.*)\.tabular" visible="true" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
314 </collection>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
315 <collection label="For all target indices: minimal energy of any interaction covering the position, on ${on_string}" name="tMinE_output" type="list">
0
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
316 <filter>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
317 ((
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
318 advancedOptions['advancedSelector'] == "advanced" and
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
319 advancedOptions['output']['add_output_cond']['selector'] == "add" and
7
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
320 'tMinE' in advancedOptions['output']['add_output_cond']['add_output']
0
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
321 ))
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
322 </filter>
7
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
323 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;tMinE.*)\.tabular" visible="true" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
324 </collection>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
325 <collection label="For all index combinations: minimal energy of any interaction covering the index pair, on ${on_string}" name="pMinE_output" type="list">
0
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
326 <filter>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
327 ((
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
328 advancedOptions['advancedSelector'] == "advanced" and
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
329 advancedOptions['output']['add_output_cond']['selector'] == "add" and
7
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
330 'pMinE' in advancedOptions['output']['add_output_cond']['add_output']
0
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
331 ))
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
332 </filter>
7
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
333 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;pMinE.*)\.tabular" visible="true" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
334 </collection>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
335 <collection label="Query local accessibility penalties (ED values), on ${on_string}" name="qAcc_output" type="list">
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
336 <filter>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
337 ((
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
338 advancedOptions['advancedSelector'] == "advanced" and
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
339 advancedOptions['output']['add_output_cond']['selector'] == "add" and
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
340 'qAcc' in advancedOptions['output']['add_output_cond']['add_output']
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
341 ))
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
342 </filter>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
343 <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;qAcc.*)\.led" visible="true" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
344 </collection>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
345 <collection label="Target local accessibility penalties (ED values), on ${on_string}" name="tAcc_output" type="list">
0
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
346 <filter>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
347 ((
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
348 advancedOptions['advancedSelector'] == "advanced" and
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
349 advancedOptions['output']['add_output_cond']['selector'] == "add" and
7
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
350 'tAcc' in advancedOptions['output']['add_output_cond']['add_output']
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
351 ))
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
352 </filter>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
353 <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;tAcc.*)\.led" visible="true" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
354 </collection>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
355 <collection label="Query local unpaired probabilities, on ${on_string}" name="qPu_output" type="list">
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
356 <filter>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
357 ((
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
358 advancedOptions['advancedSelector'] == "advanced" and
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
359 advancedOptions['output']['add_output_cond']['selector'] == "add" and
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
360 'qPu' in advancedOptions['output']['add_output_cond']['add_output']
0
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
361 ))
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
362 </filter>
7
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
363 <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;qPu.*)\.lpu" visible="true" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
364 </collection>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
365 <collection label="Target local unpaired probabilities, on ${on_string}" name="tPu_output" type="list">
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
366 <filter>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
367 ((
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
368 advancedOptions['advancedSelector'] == "advanced" and
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
369 advancedOptions['output']['add_output_cond']['selector'] == "add" and
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
370 'tPu' in advancedOptions['output']['add_output_cond']['add_output']
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
371 ))
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
372 </filter>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
373 <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;tPu.*)\.lpu" visible="true" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
374 </collection>
0
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
375 </outputs>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
376 <tests>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
377 <test>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
378 <conditional name="advancedOptions">
7
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
379 <param name="advancedSelector" value="basic" />
0
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
380 <section name="query">
7
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
381 <param name="query" value="intarna_query.fa" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
382 </section>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
383 <section name="target">
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
384 <param name="target" value="intarna_target.fa" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
385 </section>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
386 </conditional>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
387 <output file="intarna_result.tabular" name="outfile" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
388 </test>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
389 <test>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
390 <conditional name="advancedOptions">
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
391 <param name="advancedSelector" value="advanced" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
392 <section name="query">
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
393 <param name="query" value="intarna_query.fa" />
0
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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diff changeset
394 </section>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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395 <section name="target">
7
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
396 <param name="target" value="intarna_target.fa" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
397 </section>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
398 <section name="output">
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
399 <conditional name="add_output_cond">
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
400 <param name="selector" value="add" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
401 <param name="add_output" value="spotProb,qMinE,tAcc,qPu" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
402 </conditional>
0
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
403 </section>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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404 </conditional>
7
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
405 <output file="intarna_result.tabular" name="outfile" />
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
406 <output_collection count="4" name="spotProb_output" type="list">
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
407 </output_collection>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
408 <output_collection count="4" name="qMinE_output" type="list">
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
409 </output_collection>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
410 <output_collection count="2" name="qPu_output" type="list">
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
411 </output_collection>
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
412 <output_collection count="2" name="tAcc_output" type="list">
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
413 </output_collection>
0
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
414 </test>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
415 </tests>
7
e4e4f33d95c3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
416 <help><![CDATA[
0
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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417
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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418 **What it does**
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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419 Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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420 During the last few years, several new small regulatory RNAs (sRNAs) have been discovered in bacteria. Most of them act as post-transcriptional regulators by base pairing to a target mRNA, causing translational repression or activation, or mRNA degradation. Numerous sRNAs have already been identified, but the number of experimentally verified targets is considerably lower. Consequently, computational target prediction is in great demand. Many existing target prediction programs neglect the accessibility of target sites and the existence of a seed, while other approaches are either specialized to certain types of RNAs or too slow for genome-wide searches.
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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421 IntaRNA, developed by `Prof. Backofen's bioinformatics group at Freiburg University <http://www.bioinf.uni-freiburg.de/>`_, is a general and fast approach to the prediction of RNA-RNA interactions incorporating both the accessibility of interacting sites as well as the existence of a user-definable seed interaction. We successfully applied IntaRNA to the prediction of bacterial sRNA targets and determined the exact locations of the interactions with a higher accuracy than competing programs.
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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diff changeset
422 .. class:: infomark
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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423 Please refer to `IntaRNA github repository <https://github.com/BackofenLab/IntaRNA>`_ for use cases and additional information.
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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424 **Input**
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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425 RNA sequences in *FASTA* format
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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diff changeset
426 **Output**
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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diff changeset
427 RNA-RNA interaction information in CSV format and additional information/files on demand
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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428
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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429 ]]>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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430 </help>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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431 <citations>
3
bfb4f2132c89 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 0d69e178bbd7019a51a50fda5e5cf6721770083d
rnateam
parents: 2
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432 <citation type="doi">10.1093/nar/gkx279</citation>
0
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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433 <citation type="doi">10.1093/nar/gku359</citation>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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434 <citation type="doi">10.1093/bioinformatics/btn544</citation>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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435 </citations>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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436 </tool>