viennarna_rnafold: rnafold.xml annotate

annotate rnafold.xml @ 0:14817dcab062 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374

author	bgruening
date	Wed, 05 Oct 2016 11:50:25 -0400
parents
children

rev	line source
0 14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	1 <tool id="viennarna_rnafold" name="@EXECUTABLE@" version="@VERSION@.0">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	2 <description>Calculate minimum free energy secondary structures and partition function of RNAs</description>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	3 <macros>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	4 <token name="@EXECUTABLE@">RNAfold</token>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	5 <import>macros.xml</import>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	6 </macros>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	7 <expand macro="requirements" />
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	8 <expand macro="stdio" />
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	9 <expand macro="version_command" />
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	10 <command>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	11 <![CDATA[
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	12 #if str($input_source.select_fasta) == "false"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	13 #if str($input_source.input_sequence).lstrip()[0] == ">"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	14 echo "${input_source.input_sequence}" > "input.fasta" &&
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	15 #else
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	16 echo ">Sequence" > "input.fasta" &&
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	17 echo "${input_source.input_sequence}" >> "input.fasta" &&
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	18 #end if
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	19 #end if
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	20 RNAfold
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	21 -T $temperature
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	22 --dangles=$dangling
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	23 #if $layout_type ==0
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	24 --layout-type=$general_options.layout_type
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	25 #end if
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	26 #if $measelect.mea == "yes":
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	27 --MEA=$measelect.meavalue
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	28 #if $measelect.pfScale <> 1.07
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	29 --pfScale=$measelect.pfScale
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	30 #end if
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	31 #else
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	32 $measelect.pf
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	33 #if $measelect.pfScale <> 1.07
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	34 --pfScale=$measelect.pfScale
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	35 #end if
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	36 #end if
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	37 $advancedOptions.noconversion
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	38 $advancedOptions.gquad
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	39 $advancedOptions.nolp
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	40 $advancedOptions.nogu
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	41 $advancedOptions.noclosinggu
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	42 $advancedOptions.notetra
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	43 $advancedOptions.circular
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	44 #if $advancedOptions.bppmThreshold <> 1e-5
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	45 --bppmThreshold=$advancedOptions.bppmThreshold
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	46 #end if
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	47 #if $advancedOptions.nsp
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	48 --nsp='$advancedOptions.nsp'
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	49 #end if
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	50 #if $advancedOptions.betaScale <> 1.0
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	51 --betaScale=$advancedOptions.betaScale
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	52 #end if
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	53 #if $constraints.maxBPspan <> -1
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	54 --maxBPspan=$constraints.maxBPspan
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	55 #end if
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	56 #if str($constraints.constraintLocation.constraintSelector) == "fromFile"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	57 --constraint='$constraints.constraintLocation.constraintsFile'
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	58 $constraints.constraintLocation.batch
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	59 $constraints.constraintLocation.canonicalBPonly
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	60 $constraints.constraintLocation.enforceConstraint
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	61 #end if
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	62 #if str($constraints.shapeOption.shapeSelector) == "isUsed"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	63 --shape='$constraints.shapeOption.shapeFile'
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	64 #if str($constraints.shapeOption.shapeMethod.methodSelector) == "W"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	65 #set $s="W"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	66 --shapeMethod=$s
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	67 #else if str($constraints.shapeOption.shapeMethod.methodSelector) == "Z"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	68 #set $s="Zb"+str($constraints.shapeOption.shapeMethod.b)
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	69 --shapeMethod=$s
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	70 #if str($constraints.shapeOption.shapeMethod.shapeConversion.conversionSelector) == "C"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	71 #set $c="C"+str($constraints.shapeOption.shapeMethod.shapeConversion.c)
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	72 --shapeConversion=$c
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	73 #else if str($constraints.shapeOption.shapeMethod.shapeConversion.conversionSelector) == "L"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	74 #set $c="Ls"+str($constraints.shapeOption.shapeMethod.shapeConversion.s)+"i"+ str($constraints.shapeOption.shapeMethod.shapeConversion.i)
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	75 --shapeConversion=$c
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	76 #else if str($constraints.shapeOption.shapeMethod.shapeConversion.conversionSelector) == "O"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	77 #set $c="Os"+str($constraints.shapeOption.shapeMethod.shapeConversion.s)+"i"+ str($constraints.shapeOption.shapeMethod.shapeConversion.i)
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	78 --shapeConversion=$c
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	79 #else
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	80 #set $c=str($constraints.shapeOption.shapeMethod.shapeConversion.conversionSelector)
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	81 --shapeConversion=$c
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	82 #end if
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	83 #else if str($constraints.shapeOption.shapeMethod.methodSelector) == "D"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	84 #set $s="Dm"+str($constraints.shapeOption.shapeMethod.m)+"b"+str($constraints.shapeOption.shapeMethod.b)
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	85 --shapeMethod=$s
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	86 #end if
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	87 #end if
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	88 #if $constraints.motif
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	89 --motif='$constraints.motif'
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	90 #end if
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	91 <
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	92 #if str($input_source.select_fasta) == "false"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	93 "input.fasta"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	94 #else
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	95 "${input_source.fasta_input}"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	96 #end if
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	97 > '$tabular_file'
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	98 ]]>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	99 </command>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	100
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	101 <inputs>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	102 <conditional name="input_source">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	103 <param name="select_fasta" type="select" label="Input from FASTA file">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	104 <option value="true" selected="true">Use FASTA</option>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	105 <option value="false">Provide sequence as text-field</option>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	106 </param>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	107 <when value="true">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	108 <param format="fasta" name="fasta_input" type="data" label="Sequence to fold (FASTA file)"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	109 </when>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	110 <when value="false">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	111 <param name="input_sequence" type="text" label="Input sequence"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	112 </when>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	113 </conditional>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	114 <param name="temperature" type="float" value="37.0" label="Temperature [°C]" argument="-T"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	115 <param name="dangling" type="select" label="How to treat dangling end energies" argument="-d">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	116 <option value="0">0: ignore dangling ends</option>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	117 <option value="1">1: unpaired bases participate in one dangling end only</option>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	118 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	119 <option value="3">3: allow coaxial stacking</option>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	120 </param>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	121 <param name="layout_type" type="select" label="Layout algorithm" argument="--layout_type" >
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	122 <option value="1" selected="true">Default: Naview layout</option>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	123 <option value="0">Simple radial layout</option>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	124 </param>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	125 <conditional name="measelect">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	126 <param name="mea" type="select" label="Calculate Maximum Expected accuracy" argument="--MEA">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	127 <option value="no">No</option>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	128 <option value="yes">Yes</option>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	129 </param>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	130 <when value="yes">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	131 <param name="meavalue" type="float" value="1.0" label="Gamma Value"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	132 <param argument="--pfScale" type="float" value="1.07" label="Scaling factor" help="In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows). The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences."/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	133 </when>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	134 <when value="no">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	135 <param name="pf" type="boolean" checked="false" truevalue="--partfunc" falsevalue="" label="Calculate Partition Function" help="--partfunc"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	136 <param argument="--pfScale" type="float" value="1.07" label="Scaling factor" help="In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows). The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences."/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	137 </when>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	138 </conditional>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	139 <section name="advancedOptions" title="Advanced options">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	140 <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	141 <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	142 <param name="noclosinggu" type="boolean" truevalue="" falsevalue="--noClosingGU" checked="true" label="Allow GU pairing at the ends" help="Allow pairing of G and U at the ends of helices. --noClosingGU"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	143 <param name="notetra" type="boolean" truevalue="" falsevalue="--noTetra" checked="true" label="Allow stabilization for loops, hairpins etc." help=" Include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing. (--noTetra)"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	144 <param name="noconversion" type="boolean" truevalue="" falsevalue="--noconv" checked="true" label="Convert Thymine to Uracil (T -> U)" help="Avoids confusion with DNA sequences (--noconv)"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	145 <param name="gquad"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	146 type="boolean"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	147 truevalue="--gquad"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	148 falsevalue=""
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	149 checked="false"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	150 label="Take G Quadruplex formation into account"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	151 argument="-g"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	152 <param name="circular"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	153 type="boolean"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	154 truevalue="--circ"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	155 falsevalue=""
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	156 checked="false"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	157 label="Model as circular RNA structure"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	158 argument="--circ"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	159 <param name="bppmThreshold"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	160 type="float"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	161 value="1e-5"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	162 label="Threshold for base pair probabilities"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	163 help="By setting the threshold the base pair probabilities that are included in the output can be varied. By default only those exceeding 1e−5 in probability will be shown as squares in the dot plot. Changing the threshold to any other value allows for increase or decrease of data."
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	164 argument="--bppmThreshold"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	165 <param name="nsp"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	166 type="text"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	167 value=""
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	168 label="Allow other pairs in addition to the usual AU,GC,and GU pairs."
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	169 help="Its argument is a comma separated list of additionally allowed pairs. If the first character is '-' then AB will imply that AB and BA are allowed pairs. e.g. RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy."
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	170 argument="--nsp"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	171 <param name="betaScale"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	172 type="float"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	173 value="1.0"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	174 label="Scaling of Boltzman factors"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	175 help=" The argument provided with this option enables to scale the thermodynamic temperature used in the Boltzmann factors independently from the temperature used to scale the individual energy contributions of the loop types."
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	176 argument="--betaScale"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	177 </section>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	178 <section name="constraints" title="Structure constraints">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	179 <param name="maxBPspan" type="integer" value="-1" label="Set the maximum base pair span" help="" argument="--maxBPspan"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	180 <conditional name="constraintLocation">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	181 <param name="constraintSelector" type="select" label="Constraints">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	182 <!-- <option value="fromInput">The constraints are included in the input file</option> -->
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	183 <option value="fromFile">The constraints are in a seperate file</option>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	184 <option value="none" selected="true">Don't use constraints</option>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	185 </param>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	186 <!-- <when value="fromInput"></when> -->
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	187 <when value="none"></when>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	188 <when value="fromFile">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	189 <param name="constraintsFile" type="data" format="*" label="Constraints file" argument="--constraint"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	190 <param name="batch" type="boolean" checked="false" truevalue="--batch" falsevalue=""
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	191 label="Use constraints for all alignment records"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	192 help="Usually, constraints provided from input file are only applied to a single sequence alignment. Therefore, RNAalifold will stop its computation and quit after the first input alignment was processed. Using this switch, RNAalifold processes all sequence alignments in the input and applies the same provided constraints to each of them."
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	193 argument="--batch"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	194 <param argument="--canonicalBPonly" type="boolean" truevalue="--canonicalBPonly" falsevalue="" checked="false" label="Remove non-canonical base pairs from he structure constraint" />
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	195 <param argument="--enforceConstraint" type="boolean" truevalue="--enforceConstraint" falsevalue="" checked="false" label="Enforce base pair given by round brackets () in structure constraint" />
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	196 </when>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	197 </conditional>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	198 <conditional name="shapeOption">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	199 <param name="shapeSelector" type="select" label="Shape reactivity data">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	200 <option value="isUsed">Use shape reactivity data</option>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	201 <option value="notUsed" selected="true">Don't use shape reactivity data</option>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	202 </param>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	203 <when value ="isUsed">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	204 <param type="data" name="shapeFile" format="shape,*" label="Shape file" argument="--shape"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	205 <conditional name="shapeMethod">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	206 <param name="methodSelector" type="select" label="Shape reactivity data" argument="--shapeMethod">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	207 <option value="D" selected="true">D: Convert by using a linear equation according to Deigan et al 2009</option>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	208 <option value="Z">Z: Convert SHAPE reactivities to pseudo energies according to Zarringhalam et al 2012.</option>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	209 <option value="W">W: Apply a given vector of perturbation energies to unpaired nucleotides according to Washietl et al 2012</option>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	210 </param>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	211 <when value="D">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	212 <param name="m" type="float" value="1.8" label="Slope m"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	213 <param name="b" type="float" value="-0.6" label="Intercept"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	214 </when>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	215 <when value="Z">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	216 <param name="b" type="float" value="-0.6" label="Intercept"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	217 <conditional name="shapeConversion">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	218 <param name="conversionSelector" type="select" label="shape reactivity data">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	219 <option value="M">M: Use linear mapping according to Zarringhalam et al</option>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	220 <option value="C">C: Use a cutoff−approach to divide into paired and unpaired nucleotides</option>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	221 <option value="S">S: Skip the normalizing step since the input data already represents probabilities for being unpaired rather than raw reactivity values</option>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	222 <option value="L">L: Use a linear model to convert the reactivity into a probability for being unpaired</option>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	223 <option value="O" selected="true">O: Use a linear model to convert the log of the reactivity into a probability for being unpaired</option>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	224 </param>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	225 <when value="M">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	226 </when>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	227 <when value="C">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	228 <param name="c" type="float" value="0.25" label="Cutoff"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	229 </when>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	230 <when value="S">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	231 </when>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	232 <when value="L">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	233 <param name="s" type="float" value="0.68" label="Slope"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	234 <param name="i" type="float" value="0.2" label="Intercept"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	235 </when>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	236 <when value="O">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	237 <param name="s" type="float" value="1.6" label="Slope s"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	238 <param name="i" type="float" value="-2.29" label="Intercept"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	239 </when>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	240 </conditional>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	241 </when>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	242 <when value="W">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	243 </when>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	244 </conditional>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	245 </when>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	246 <when value="notUsed">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	247 </when>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	248 </conditional>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	249 <param argument="--motif" type="text" value="" label="Sequence structure energy" help="Specify stabilizing effect of ligand binding to a particular sequence/structure motif. Some ligands binding to RNAs require and/or induce particular sequence and structure motifs. For instance they bind to an interior loop, or small hairpin loop. If for such cases a binding free energy is known, the binding and therefore stabilizing effect of the ligand can be included in the folding recursions. Interior loop motifs are specified as concatenations of 5’ and 3’ motif, separated by an ’&’ character. Energy contributions must be specified in kcal/mol."/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	250 </section>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	251 <section name="IDs" title="Naming Conventions">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	252 <param name="auto_id"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	253 type="boolean" truevalue="--auto-id" falsevalue="" checked="false"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	254 label="Automatically generate an ID for each alignment."
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	255 help="If this flag is active, RNAalifold ignores any IDs retrieved from the input and automatically generates an ID for each alignment."
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	256 argument="--auto-id"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	257 <param name="id_prefix"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	258 type="text" value="alignment"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	259 label="Prefix for automatically generated IDs (as used in output file names)"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	260 help="If this parameter is set, each alignment will be prefixed with the provided string. Hence, the output files will obey the following naming scheme: 'prefix_xxxx_ss.ps' (secondary structure plot), 'prefix_xxxx_dp.ps' (dot−plot), 'prefix_xxxx_aln.ps' (annotated alignment), etc. where xxxx is the alignment number beginning with the second alignment in the input. Use this setting in conjunction with the −−continuous−ids flag to assign IDs beginning with the first input alignment."
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	261 argument="--id-prefix"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	262 <param name="id_digits"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	263 type="integer" value="4" min="1" max="18"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	264 label="The number of digits of the counter in automatically generated alignment IDs"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	265 help="When alignments IDs are automatically generated, they receive an increasing number, starting with 1. This number will always be left−padded by leading zeros, such that the number takes up a certain width. Using this parameter, the width can be specified to the users need. We allow numbers in the range [1:18]."
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	266 argument="--id-digits"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	267 <param name="id_start"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	268 type="integer" value="1" min="0"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	269 label="First number in automatically generated alignment IDs"
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	270 help="When alignment IDs are automatically generated, they receive an increasing number, usually starting with 1. Using this parameter, the first number can be specified to the users requirements. Note: negative numbers are not allowed. Note: Setting this parameter implies continuous alignment IDs, i.e. it activates the −−continuous−ids flag.."
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	271 argument="--id-start"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	272 </section>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	273 </inputs>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	274 <outputs>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	275 <data format="dbn" name="tabular_file"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	276 <collection name="sequence_outputs" type="list" label="rna_eps outputs">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	277 <discover_datasets pattern="(?P<designation>.+)_ss\.ps" ext="eps" />
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	278 </collection>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	279 <collection name="matrix_outputs" type="list" label="rna_eps outputs">
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	280 <filter>measelect['pf'] is True</filter>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	281 <discover_datasets pattern="(?P<designation>.+)_dp\.ps" ext="rna_eps" visible="true"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	282 </collection>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	283 </outputs>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	284 <tests>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	285 <test>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	286 <param name="select_fasta" value="true" />
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	287 <param name="fasta_input" value="rnafold_input1.fa"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	288 <output name="out_file1" file="rnafold_result1.txt"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	289 </test>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	290
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	291 <test>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	292 <param name="select_fasta" value="true" />
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	293 <param name="fasta_input" value="rnafold_input2.fa"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	294 <param name="temperature" value="75"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	295 <output name="out_file1" file="rnafold_result2.txt"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	296 </test>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	297
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	298 <test>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	299 <param name="select_fasta" value="false" />
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	300 <param name="input_sequence" value="TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	301 <output name="out_file1" file="rnafold_result3.txt"/>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	302 </test>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	303 </tests>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	304 <help>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	305 <![CDATA[
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	306 RNAfold
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	307
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	308 The program reads RNA sequences, calculates their minimum free
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	309 energy (mfe) structure and the mfe structure in dot-bracket notation.
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	310
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	311 If the -p option was given it also computes the
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	312 partition function (pf) and base pairing probability matrix.
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	313
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	314 The dot plot of the base pairing probability matrix shows a matrix of squares with area proportional to the pairing
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	315 probability in the upper right half, and one square for each pair in the
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	316 minimum free energy structure in the lower left half. For each pair i-j with
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	317 probability p>10E-6 there is a line of the form
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	318
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	319 i j sqrt(p) ubox
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	320
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	321 in the PostScript file, so that the pair probabilities can be easily extracted.
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	322
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	323 The sequences have to be provided in FASTA format. The first word (max. 42 char) of the FASTA header will be used for output file names. PostScript files "name_ss.ps" and "name_dp.ps" are produced for the structure and dot plot, respectively.
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	324 The program will read the whole FASTA input file and provide output for each found sequence.
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	325
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	326
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	327 -----
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	328
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	329 Input format
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	330
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	331 RNAfold requires one input file or a plain RNA sequence
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	332
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	333 ------
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	334
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	335 Outputs
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	336
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	337 - Secondary structures in dot-bracket notation
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	338
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	339 - several possible postscript images bundled together in a tar file
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	340 - secondary structure for each sequence in the input file
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	341 - if partition function is calculated (--MEA or --partfunc is set) then also the pairing probabilty matrix is generated for each sequence
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	342
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	343 ]]>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	344 </help>
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	345 <expand macro="citations" />
14817dcab062 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374 bgruening parents: diff changeset	346 </tool>

Mercurial > repos > bgruening > viennarna_rnafold

annotate rnafold.xml @ 0:14817dcab062 draft default tip