viennarna_rnafold: rnafold.xml annotate

annotate rnafold.xml @ 8:bdb786715d28 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29

author	rnateam
date	Wed, 20 Dec 2017 08:34:54 -0500
parents	86f517dcfdfb
children

rev	line source
8 bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	1 <tool id="viennarna_rnafold" name="@EXECUTABLE@" version="@VERSION@.4">
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	2 <description>Calculate minimum free energy secondary structures and partition function of RNAs</description>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	3 <macros>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	4 <token name="@EXECUTABLE@">RNAfold</token>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	5 <import>macros.xml</import>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	6 </macros>
2 84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	7 <expand macro="requirements">
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	8 <requirement type="package" version="1.65">biopython</requirement>
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	9 </expand>
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	10 <expand macro="stdio" />
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	11 <expand macro="version_command" />
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	12 <command>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	13 <![CDATA[
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	14 #if str($input_source.select_fasta) == "false"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	15 #if str($input_source.input_sequence).lstrip()[0] == ">"
2 84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	16 echo '${input_source.input_sequence}' > "input.fasta" &&
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	17 #else
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	18 echo ">Sequence" > "input.fasta" &&
2 84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	19 echo '${input_source.input_sequence}' >> "input.fasta" &&
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	20 #end if
2 84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	21 #end if
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	22
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	23 #if str($constraints.shapeOption.shapeSelector) == "isUsed"
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	24 python '$__tool_directory__/rnafold_SHAPE.py'
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	25 #else
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	26 RNAfold
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	27 #end if
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	28
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	29 -T $temperature
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	30 --dangles=$dangling
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	31 #if $layout_type ==0
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	32 --layout-type=$general_options.layout_type
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	33 #end if
8 bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	34
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	35 #if $mea:
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	36 #if $meagamma:
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	37 --MEA=$meagamma
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	38 #else
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	39 --MEA
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	40 #end if
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	41 #end if
8 bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	42
7 86f517dcfdfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d9f13fd859165e4280412ec73f8f3f8b258d351d-dirty rnateam parents: 6 diff changeset	43 #if $pf
86f517dcfdfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d9f13fd859165e4280412ec73f8f3f8b258d351d-dirty rnateam parents: 6 diff changeset	44 $pf
2 84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	45 #end if
8 bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	46
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	47 #if $pfscale:
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	48 --pfScale=$pfscale
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	49 #end if
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	50
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	51 $advancedOptions.noconversion
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	52 $advancedOptions.gquad
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	53 $advancedOptions.nolp
3 fcf2463f85c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 04c9cc19a39fea2e20986ca27d364f86f65184fd rnateam parents: 2 diff changeset	54 $advancedOptions.nops
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	55 $advancedOptions.nogu
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	56 $advancedOptions.noclosinggu
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	57 $advancedOptions.notetra
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	58 $advancedOptions.circular
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	59 #if $advancedOptions.bppmThreshold <> 1e-5
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	60 --bppmThreshold=$advancedOptions.bppmThreshold
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	61 #end if
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	62 #if $advancedOptions.nsp
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	63 --nsp='$advancedOptions.nsp'
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	64 #end if
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	65 #if $advancedOptions.betaScale <> 1.0
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	66 --betaScale=$advancedOptions.betaScale
2 84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	67 #end if
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	68 #if $constraints.maxBPspan <> -1
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	69 --maxBPspan=$constraints.maxBPspan
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	70 #end if
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	71 #if str($constraints.constraintLocation.constraintSelector) == "fromFile"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	72 --constraint='$constraints.constraintLocation.constraintsFile'
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	73 $constraints.constraintLocation.batch
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	74 $constraints.constraintLocation.canonicalBPonly
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	75 $constraints.constraintLocation.enforceConstraint
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	76 #end if
1 f87325531be8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 14f0b39f64982773ef0367379b915f742eabcc1b rnateam parents: 0 diff changeset	77 #if str($constraints.constraintLocation.constraintSelector) == "inFile"
f87325531be8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 14f0b39f64982773ef0367379b915f742eabcc1b rnateam parents: 0 diff changeset	78 -C
f87325531be8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 14f0b39f64982773ef0367379b915f742eabcc1b rnateam parents: 0 diff changeset	79 #end if
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	80 #if str($constraints.shapeOption.shapeSelector) == "isUsed"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	81 --shape='$constraints.shapeOption.shapeFile'
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	82 #if str($constraints.shapeOption.shapeMethod.methodSelector) == "W"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	83 #set $s="W"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	84 --shapeMethod=$s
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	85 #else if str($constraints.shapeOption.shapeMethod.methodSelector) == "Z"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	86 #set $s="Zb"+str($constraints.shapeOption.shapeMethod.b)
2 84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	87 --shapeMethod=$s
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	88 #if str($constraints.shapeOption.shapeMethod.shapeConversion.conversionSelector) == "C"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	89 #set $c="C"+str($constraints.shapeOption.shapeMethod.shapeConversion.c)
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	90 --shapeConversion=$c
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	91 #else if str($constraints.shapeOption.shapeMethod.shapeConversion.conversionSelector) == "L"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	92 #set $c="Ls"+str($constraints.shapeOption.shapeMethod.shapeConversion.s)+"i"+ str($constraints.shapeOption.shapeMethod.shapeConversion.i)
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	93 --shapeConversion=$c
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	94 #else if str($constraints.shapeOption.shapeMethod.shapeConversion.conversionSelector) == "O"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	95 #set $c="Os"+str($constraints.shapeOption.shapeMethod.shapeConversion.s)+"i"+ str($constraints.shapeOption.shapeMethod.shapeConversion.i)
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	96 --shapeConversion=$c
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	97 #else
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	98 #set $c=str($constraints.shapeOption.shapeMethod.shapeConversion.conversionSelector)
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	99 --shapeConversion=$c
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	100 #end if
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	101 #else if str($constraints.shapeOption.shapeMethod.methodSelector) == "D"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	102 #set $s="Dm"+str($constraints.shapeOption.shapeMethod.m)+"b"+str($constraints.shapeOption.shapeMethod.b)
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	103 --shapeMethod=$s
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	104 #end if
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	105 #end if
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	106 #if $constraints.motif
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	107 --motif='$constraints.motif'
2 84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	108 #end if
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	109 <
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	110 #if str($input_source.select_fasta) == "false"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	111 "input.fasta"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	112 #else
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	113 "${input_source.fasta_input}"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	114 #end if
8 bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	115 > '$dot_bracket_stdout'
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	116 ]]>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	117 </command>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	118
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	119 <inputs>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	120 <conditional name="input_source">
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	121 <param name="select_fasta" type="select" label="Input from FASTA file">
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	122 <option value="true" selected="true">Use FASTA</option>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	123 <option value="false">Provide sequence as text-field</option>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	124 </param>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	125 <when value="true">
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	126 <param format="fasta" name="fasta_input" type="data" label="Sequence to fold (FASTA file)"/>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	127 </when>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	128 <when value="false">
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	129 <param name="input_sequence" type="text" label="Input sequence"/>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	130 </when>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	131 </conditional>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	132 <param name="temperature" type="float" value="37.0" label="Temperature [°C]" argument="-T"/>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	133 <param name="dangling" type="select" label="How to treat dangling end energies" argument="-d">
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	134 <option value="0">0: ignore dangling ends</option>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	135 <option value="1">1: unpaired bases participate in one dangling end only</option>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	136 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	137 <option value="3">3: allow coaxial stacking</option>
2 84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	138 </param>
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	139 <param name="layout_type" type="select" label="Layout algorithm" argument="--layout_type" >
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	140 <option value="1" selected="true">Default: Naview layout</option>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	141 <option value="0">Simple radial layout</option>
2 84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	142 </param>
8 bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	143
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	144 <param name="mea" type="boolean" checked="false" falsevalue="" label="Calculate Maximum Expected accuracy" help="--MEA"/>
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	145 <param name="meagamma" type="float" optional="true" label="MEA-Gamma Value"/>
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	146
7 86f517dcfdfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d9f13fd859165e4280412ec73f8f3f8b258d351d-dirty rnateam parents: 6 diff changeset	147 <param name="pf" type="boolean" checked="false" truevalue="--partfunc" falsevalue="" label="Calculate Partition Function" help="--partfunc"/>
8 bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	148 <param name="pfscale" type="float" optional="true" 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."/>
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	149 <section name="advancedOptions" title="Advanced options">
3 fcf2463f85c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 04c9cc19a39fea2e20986ca27d364f86f65184fd rnateam parents: 2 diff changeset	150 <param name="nops" type="boolean" truevalue="--noPS" falsevalue="" checked="false" label="Do not produce postscript drawing of the mfe structure (reduces run-time)" help="(--noPS)"/>
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	151 <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	152 <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	153 <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"/>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	154 <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)"/>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	155 <param name="noconversion" type="boolean" truevalue="" falsevalue="--noconv" checked="true" label="Convert Thymine to Uracil (T -> U)" help="Avoids confusion with DNA sequences (--noconv)"/>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	156 <param name="gquad"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	157 type="boolean"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	158 truevalue="--gquad"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	159 falsevalue=""
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	160 checked="false"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	161 label="Take G Quadruplex formation into account"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	162 argument="-g"/>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	163 <param name="circular"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	164 type="boolean"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	165 truevalue="--circ"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	166 falsevalue=""
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	167 checked="false"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	168 label="Model as circular RNA structure"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	169 argument="--circ"/>
2 84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	170 <param name="bppmThreshold"
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	171 type="float"
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	172 value="1e-5"
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	173 label="Threshold for base pair probabilities"
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	174 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."
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	175 argument="--bppmThreshold"/>
2 84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	176 <param name="nsp"
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	177 type="text"
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	178 value=""
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	179 label="Allow other pairs in addition to the usual AU,GC,and GU pairs."
2 84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	180 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."
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	181 argument="--nsp"/>
2 84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	182 <param name="betaScale"
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	183 type="float"
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	184 value="1.0"
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	185 label="Scaling of Boltzman factors"
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	186 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."
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	187 argument="--betaScale"/>
2 84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	188 </section>
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	189 <section name="constraints" title="Structure constraints">
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	190 <param name="maxBPspan" type="integer" value="-1" label="Set the maximum base pair span" help="" argument="--maxBPspan"/>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	191 <conditional name="constraintLocation">
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	192 <param name="constraintSelector" type="select" label="Constraints">
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	193 <!-- <option value="fromInput">The constraints are included in the input file</option> -->
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	194 <option value="fromFile">The constraints are in a seperate file</option>
7 86f517dcfdfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d9f13fd859165e4280412ec73f8f3f8b258d351d-dirty rnateam parents: 6 diff changeset	195 <option value="inFile">The constraints are in the fasta input file</option>
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	196 <option value="none" selected="true">Don't use constraints</option>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	197 </param>
7 86f517dcfdfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d9f13fd859165e4280412ec73f8f3f8b258d351d-dirty rnateam parents: 6 diff changeset	198 <!-- <when value="fromInput"></when> -->
86f517dcfdfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d9f13fd859165e4280412ec73f8f3f8b258d351d-dirty rnateam parents: 6 diff changeset	199 <when value="none"></when>
86f517dcfdfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d9f13fd859165e4280412ec73f8f3f8b258d351d-dirty rnateam parents: 6 diff changeset	200 <when value="inFile"></when>
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	201 <when value="fromFile">
6 b31dcdb31209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit e3c20fec5dafc424d55a4de77304e79e3c88b76b-dirty rnateam parents: 3 diff changeset	202 <param name="constraintsFile" type="data" format="txt" label="Constraints file" argument="--constraint"/>
2 84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	203 <param name="batch" type="boolean" checked="false" truevalue="--batch" falsevalue=""
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	204 label="Use constraints for all alignment records"
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	205 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, RNAfold processes all sequence alignments in the input and applies the same provided constraints to each of them."
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	206 argument="--batch"/>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	207 <param argument="--canonicalBPonly" type="boolean" truevalue="--canonicalBPonly" falsevalue="" checked="false" label="Remove non-canonical base pairs from he structure constraint" />
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	208 <param argument="--enforceConstraint" type="boolean" truevalue="--enforceConstraint" falsevalue="" checked="false" label="Enforce base pair given by round brackets () in structure constraint" />
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	209 </when>
2 84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	210 </conditional>
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	211 <conditional name="shapeOption">
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	212 <param name="shapeSelector" type="select" label="Shape reactivity data">
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	213 <option value="isUsed">Use shape reactivity data</option>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	214 <option value="notUsed" selected="true">Don't use shape reactivity data</option>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	215 </param>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	216 <when value ="isUsed">
3 fcf2463f85c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 04c9cc19a39fea2e20986ca27d364f86f65184fd rnateam parents: 2 diff changeset	217 <param type="data" name="shapeFile" format="txt" label="Shape file" argument="--shape"/>
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	218 <conditional name="shapeMethod">
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	219 <param name="methodSelector" type="select" label="Shape reactivity data" argument="--shapeMethod">
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	220 <option value="D" selected="true">D: Convert by using a linear equation according to Deigan et al 2009</option>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	221 <option value="Z">Z: Convert SHAPE reactivities to pseudo energies according to Zarringhalam et al 2012.</option>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	222 <option value="W">W: Apply a given vector of perturbation energies to unpaired nucleotides according to Washietl et al 2012</option>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	223 </param>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	224 <when value="D">
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	225 <param name="m" type="float" value="1.8" label="Slope m"/>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	226 <param name="b" type="float" value="-0.6" label="Intercept"/>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	227 </when>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	228 <when value="Z">
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	229 <param name="b" type="float" value="-0.6" label="Intercept"/>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	230 <conditional name="shapeConversion">
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	231 <param name="conversionSelector" type="select" label="shape reactivity data">
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	232 <option value="M">M: Use linear mapping according to Zarringhalam et al</option>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	233 <option value="C">C: Use a cutoff−approach to divide into paired and unpaired nucleotides</option>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	234 <option value="S">S: Skip the normalizing step since the input data already represents probabilities for being unpaired rather than raw reactivity values</option>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	235 <option value="L">L: Use a linear model to convert the reactivity into a probability for being unpaired</option>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	236 <option value="O" selected="true">O: Use a linear model to convert the log of the reactivity into a probability for being unpaired</option>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	237 </param>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	238 <when value="M">
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	239 </when>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	240 <when value="C">
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	241 <param name="c" type="float" value="0.25" label="Cutoff"/>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	242 </when>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	243 <when value="S">
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	244 </when>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	245 <when value="L">
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	246 <param name="s" type="float" value="0.68" label="Slope"/>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	247 <param name="i" type="float" value="0.2" label="Intercept"/>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	248 </when>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	249 <when value="O">
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	250 <param name="s" type="float" value="1.6" label="Slope s"/>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	251 <param name="i" type="float" value="-2.29" label="Intercept"/>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	252 </when>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	253 </conditional>
2 84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	254 </when>
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	255 <when value="W">
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	256 </when>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	257 </conditional>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	258 </when>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	259 <when value="notUsed">
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	260 </when>
2 84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	261 </conditional>
6 b31dcdb31209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit e3c20fec5dafc424d55a4de77304e79e3c88b76b-dirty rnateam parents: 3 diff changeset	262 <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.">
b31dcdb31209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit e3c20fec5dafc424d55a4de77304e79e3c88b76b-dirty rnateam parents: 3 diff changeset	263 <sanitizer>
b31dcdb31209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit e3c20fec5dafc424d55a4de77304e79e3c88b76b-dirty rnateam parents: 3 diff changeset	264 <valid initial="string.printable">
b31dcdb31209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit e3c20fec5dafc424d55a4de77304e79e3c88b76b-dirty rnateam parents: 3 diff changeset	265 </valid>
b31dcdb31209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit e3c20fec5dafc424d55a4de77304e79e3c88b76b-dirty rnateam parents: 3 diff changeset	266 </sanitizer>
b31dcdb31209 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit e3c20fec5dafc424d55a4de77304e79e3c88b76b-dirty rnateam parents: 3 diff changeset	267 </param>
2 84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	268 </section>
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	269 <section name="IDs" title="Naming Conventions">
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	270 <param name="auto_id"
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	271 type="boolean" truevalue="--auto-id" falsevalue="" checked="false"
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	272 label="Automatically generate an ID for each alignment."
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	273 help="If this flag is active, RNAfold ignores any IDs retrieved from the input and automatically generates an ID for each sequence."
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	274 argument="--auto-id"/>
2 84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	275 <param name="id_prefix"
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	276 type="text" value="sequence"
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	277 label="Prefix for automatically generated IDs (as used in output file names)"
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	278 help="If this parameter is set, each sequence 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 sequence), etc. where xxxx is the sequence number beginning with the second sequence in the input. Use this setting in conjunction with the −−continuous−ids flag to assign IDs beginning with the first input sequence."
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	279 argument="--id-prefix"/>
2 84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	280 <param name="id_digits"
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	281 type="integer" value="4" min="1" max="18"
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	282 label="The number of digits of the counter in automatically generated sequence IDs"
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	283 help="When sequences 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]."
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	284 argument="--id-digits"/>
2 84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	285 <param name="id_start"
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	286 type="integer" value="1" min="0"
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	287 label="First number in automatically generated sequence IDs"
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	288 help="When sequence 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 sequence IDs, i.e. it activates the −−continuous−ids flag.."
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	289 argument="--id-start"/>
2 84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	290 </section>
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	291 </inputs>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	292 <outputs>
8 bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	293 <data format="dbn" name="dot_bracket_stdout"/>
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	294 <collection name="structure_outputs" type="list" label="rna_strcuture_eps outputs">
3 fcf2463f85c1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 04c9cc19a39fea2e20986ca27d364f86f65184fd rnateam parents: 2 diff changeset	295 <filter>advancedOptions['nops'] is False</filter>
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	296 <discover_datasets pattern="(?P<designation>.+)_ss\.ps" ext="eps" />
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	297 </collection>
8 bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	298 <collection name="matrix_outputs" type="list" label="rna_matrix_eps outputs">
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	299 <filter>pf is True</filter>
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	300 <discover_datasets pattern="(?P<designation>.+)_dp\.ps" ext="rna_eps" visible="true"/>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	301 </collection>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	302 </outputs>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	303 <tests>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	304 <test>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	305 <param name="select_fasta" value="true" />
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	306 <param name="fasta_input" value="rnafold_input1.fa"/>
8 bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	307 <output name="dot_bracket_stdout" file="rnafold_result1.txt"/>
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	308 </test>
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	309
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	310 <test>
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	311 <param name="select_fasta" value="true" />
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	312 <param name="mea" value="true" />
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	313 <param name="fasta_input" value="rnafold_input1.fa"/>
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	314 <output name="dot_bracket_stdout" file="rnafold_result1_mea.txt"/>
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	315 </test>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	316 <test>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	317 <param name="select_fasta" value="true" />
8 bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	318 <param name="pf" value="true" />
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	319 <param name="fasta_input" value="rnafold_input1.fa"/>
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	320 <output name="dot_bracket_stdout" file="rnafold_result1_pf.txt"/>
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	321 <output_collection name="structure_outputs" type="list">
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	322 <element name="Anolis_caro_chrUn_GL343590.trna2_AlaAGC" file="Anolis_caro_chrUn_GL343590.trna2_AlaAGC_ss.ps" compare="sim_size" />
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	323 <element name="Anolis_caro_chrUn_GL343207.trna3_AlaAGC" file="Anolis_caro_chrUn_GL343207.trna3_AlaAGC_ss.ps" compare="sim_size" />
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	324 </output_collection>
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	325
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	326 <output_collection name="matrix_outputs" type="list">
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	327 <element name="Anolis_caro_chrUn_GL343590.trna2_AlaAGC" file="Anolis_caro_chrUn_GL343590.trna2_AlaAGC_dp.ps" compare="sim_size" />
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	328 <element name="Anolis_caro_chrUn_GL343207.trna3_AlaAGC" file="Anolis_caro_chrUn_GL343207.trna3_AlaAGC_dp.ps" compare="sim_size" />
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	329 </output_collection>
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	330 </test>
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	331 <test>
bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	332 <param name="select_fasta" value="true" />
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	333 <param name="fasta_input" value="rnafold_input2.fa"/>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	334 <param name="temperature" value="75"/>
8 bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	335 <output name="dot_bracket_stdout" file="rnafold_result2.txt"/>
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	336 </test>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	337 <test>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	338 <param name="select_fasta" value="false" />
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	339 <param name="input_sequence" value="TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA"/>
8 bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	340 <output name="dot_bracket_stdout" file="rnafold_result3.txt"/>
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	341 </test>
2 84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	342 <test>
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	343 <param name="select_fasta" value="true" />
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	344 <param name="fasta_input" value="sample_3.fa"/>
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	345 <conditional name="shapeOption">
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	346 <param name="shapeSelector" value="isUsed"/>
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	347 </conditional>
84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	348 <param name="shapeFile" value="sample_3.react"/>
8 bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	349 <output name="dot_bracket_stdout" file="sample_3_result.txt"/>
2 84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	350 </test>
8 bdb786715d28 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29 rnateam parents: 7 diff changeset	351
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	352 </tests>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	353 <help>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	354 <![CDATA[
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	355 RNAfold
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	356
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	357 The program reads RNA sequences, calculates their minimum free
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	358 energy (mfe) structure and the mfe structure in dot-bracket notation.
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	359
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	360 If the -p option was given it also computes the
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	361 partition function (pf) and base pairing probability matrix.
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	362
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	363 The dot plot of the base pairing probability matrix shows a matrix of squares with area proportional to the pairing
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	364 probability in the upper right half, and one square for each pair in the
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	365 minimum free energy structure in the lower left half. For each pair i-j with
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	366 probability p>10E-6 there is a line of the form
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	367
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	368 i j sqrt(p) ubox
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	369
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	370 in the PostScript file, so that the pair probabilities can be easily extracted.
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	371
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	372 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.
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	373 The program will read the whole FASTA input file and provide output for each found sequence.
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	374
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	375
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	376 -----
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	377
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	378 Input format
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	379
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	380 RNAfold requires one input file or a plain RNA sequence
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	381
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	382 ------
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	383
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	384 Outputs
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	385
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	386 - Secondary structures in dot-bracket notation
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	387
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	388 - several possible postscript images bundled together in a tar file
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	389 - secondary structure for each sequence in the input file
2 84aad99aca1f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n' rnateam parents: 1 diff changeset	390 - if partition function is calculated (--MEA or --partfunc is set) then also the pairing probabilty matrix is generated for each sequence
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	391
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	392 ]]>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	393 </help>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	394 <expand macro="citations" />
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	395 </tool>

Mercurial > repos > rnateam > viennarna_rnafold

annotate rnafold.xml @ 8:bdb786715d28 draft default tip