viennarna_rnafold: rnafold.xml annotate

annotate rnafold.xml @ 7:86f517dcfdfb draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d9f13fd859165e4280412ec73f8f3f8b258d351d-dirty

author	rnateam
date	Thu, 28 Sep 2017 16:24:39 -0400
parents	b31dcdb31209
children	bdb786715d28

rev	line source
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	1 <tool id="viennarna_rnafold" name="@EXECUTABLE@" version="@VERSION@.3">
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
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	34 #if $mea:
86f517dcfdfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d9f13fd859165e4280412ec73f8f3f8b258d351d-dirty rnateam parents: 6 diff changeset	35 --MEA=$mea
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	36 #end if
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	37 #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	38 $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	39 #if $pfscale:
86f517dcfdfb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d9f13fd859165e4280412ec73f8f3f8b258d351d-dirty rnateam parents: 6 diff changeset	40 --pfScale=$pfscale
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
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	42 #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	43 $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	44 $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	45 $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	46 $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	47 $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	48 $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	49 $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	50 $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	51 #if $advancedOptions.bppmThreshold <> 1e-5
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	52 --bppmThreshold=$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	53 #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	54 #if $advancedOptions.nsp
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	55 --nsp='$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	56 #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	57 #if $advancedOptions.betaScale <> 1.0
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	58 --betaScale=$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	59 #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	60 #if $constraints.maxBPspan <> -1
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	61 --maxBPspan=$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	62 #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	63 #if str($constraints.constraintLocation.constraintSelector) == "fromFile"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	64 --constraint='$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	65 $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	66 $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	67 $constraints.constraintLocation.enforceConstraint
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	68 #end if
1 f87325531be8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 14f0b39f64982773ef0367379b915f742eabcc1b rnateam parents: 0 diff changeset	69 #if str($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	70 -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	71 #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	72 #if str($constraints.shapeOption.shapeSelector) == "isUsed"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	73 --shape='$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	74 #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	75 #set $s="W"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	76 --shapeMethod=$s
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	77 #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	78 #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	79 --shapeMethod=$s
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	80 #if str($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	81 #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	82 --shapeConversion=$c
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	83 #else if str($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	84 #set $c="Ls"+str($constraints.shapeOption.shapeMethod.shapeConversion.s)+"i"+ str($constraints.shapeOption.shapeMethod.shapeConversion.i)
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	85 --shapeConversion=$c
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	86 #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	87 #set $c="Os"+str($constraints.shapeOption.shapeMethod.shapeConversion.s)+"i"+ str($constraints.shapeOption.shapeMethod.shapeConversion.i)
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	88 --shapeConversion=$c
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	89 #else
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	90 #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	91 --shapeConversion=$c
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	92 #end if
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	93 #else if str($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	94 #set $s="Dm"+str($constraints.shapeOption.shapeMethod.m)+"b"+str($constraints.shapeOption.shapeMethod.b)
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	95 --shapeMethod=$s
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	96 #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	97 #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	98 #if $constraints.motif
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	99 --motif='$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	100 #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	101 <
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	102 #if str($input_source.select_fasta) == "false"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	103 "input.fasta"
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	104 #else
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	105 "${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	106 #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	107 > '$tabular_file'
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	108 ]]>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	109 </command>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	110
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	111 <inputs>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	112 <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	113 <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	114 <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	115 <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	116 </param>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	117 <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	118 <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	119 </when>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	120 <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	121 <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	122 </when>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	123 </conditional>
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 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	125 <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	126 <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	127 <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	128 <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	129 <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	130 </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	131 <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	132 <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	133 <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	134 </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	135 <param argument="--MEA" name="mea" type="float" value="1.0" optional="true" label="Gamma Value" help="Used for the calculation of the Maximum Expected accuracy"/>
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	136 <param name="pf" type="boolean" checked="false" truevalue="--partfunc" falsevalue="" label="Calculate Partition Function" help="--partfunc"/>
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	137 <param name="pfscale" type="float" value="1.07" 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	138 <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	139 <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	140 <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	141 <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	142 <param name="noclosinggu" type="boolean" truevalue="" falsevalue="--noClosingGU" checked="true" label="Allow GU pairing at the ends" help="Allow pairing of G and U at the ends of helices. --noClosingGU"/>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	143 <param name="notetra" type="boolean" truevalue="" falsevalue="--noTetra" checked="true" label="Allow stabilization for loops, hairpins etc." help=" Include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing. (--noTetra)"/>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	144 <param name="noconversion" type="boolean" truevalue="" falsevalue="--noconv" checked="true" label="Convert Thymine to Uracil (T -> U)" help="Avoids confusion with DNA sequences (--noconv)"/>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	145 <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	146 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	147 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	148 falsevalue=""
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	149 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	150 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	151 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	152 <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	153 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	154 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	155 falsevalue=""
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	156 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	157 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	158 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	159 <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	160 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	161 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	162 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	163 help="By setting the threshold the base pair probabilities that are included in the output can be varied. By default only those exceeding 1e−5 in probability will be shown as squares in the dot plot. Changing the threshold to any other value allows for increase or decrease of data."
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	164 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	165 <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	166 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	167 value=""
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="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	169 help="Its argument is a comma separated list of additionally allowed pairs. If the first character is '-' then AB will imply that AB and BA are allowed pairs. e.g. RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy."
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	170 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	171 <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	172 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	173 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	174 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	175 help=" The argument provided with this option enables to scale the thermodynamic temperature used in the Boltzmann factors independently from the temperature used to scale the individual energy contributions of the loop types."
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	176 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	177 </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	178 <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	179 <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	180 <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	181 <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	182 <!-- <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	183 <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	184 <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	185 <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	186 </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	187 <!-- <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	188 <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	189 <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	190 <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	191 <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	192 <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	193 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	194 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	195 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	196 <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	197 <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	198 </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	199 </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	200 <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	201 <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	202 <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	203 <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	204 </param>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	205 <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	206 <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	207 <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	208 <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	209 <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	210 <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	211 <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	212 </param>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	213 <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	214 <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	215 <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	216 </when>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	217 <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	218 <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	219 <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	220 <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	221 <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	222 <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	223 <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	224 <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	225 <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	226 </param>
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 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	228 </when>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	229 <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	230 <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	231 </when>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	232 <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	233 </when>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	234 <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	235 <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	236 <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	237 </when>
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="O">
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	239 <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	240 <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	241 </when>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	242 </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	243 </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	244 <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	245 </when>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	246 </conditional>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	247 </when>
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 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	249 </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	250 </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	251 <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	252 <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	253 <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	254 </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	255 </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	256 </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	257 </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	258 <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	259 <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	260 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	261 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	262 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	263 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	264 <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	265 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	266 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	267 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	268 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	269 <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	270 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	271 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	272 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	273 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	274 <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	275 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	276 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	277 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	278 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	279 </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	280 </inputs>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	281 <outputs>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	282 <data format="dbn" name="tabular_file"/>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	283 <collection name="sequence_outputs" type="list" label="rna_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	284 <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	285 <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	286 </collection>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	287 <collection name="matrix_outputs" type="list" label="rna_eps outputs">
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	288 <filter>measelect['pf'] is True</filter>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	289 <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	290 </collection>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	291 </outputs>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	292 <tests>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	293 <test>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	294 <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	295 <param name="fasta_input" value="rnafold_input1.fa"/>
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	296 <output name="tabular_file" file="rnafold_result1.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	297 </test>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	298 <test>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	299 <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	300 <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	301 <param name="temperature" value="75"/>
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	302 <output name="tabular_file" 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	303 </test>
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="false" />
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="input_sequence" value="TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA"/>
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	307 <output name="tabular_file" 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	308 </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	309 <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	310 <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	311 <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	312 <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	313 <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	314 </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	315 <param name="shapeFile" value="sample_3.react"/>
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	316 <output name="tabular_file" 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	317 </test>
0 d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	318 </tests>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	319 <help>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	320 <![CDATA[
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	321 RNAfold
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	322
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	323 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	324 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	325
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	326 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	327 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	328
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	329 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	330 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	331 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	332 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	333
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	334 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	335
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	336 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	337
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	338 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	339 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	340
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	341
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	342 -----
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	343
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	344 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	345
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	346 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	347
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	348 ------
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	349
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	350 Outputs
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	351
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	352 - 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	353
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	354 - 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	355 - 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	356 - 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	357
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	358 ]]>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	359 </help>
d6044fad075f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9 rnateam parents: diff changeset	360 <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	361 </tool>

Mercurial > repos > rnateam > viennarna_rnafold

annotate rnafold.xml @ 7:86f517dcfdfb draft