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comparison mea.xml @ 3:8c457c7a7bd7 draft

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planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty
author rnateam
date Wed, 01 Jul 2015 10:41:03 -0400
parents a041bcbb77fc
children 00e0ba24886a
comparison
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2:34fc6f78ed7c 3:8c457c7a7bd7
9 9
10 <stdio> 10 <stdio>
11 <exit_code range="1:" /> 11 <exit_code range="1:" />
12 </stdio> 12 </stdio>
13 13
14 <command><![CDATA[ 14 <command><![CDATA[mea
15 mea
16 #if str($mode.mode_selector) == "predict" 15 #if str($mode.mode_selector) == "predict"
17 $mode.dotplot 16 $mode.dotplot
17 --alpha $mode.alpha
18 --beta $mode.beta
19 --gamma $mode.gamma
20 --delta $mode.delta
18 #else 21 #else
19 --structure `cat $mode.structure` 22 --structure `cat $mode.structure`
20 #end if 23 #end if
21 #if str($reference) != "" 24 #if str($reference) != ""
22 --reference `cat $reference` 25 --reference `cat $reference`
23 #end if 26 #end if
24 --alpha $mode.alpha
25 --beta $mode.beta
26 --gamma $mode.gamma
27 --delta $mode.delta
28 $slide_rule 27 $slide_rule
29 $conflict_rule 28 $conflict_rule
30 > $stdout 29 > $stdout
31 ]]></command> 30 ]]></command>
32 31
38 </param> 37 </param>
39 <when value="predict"> 38 <when value="predict">
40 <param name="dotplot" type="data" format="rna_eps" label="Dotplot" 39 <param name="dotplot" type="data" format="rna_eps" label="Dotplot"
41 optional="false" help="Dotplot file (RNA base pair probabilities)"/> 40 optional="false" help="Dotplot file (RNA base pair probabilities)"/>
42 <param name="alpha" label="Alpha" type="float" 41 <param name="alpha" label="Alpha" type="float"
43 optional="false" value="0.012" 42 optional="false" value="0.012"
44 help="Slope of base pair distance penalty"/> 43 help="Slope of base pair distance penalty"/>
45 <param name="beta" label="Beta" type="float" 44 <param name="beta" label="Beta" type="float"
46 optional="false" value="315" 45 optional="false" value="315"
47 help="Turning point of base pair distance penalty" /> 46 help="Turning point of base pair distance penalty" />
48 <param name="gamma" label="Gamma" type="float" 47 <param name="gamma" label="Gamma" type="float"
49 optional="false" value="0.5" 48 optional="false" value="0.5"
56 <param name="structure" format="txt" type="data" label="Structure" 55 <param name="structure" format="txt" type="data" label="Structure"
57 optional="false" help="(Predicted) RNA secondary structure" /> 56 optional="false" help="(Predicted) RNA secondary structure" />
58 </when> 57 </when>
59 </conditional> 58 </conditional>
60 59
61 <param name="reference" format="txt" type="data" label="Reference" /> 60 <param name="reference" optional="true" format="txt" type="data" label="Reference" />
62 61
63 <param name="slide_rule" label="Slide Rule" type="boolean" 62 <param name="slide_rule" label="Slide Rule" type="boolean"
64 optional="false" 63 optional="false"
65 checked="yes" 64 checked="yes"
66 falsevalue="--no-slide-rule" truevalue="" 65 falsevalue="--no-slide-rule" truevalue=""