diff rnaalifold.xml @ 1:10b56bba8dee draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 14f0b39f64982773ef0367379b915f742eabcc1b

--- a/rnaalifold.xml	Tue Dec 06 12:31:07 2016 -0500
+++ b/rnaalifold.xml	Wed Dec 21 17:31:51 2016 -0500
@@ -99,12 +99,12 @@
                 <option value="0">0: Deactivates the calculation of the pair probabilities, saving about 50% in runtime</option>
                 <option value="1" >1: Calculate the partition function and base pairing probability matrix</option>				
             </param>
-            <param name="mea" type="float" value="1.0" label="Gamma Value" help="Calculate an MEA (maximum expected accuracy) structure. The parameter gamma tunes the importance of correctly predicted pairs versus unpaired bases. Thus, for small values of gamma the MEA structure will contain only pairs with very high probability. where the expected accuracy is computed from the pair probabilities: each base pair (i,j) gets a score 2*gamma*p_ij and the score of an unpaired base is given by the probability of not forming a pair." argumen="--MEA"/>
+            <param name="mea" type="float" value="1.0" label="Gamma Value" help="Calculate an MEA (maximum expected accuracy) structure. The parameter gamma tunes the importance of correctly predicted pairs versus unpaired bases. Thus, for small values of gamma the MEA structure will contain only pairs with very high probability. where the expected accuracy is computed from the pair probabilities: each base pair (i,j) gets a score 2*gamma*p_ij and the score of an unpaired base is given by the probability of not forming a pair." argument="--MEA"/>
             <param argument="--mis" type="boolean" checked="false" truevalue="--mis" falsevalue="" label="Most Informative Sequence" help="Output 'most informative sequence' instead of simple consensu"/>							
             <param name="stochBT_en" type="integer" value="1" label="Number of random structures." help="Compute a certain number of random structures with a probability dependend on the partition function. Print out the energies and probabilities of the backtraced structures. " argument="--stochBT_en"/>	        
-            <param name="pfScale" type="float" value="1.07" label="Scaling factor" help="In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows). The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences." argumen="--pfScale"/>						
+            <param name="pfScale" type="float" value="1.07" label="Scaling factor" help="In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows). The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences." argument="--pfScale"/>						
             <param name="circular" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA structure" help="--circ"/>
-            <param name="bppmThreshold" type="float" value="1e-6" label="Threshold for base pair probabilities" 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." argumen="--bppmThreshold"/>
+            <param name="bppmThreshold" type="float" value="1e-6" label="Threshold for base pair probabilities" 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." argument="--bppmThreshold"/>
             <param name="gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="G Quadruplex formation" help="Take into account G Quadruplex formation (-g)"/>
             <param name="sci" type="boolean" truevalue="--sci" falsevalue="" checked="false" label="Structure conservation index" 
                 help="Compute the structure conservation index (SCI) for the MFE consensus structure of the alignment" argument="--sci"/>
@@ -178,8 +178,8 @@
                             <option value="notUsed" selected="true">Don't use shape reactivity data</option>
                         </param>
                         <when value ="isUsed">
-                            <repeat name="shape_files" title="Shape File" default="0" argument="--shape">
-                                <param type="data" name="shape" format="shape,*" label="Shape file"/>
+                            <repeat name="shape_files" title="Shape File" default="0">
+                                <param type="data" name="shape" format="shape,*" label="Shape file" argument="--shape"/>
                             </repeat>
                                 <param name="m" type="float" value="1.8" label="Slope m" />
                                 <param name="b" type="float" value="-0.6" label="Intercept b" help="Currently, the only data conversion method available is that of to Deigan et al 2009. This method is the default. The slope 'm' and the intercept 'b' can be set to a non−default value if necessary. Otherwise m=1.8 and b=−0.6 as stated in the paper mentioned before."/>