changeset 1:b2dbc72b50d4 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha commit ba69207568a546d7c3b71a144f78095811e3e99a-dirty

--- a/piranha.xml	Wed Jul 15 11:57:07 2015 -0400
+++ b/piranha.xml	Fri Jul 24 06:04:53 2015 -0400
@@ -32,16 +32,16 @@
         #else:
             -u $merge_bins.merge
         #end if
-        $suppress_covars
+        $print_covars
         $fit
         #if $dist:
             -d $dist
         #end if
         $fitMethod
-        #if $use_model.model_select=="yes":
-            -m $use_model.model
+        #if $model:
+            -m $model
         #end if
-        $unstranded
+        $stranded
         $no_normalisation
         $log_covars
         ./foo.$input.ext
@@ -77,7 +77,7 @@
                 help="Default is 1 (merge adjacent)"/>
             </when>
         </conditional>
-        <param name="suppress_covars" type="boolean" checked="False" truevalue="-r" falsevalue="" label="Don't print covariate values in output" />
+        <param name="print_covars" type="boolean" checked="True" truevalue="" falsevalue="-r"  label="Print covariate values in output" help="(-r)" />
         <param name="fit" type="boolean" checked="False" truevalue="-f" falsevalue="" label="Fit only" />
         <param name="dist" type="select" label="Select distribution type">
             <option value="">None</option>
@@ -91,23 +91,16 @@
             <option value="ZeroTruncatedNegativeBinomialRegression">ZeroTruncatedNegativeBinomialRegression</option>
         </param>
         <param name="fitMethod" type="boolean" checked="False" truevalue="-t"
-            falsevalue="" label="Component fitting method" help=""/>
-        <conditional name="use_model">
-            <param name="model_select" type="select" label="Use the specified model file instead of fitting to input data?">
-                <option value="yes">Yes</option>
-                <option value="no" selected="true">No</option>
-            </param>
-            <when value="yes">
-                <param name="model" type="data" multiple="false" format="xml" label="Select the model file"/>
-            </when>
-        </conditional>  
+            falsevalue="" label="Use component fitting method"  help="(-t)"/>
+        <param name="model" type="data" optional="True" format="xml" label="Select the model file"/>
 
-        <param name="unstranded" type="boolean" checked="False" truevalue="-x"
-            falsevalue="" label="Don't preserve strand (puts all the peaks in positive strand)"/>
+        <param name="stranded" type="boolean" checked="True" truevalue=""
+            falsevalue="-x" label="Preserve strand information"
+            help="If not set all the peaks will be associated to the positive strand. (-x)"/>
         <param name="no_normalisation" type="boolean" checked="yes" falsevalue="-n" 
-            truevalue="" label="Normalise covariates?"/>
+            truevalue="" label="Normalise covariates?" help="(-n)"/>
         <param name="log_covars" type="boolean" checked="False" truevalue="-l" 
-            falsevalue="" label="Convert covariates to log scale?"/>
+            falsevalue="" label="Convert covariates to log scale?" help="(-l)"/>
     </inputs>
     <outputs>
         <data format="tabular" name="output_bed" from_work_dir="piranha.out"