# HG changeset patch
# User bgruening
# Date 1462220332 14400
# Node ID 693b42e3bfbe6f3e217a464ad7493fdeeddb85bb
# Parent  5c975980f94df6c15474544f6a70edd4449290b1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty

diff -r 5c975980f94d -r 693b42e3bfbe macros.xml
--- a/macros.xml	Sat Mar 12 14:26:07 2016 -0500
+++ b/macros.xml	Mon May 02 16:18:52 2016 -0400
@@ -17,7 +17,7 @@
               <option value="predict">Load a model and predict</option>
           </param>
           <when value="predict">
-              <param name="infile_model" type="data" format="eden_model" label="Models" help="Select a model file." />
+              <param name="infile_model" type="data" format="zip" label="Models" help="Select a model file." />
               <param name="infile_data" type="data" format="fasta" label="Data (fasta)" help="Select the FASTA sequences you want to classify."/>
           </when>
           <when value="fit">
diff -r 5c975980f94d -r 693b42e3bfbe protease.xml
--- a/protease.xml	Sat Mar 12 14:26:07 2016 -0500
+++ b/protease.xml	Mon May 02 16:18:52 2016 -0400
@@ -14,6 +14,8 @@
         --negative-ratio $selected_tasks.options.negative_ratio
         --shuffle-order $selected_tasks.options.shuffle_order
         -r  $selected_tasks.options.random_state
+        -e  $selected_tasks.options.n_iter
+        --max-total-time $selected_tasks.options.max_total_time
     #else:
         predict
         -m $selected_tasks.infile_model
@@ -28,7 +30,9 @@
                     help="Relative size ratio for the randomly permuted negative instances w.r.t. the positive instances." />
                 <param name="shuffle_order" type="integer" optional="true" value="2" label="Order of k-mer shuffling"
                     help="Order of the k-mer for the random shuffling procedure." />
-                <param name="random_state" type="integer" value="1" label="Random seed" />
+                <param name="random_state" type="integer" value="1" label="Random seed" help="Integer number. The seed of the pseudo random number generator. A fixed seed allows reproducible results." />
+                <param name="n_iter" type="integer" value="1" label="Number of randomly generated hyper parameter configurations" help="Tried during the discriminative model optimization. A value of 1 implies using the estimator default values."/>
+                <param name="max_total_time" type="integer" value="-1" label="Maximal number of seconds for the duration of the optimization phase" help="After max_total_time is elapsed, the procedure is forcefully stopped. A value of -1 means no time limit." />
             </section>
         </expand>
     </inputs>
@@ -36,7 +40,7 @@
         <data format="tabular" name="outfile_predict" from_work_dir="out/predictions.txt">
             <filter>selected_tasks['selected_task'] == 'predict'</filter>
         </data>
-        <data format="eden_model" name="outfile_fit" from_work_dir="out/model">
+        <data format="zip" name="outfile_fit" from_work_dir="out/model">
             <filter>selected_tasks['selected_task'] == 'fit'</filter>
         </data>
     </outputs>
@@ -45,10 +49,12 @@
             <param name="infile_train" value="CTSL_train.fasta" ftype="fasta"/>
             <param name="selected_task" value="fit"/>
             <param name="shuffle_order" value="3"/>
-            <output name="outfile_fit" file="model" ftpye="eden_model" compare="sim_size" delta="100000"/>
+            <param name="n_iter" value="5"/>
+            <!--param name="max_total_time" value="60"/-->
+            <output name="outfile_fit" file="model" ftype="zip" compare="sim_size" delta="500000"/>
         </test>
         <test>
-            <param name="infile_model" value="model" ftype="eden_model"/>
+            <param name="infile_model" value="model" ftype="zip"/>
             <param name="infile_data" value="CTSL_test.fasta" ftype="fasta"/>
             <param name="selected_task" value="predict"/>
             <output name="outfile_predict" file="predictions.txt" ftpye="tabular"/>
@@ -75,6 +81,14 @@
   >CTSL1
   SSLGGTVV
 
+**Estimator optimization time parameters**
+The time spent for optimization phase is controlled by two parameters:
+
+ n_iter : defines the number of hyperparameter configurations used for optimization.
+
+ max_total_time : defines the time in seconds spent in total for optimization.
+
+If both parameters are set, the algorithm would stop at the time lapse which is shorter among these two. 
 
     ]]></help>
     <expand macro="eden_citation"/>
diff -r 5c975980f94d -r 693b42e3bfbe protease_prediction.tar.gz
Binary file protease_prediction.tar.gz has changed
diff -r 5c975980f94d -r 693b42e3bfbe test-data/model
Binary file test-data/model has changed
diff -r 5c975980f94d -r 693b42e3bfbe test-data/predictions.txt
--- a/test-data/predictions.txt	Sat Mar 12 14:26:07 2016 -0500
+++ b/test-data/predictions.txt	Mon May 02 16:18:52 2016 -0400
@@ -1,75 +1,75 @@
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