# HG changeset patch
# User galaxyp
# Date 1630049323 0
# Node ID f831f7d721f8aa17d0f705c3af62472a6fbfe92b
# Parent  b8590dea5e2dc7ba13caf4525da14abc2ff250d7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics commit 28244fe226c9bd5326886bf21960cbb43a4be2ec"

diff -r b8590dea5e2d -r f831f7d721f8 proteomiqon_psmstatistics.xml
--- a/proteomiqon_psmstatistics.xml	Sun Jul 18 13:53:08 2021 +0000
+++ b/proteomiqon_psmstatistics.xml	Fri Aug 27 07:28:43 2021 +0000
@@ -3,7 +3,7 @@
         utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.
     </description>
     <macros>
-        <token name="@VERSION@">0.0.6</token>
+        <token name="@VERSION@">0.0.7</token>
     </macros>
     <requirements>
         <requirement type="package" version="@VERSION@">proteomiqon-psmstatistics</requirement>
@@ -35,7 +35,7 @@
                             "MaxIterations" : $ThresholdCond.MaxIterations,
                             "MinimumIncreaseBetweenIterations" : $ThresholdCond.MinimumIncreaseBetweenIterations,
                             "PepValueFittingMethod" : {
-                                "Case":"$ThresholdCond.PepValueFittingMethod"
+                                "Case":"LinearLogit"
                             }
                         }
                     ]
@@ -69,10 +69,6 @@
                 <param name="PepValueThreshold" type="float" value="0.05" label="Pep-Value threshold" />
                 <param name="MaxIterations" type="integer" value="15" label="Max iterations" />
                 <param name="MinimumIncreaseBetweenIterations" type="float" value="0.005" label="Minimum increase between iterations" />
-                <param name="PepValueFittingMethod" type="select" label="Pep-Value fitting method">
-                    <option value="LinearSpline">Linear Spline</option>
-                    <option value="LogisticRegressionLogit" selected="true">Logistic Regression Logit</option>
-                </param>
             </when>
             <when value="Fixed">
                 <param name="SequestLike" type="float" value="5.0" label="Sequest like" />
@@ -102,7 +98,6 @@
                 <param name="PepValueThreshold" value="0.05"/>
                 <param name="MaxIterations" value="15"/>
                 <param name="MinimumIncreaseBetweenIterations" value="0.005"/>
-                <param name="PepValueFittingMethod" value="LinearSpline"/>
             </conditional>
         </test>
         <test expect_num_outputs="2">
@@ -116,7 +111,6 @@
                 <param name="PepValueThreshold" value="0.05"/>
                 <param name="MaxIterations" value="15"/>
                 <param name="MinimumIncreaseBetweenIterations" value="0.005"/>
-                <param name="PepValueFittingMethod" value="LinearSpline"/>
             </conditional>
             <output name="out_paramfile" file="result_1.json"/>
         </test>
@@ -131,7 +125,6 @@
                 <param name="PepValueThreshold" value="0.05"/>
                 <param name="MaxIterations" value="15"/>
                 <param name="MinimumIncreaseBetweenIterations" value="0.005"/>
-                <param name="PepValueFittingMethod" value="LogisticRegressionLogit"/>
             </conditional>
             <output name="out_paramfile" file="result_2.json"/>
         </test>
diff -r b8590dea5e2d -r f831f7d721f8 test-data/result_1.json
--- a/test-data/result_1.json	Sun Jul 18 13:53:08 2021 +0000
+++ b/test-data/result_1.json	Fri Aug 27 07:28:43 2021 +0000
@@ -12,7 +12,7 @@
                             "MaxIterations" : 15,
                             "MinimumIncreaseBetweenIterations" : 0.005,
                             "PepValueFittingMethod" : {
-                                "Case":"LinearSpline"
+                                "Case":"LinearLogit"
                             }
                         }
                     ]
diff -r b8590dea5e2d -r f831f7d721f8 test-data/result_2.json
--- a/test-data/result_2.json	Sun Jul 18 13:53:08 2021 +0000
+++ b/test-data/result_2.json	Fri Aug 27 07:28:43 2021 +0000
@@ -12,7 +12,7 @@
                             "MaxIterations" : 15,
                             "MinimumIncreaseBetweenIterations" : 0.005,
                             "PepValueFittingMethod" : {
-                                "Case":"LogisticRegressionLogit"
+                                "Case":"LinearLogit"
                             }
                         }
                     ]