Merge pull request #5 from ieguinoa/moFF_2_0

fix filtering of matched peptides for task=all
galaxyproteomics · Mar 21, 2019 · fbbe8a7 · fbbe8a7
2 parents 07adbff + 5c79812
commit fbbe8a7
Showing 1 changed file with 5 additions and 5 deletions.
diff --git a/tools/moFF/moff.xml b/tools/moFF/moff.xml
@@ -206,10 +206,10 @@
                #end if
                #if ($task.match_filter.match_filter_selection):
                     --match_filter
-                    --sample_size $task.sample_size
-                    --quantile_thr_filtering $task.quantile_thr_filtering
-                    #if ($ptm_file):
-                        --ptm_file '$task.ptm_file'
+                    --sample_size $task.match_filter.sample_size
+                    --quantile_thr_filtering $task.match_filter.quantile_thr_filtering
+                    #if ($task.match_filter.ptm_file):
+                        --ptm_file '$task.match_filter.ptm_file'
                     #else:
                         --ptm_file $__tool_directory__/tool-data/ptm_setting_ps.json
                     #end if
@@ -283,7 +283,7 @@
 					          <when value="true">
                         <param argument="--sample_size" label="sample_size"  type="float" value="0.20" help="percentage of MS2 peptide used to estimated the threshold. Default value: 0.20" />
 						             <param argument="--quantile_thr_filtering" label="-quantile_thr_filtering" type="float" value="0.75" help="quantile value used to compute the filtering threshold for the matched peak"/>
-					               <param argument="--ptm_file " type="data" format="json" label="ptm_file"  optional= "False"  help="load your ptm file in order to overwrite internal method"/>
+					               <param argument="--ptm_file" type="data" format="json" label="ptm_file"  optional= "True"  help="load your ptm file in order to overwrite internal method"/>
                     </when>
                     <when value="false">
                     </when>