diff search_model_validation.xml @ 19:cb5635e30842 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"

--- a/search_model_validation.xml	Fri Oct 02 08:41:16 2020 +0000
+++ b/search_model_validation.xml	Tue Apr 13 18:41:36 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="sklearn_searchcv" name="Hyperparameter Search" version="@VERSION@">
+<tool id="sklearn_searchcv" name="Hyperparameter Search" version="@VERSION@" profile="20.05">
     <description>performs hyperparameter optimization using various SearchCVs</description>
     <macros>
         <import>main_macros.xml</import>
@@ -32,47 +32,41 @@
     <expand macro="python_requirements"/>
     <expand macro="macro_stdio"/>
     <version_command>echo "@VERSION@"</version_command>
-    <command>
-        <![CDATA[
+    <command><![CDATA[
         export HDF5_USE_FILE_LOCKING='FALSE';
         #if $input_options.selected_input == 'refseq_and_interval'
-        bgzip -c '$input_options.target_file' > '${target_file.element_identifier}.gz' &&
-        tabix -p bed '${target_file.element_identifier}.gz' &&
+            bgzip -c '$input_options.target_file' > '${target_file.element_identifier}.gz' &&
+            tabix -p bed '${target_file.element_identifier}.gz' &&
         #end if
         python '$__tool_directory__/search_model_validation.py'
             --inputs '$inputs'
             --estimator '$search_schemes.infile_estimator'
             #if $input_options.selected_input == 'seq_fasta'
-            --fasta_path '$input_options.fasta_path'
+                --fasta_path '$input_options.fasta_path'
             #elif $input_options.selected_input == 'refseq_and_interval'
-            --ref_seq '$input_options.ref_genome_file'
-            --interval '$input_options.interval_file'
-            --targets "`pwd`/${target_file.element_identifier}.gz"
+                --ref_seq '$input_options.ref_genome_file'
+                --interval '$input_options.interval_file'
+                --targets "`pwd`/${target_file.element_identifier}.gz"
             #else
-            --infile1 '$input_options.infile1'
+                --infile1 '$input_options.infile1'
             #end if
-            --infile2 '$input_options.infile2'
+                --infile2 '$input_options.infile2'
             #if $save != 'save_no_fit'
-            --outfile_result "`pwd`/tmp_outfile_result"
+                --outfile_result '$outfile_result'
             #end if
             #if $save == 'save_estimator'
-            --outfile_object '$outfile_object'
+                --outfile_object '$outfile_object'
             #end if
             #if $save == 'save_no_fit'
-            --outfile_object '$outfile_object_no_fit'
+                --outfile_object '$outfile_object_no_fit'
             #end if
             #if $search_schemes.is_deep_learning == 'booltrue' and $save == 'save_estimator' and $outer_split.split_mode == 'nested_cv'
-            --outfile_weights '$outfile_weights'
+                --outfile_weights '$outfile_weights'
             #end if
             #if $search_schemes.options.cv_selector.selected_cv in ['GroupKFold', 'GroupShuffleSplit', 'LeaveOneGroupOut', 'LeavePGroupsOut']
-            --groups '$search_schemes.options.cv_selector.groups_selector.infile_g'
+                --groups '$search_schemes.options.cv_selector.groups_selector.infile_g'
             #end if
-            #if $save != 'save_no_fit'
-            >'$outfile_result' && cp '$outfile_result' "`pwd`/../tool_stdout"
-            && cp "`pwd`/tmp_outfile_result" '$outfile_result';
-            #end if
-
-        ]]>
+    ]]>
     </command>
     <configfiles>
         <inputs name="inputs" />