The XML file was updated

Author: reyhaneh-tavakoli

tools/rna_tools/cleaverna/cleaverna.xml

@@ -19,8 +19,14 @@
     <command detect_errors="exit_code"><![CDATA[
         #if $mode_selector.mode == "training"
             #set $model_name = $mode_selector.model_name
-            cleaverna --params "$mode_selector.params_csv" --target_files_training $mode_selector.target_files_training --prediction_mode default --model_name "$model_name" --output_dir output 
+            cleaverna 
+                --params "$mode_selector.params_csv" 
+                --target_files_training #for $f in $mode_selector.target_files_training# "$f" #end for 
+                --prediction_mode default 
+                --model_name "$model_name" 
+                --output_dir output
         #else
+
             ## ---------- PREDICTION MODE ----------
             #if $mode_selector.prediction_mode_selector.prediction_mode == "default"
                 ## PARAMS
@@ -182,7 +188,7 @@
     </inputs>
     <outputs>
         <!-- Training outputs -->
-        <data name="training_csv" format="csv" from_work_dir="output/training_output.csv" label="${tool.name} on ${on_string}: Training CSV">
+        <data name="training_csv" format="csv" from_work_dir="output/${mode_selector.model_name}_user_merged_num.csv" label="${tool.name} on ${on_string}: Training CSV">
             <filter>mode_selector['mode'] == 'training'</filter>
         </data>
         <data name="training_cfg" format="txt" from_work_dir="output/parameters.cfg" label="${tool.name} on ${on_string}: Training Config">
@@ -212,8 +218,8 @@
             <conditional name="mode_selector">
                 <param name="mode" value="training"/>
                 <param name="params_csv" value="params.csv" ftype="csv"/>
-                <param name="target_files_training" value="BCL-1.fasta" ftype="fasta"/>
                 <param name="model_name" value="test"/>
+                <param name="target_files_training" value="BCL-1.fasta,BCL-2.fasta" ftype="fasta"/>
             </conditional>
             <output name="training_csv">
                 <assert_contents>

tools/rna_tools/cleaverna/test-data/BCL-1.fasta

@@ -9,3 +9,8 @@ TGCCACGGTGGTGGAGGAGCTCTTCAGGGACGGGGTGAACTGGGGGAGGATTGTGGCCTTCTTTGAGTTC
 GGTGGGGTCATGTGTGTGGAGAGCGTCAACCGGGAGATGTCGCCCCTGGTGGACAACATCGCCCTGTGGA
 TGACTGAGTACCTGAACCGGCACCTGCACACCTGGATCCAGGATAACGGAGGCTGGGATGCCTTTGTGGA
 ACTGTACGGCCCCAGCATGCGGCCTCTGTTTGATTTCTCCTGGCTGTCTCTGAAGACTCTGCTCAGTTTG
+GCCCTGGTGGGAGCTTGCATCACCCTGGGTGCCTATCTGGGCCACAAGTGAAGTCAACATGCCTGCCCCA
+AACAAATATGCAAAAGGTTCACTAAAGCAGTAGAAATAATATGCATTGTCAGTGATGTTCCATGAAACAA
+AGCTGCAGGCTGTTTAAGAAAAAATAACACACATATAAACATCACACACACAGACAGACACACACACACA
+
+

tools/rna_tools/cleaverna/test-data/BCL-2.fasta

@@ -0,0 +1,16 @@
+>BCL-2
+GAATCTCTTTCTCTCCCTTCAGAATCTTATCTTGGCTTTGGATCTTAGAAGAGAATCACTAACCAGAGAC
+GAGACTCAGTGAGTGAGCAGGTGTTTTGGACAATGGACTGGTTGAGCCCATCCCTATTATAAAAATGTCT
+CAGAGCAACCGGGAGCTGGTGGTTGACTTTCTCTCCTACAAGCTTTCCCAGAAAGGATACAGCTGGAGTC
+AGTTTAGTGATGTGGAAGAGAACAGGACTGAGGCCCCAGAAGGGACTGAATCGGAGATGGAGACCCCCAG
+TGCCATCAATGGCAACCCATCCTGGCACCTGGCAGACAGCCCCGCGGTGAATGGAGCCACTGCGCACAGC
+AGCAGTTTGGATGCCCGGGAGGTGATCCCCATGGCAGCAGTAAAGCAAGCGCTGAGGGAGGCAGGCGACG
+AGTTTGAACTGCGGTACCGGCGGGCATTCAGTGACCTGACATCCCAGCTCCACATCACCCCAGGGACAGC
+ATATCAGAGCTTTGAACAGGTAGTGAATGAACTCTTCCGGGATGGGGTAAACTGGGGTCGCATTGTGGCC
+TTTTTCTCCTTCGGCGGGGCACTGTGCGTGGAAAGCGTAGACAAGGAGATGCAGGTATTGGTGAGTCGGA
+TCGCAGCTTGGATGGCCACTTACCTGAATGACCACCTAGAGCCTTGGATCCAGGAGAACGGCGGCTGGGA
+TACTTTTGTGGAACTCTATGGGAACAATGCAGCAGCCGAGAGCCGAAAGGGCCAGGAACGCTTCAACCGC
+TGGTTCCTGACGGGCATGACTGTGGCCGGCGTGGTTCTGCTGGGCTCACTCTTCAGTCGGAAATGACCAG
+ACACTGACCATCCACTCTACCCTCCCACCCCCTTCTCTGCTCCACCACATCCTCCGTCCAGCCGCCATTG
+CCACCAGGAGAACCCG
+