diff cherri_train.xml @ 3:a30b9df1775a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit 8778c3f71e295ec5b62ef3998319d211fc864e35

--- a/cherri_train.xml	Mon Jan 09 19:50:32 2023 +0000
+++ b/cherri_train.xml	Wed Jan 25 18:33:19 2023 +0000
@@ -1,14 +1,14 @@
-<tool id="cherri_train" name="Train a CheRRI model using RRIs" version="@VERSION@" profile="@PROFILE@">
+<tool id="cherri_train" name="Train a CheRRI model using RRIs" version="@VERSION@+galaxy@SUFFIX_VERSION@" profile="@PROFILE@">
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         export PYTHONHASHSEED=31337 &&
-        mkdir mixed_model &&
         #set experiments = []
         #for $experiment in $rep_experiment:
             mkdir $experiment.exp_name &&
+            mkdir '$experiment.exp_name/tmp' &&
             ln -s '$experiment.ref_source.genome_fasta' '$experiment.exp_name/genome.fa' &&
             $experiments.append(str($experiment.exp_name))
             #set replicates = []
@@ -26,9 +26,11 @@
                 -i2 '$experiment.occupied_regions'
             #end if
             -o .
-            -on '$experiment.exp_name' 
+            -on '$experiment.exp_name'
+            -tp '$experiment.exp_name/tmp'
             @COMMONPARAMS@ &&
             #if len($rep_experiment) > 1:
+                mkdir -p mixed_model &&
                 ln -s '../$experiment.exp_name' 'mixed_model/$experiment.exp_name' &&
             #else:
                 ln -s $experiment.exp_name/model/optimized/full_${experiment.exp_name}_context_${context}.model final_full.model &&
@@ -40,6 +42,7 @@
             #end if
         #end for
         #if len($rep_experiment) > 1:
+            mkdir mixed_model/tmp &&
             cherri train 
                 -mi on
                 -i1 mixed_model
@@ -49,6 +52,7 @@
                 -n mixed
                 -o .
                 -on mixed_model
+                -tp mixed_model/tmp
                 @COMMONPARAMS@ &&
                 ln -s mixed_model/mixed/model/optimized/full_mixed_context_${context}.model final_full.model &&
                 #if $use_structure == 'off':