From 0b1bad89582d4d8fae8cfb722b7ecf32f8c20c9e Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Wed, 9 Jun 2021 13:57:32 +0200
Subject: [PATCH] respect the cheetah style

---
 .../interactivetool_jupyter_notebook.xml      | 76 +++++++++----------
 1 file changed, 38 insertions(+), 38 deletions(-)

diff --git a/tools/interactive/interactivetool_jupyter_notebook.xml b/tools/interactive/interactivetool_jupyter_notebook.xml
index 5f03e496a52..c7453f06f0d 100644
--- a/tools/interactive/interactivetool_jupyter_notebook.xml
+++ b/tools/interactive/interactivetool_jupyter_notebook.xml
@@ -16,47 +16,47 @@
         <environment_variable name="API_KEY" inject="api_key" />
     </environment_variables>
     <command detect_errors="aggressive"><![CDATA[
-#import re
-#import random
-#import string
-export GALAXY_WORKING_DIR=`pwd` &&
-mkdir -p ./jupyter/outputs/ &&
-mkdir -p ./jupyter/data &&
+        #import re
+        #import random
+        #import string
+        export GALAXY_WORKING_DIR=`pwd` &&
+        mkdir -p ./jupyter/outputs/ &&
+        mkdir -p ./jupyter/data &&
 
-#set $cleaned_names = []
-#for $file in $input
-    #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($file.element_identifier))
-    ## prevent overwriting data with a randomized suffix
-    #if $cleaned_name in $cleaned_names:
-        #set $cleaned_name = $cleaned_name + '_' + ''.join(random.choice(string.ascii_lowercase) for _ in range(3))
-    #end if
-    #set $cleaned_names += [$cleaned_name]
-    ln -sf '$file' './jupyter/data/${cleaned_name}' &&
-#end for
+        #set $cleaned_names = []
+        #for $file in $input
+            #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($file.element_identifier))
+            ## prevent overwriting data with a randomized suffix
+            #if $cleaned_name in $cleaned_names:
+                #set $cleaned_name = $cleaned_name + '_' + ''.join(random.choice(string.ascii_lowercase) for _ in range(3))
+            #end if
+            #set $cleaned_names += [$cleaned_name]
+            ln -sf '$file' './jupyter/data/${cleaned_name}' &&
+        #end for
 
-## change into the directory where the notebooks are located
-cd ./jupyter/ &&
-export HOME=/home/jovyan/ &&
-export PATH=/home/jovyan/.local/bin:\$PATH &&
+        ## change into the directory where the notebooks are located
+        cd ./jupyter/ &&
+        export HOME=/home/jovyan/ &&
+        export PATH=/home/jovyan/.local/bin:\$PATH &&
 
-#if $mode.mode_select == 'scratch':
-    ## copy default notebook
-    cp '$__tool_directory__/default_notebook.ipynb' ./ipython_galaxy_notebook.ipynb &&
-    jupyter trust ./ipython_galaxy_notebook.ipynb &&
-    jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
-    cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'
-#else:
-    #set $noteboook_name = re.sub('[^\w\-\.]', '_', str($mode.ipynb.element_identifier))
-    cp '$mode.ipynb' ./${noteboook_name}.ipynb &&
-    jupyter trust ./${noteboook_name}.ipynb &&
-    #if $mode.run_it:
-        jupyter nbconvert --to notebook --execute --output ./ipython_galaxy_notebook.ipynb --allow-errors  ./*.ipynb &&
-        #set $noteboook_name = 'ipython_galaxy_notebook'
-    #else:
-        jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
-    #end if
-    cp ./${noteboook_name}.ipynb '$jupyter_notebook'
-#end if
+        #if $mode.mode_select == 'scratch':
+            ## copy default notebook
+            cp '$__tool_directory__/default_notebook.ipynb' ./ipython_galaxy_notebook.ipynb &&
+            jupyter trust ./ipython_galaxy_notebook.ipynb &&
+            jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
+            cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'
+        #else:
+            #set $noteboook_name = re.sub('[^\w\-\.]', '_', str($mode.ipynb.element_identifier))
+            cp '$mode.ipynb' ./${noteboook_name}.ipynb &&
+            jupyter trust ./${noteboook_name}.ipynb &&
+            #if $mode.run_it:
+                jupyter nbconvert --to notebook --execute --output ./ipython_galaxy_notebook.ipynb --allow-errors  ./*.ipynb &&
+                #set $noteboook_name = 'ipython_galaxy_notebook'
+            #else:
+                jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
+            #end if
+            cp ./${noteboook_name}.ipynb '$jupyter_notebook'
+        #end if
     ]]>
     </command>
     <inputs>