update tutorial

tutorial/README.md

@@ -56,15 +56,15 @@ In the Galaxy welcome screen, click on the "Eco-Metabolomics" entry in the left
 ![mtbls520_workflow](mtbls520_instructions_01.jpg)
 Fig. 1: Running the module "mtbls520_01_mtbls_download".
 
-After the download has been completed successfully, data from the dataset has to be imported into Galaxy. In order to proceed, please click on the module "mtbls520_02_extract" in the left pane (Fig. 2). Please choose the dataset you have just downloaded as input. When you click on the button "Execute", the data acquired in positive mode will be extracted and imported into the Galaxy history.
+After the download has been completed successfully (Fig. 2), click on the module "mtbls520_02_extract" in the left pane to import the data from the dataset into Galaxy (Fig. 3). Choose the dataset you have just downloaded as input. When you click on the button "Execute", the data acquired in positive mode will be extracted and imported into the Galaxy history.
 
 ![mtbls520_workflow](mtbls520_instructions_02.jpg)
-Fig. 2: Successful run of the module "mtbls520_02_extract"
+Fig. 2: Successful run of the module "mtbls520_01_mtbls_download"
 
 ![mtbls520_workflow](mtbls520_instructions_03.jpg)
 Fig. 3: Data extraction
 
-After the data has been imported (which can take up several minutes), click on the “Workflow” tab on the upper pane. A new screen appears, which shows all workflows shared to you (Fig. 4). In order to process the MTBLS520 workflow, you need to import the workflow into Galaxy. Please click on the "upload" button as indicated in Fig. 4. A new window will appear. Please enter the following address in the field named "Galaxy workflow URL":
+It will take several minutes to import the data. Next, click on the “Workflow” tab on the upper pane. A new screen appears, which shows all workflows shared to you (Fig. 4). In order to process the MTBLS520 workflow, you need to import the workflow into Galaxy. Please click on the "upload" button as indicated in Fig. 4. A new window will appear. Please enter the following address in the field named "Galaxy workflow URL":
 
 ```https://raw.githubusercontent.com/korseby/container-mtbls520/master/galaxy/mtbls520_workflow.ga```
 
@@ -73,7 +73,7 @@ A click on the button "Import" will import the workflow into Galaxy.
 ![mtbls520_workflow](mtbls520_instructions_04.jpg)
 Fig. 4: Workflows
 
-After the screen has been reloaded automatically, the just imported workflow should appear in the list under the name "MTBLS520 Eco-Metabolomics Worlflow (imported from uploaded file)". Please click on the entry to edit and get an overview of the entire workflow (Fig. 5).
+After the screen has been reloaded automatically, the just imported workflow should appear in the list under the name "MTBLS520 Eco-Metabolomics Worlflow (imported from uploaded file)". Please click on the entry to "Edit" and get an overview of the entire workflow (Fig. 5).
 
 ![mtbls520_workflow](mtbls520_instructions_05.jpg)
 Fig. 5: Edit and run the MTBLS520 workflow
@@ -83,13 +83,13 @@ The window will reload and will show a graphical represention of the entire work
 ![mtbls520_workflow](mtbls520_instructions_06.jpg)
 Fig. 6: Run the workflow
 
-On the next screen, select the input variables and input datasets as listed in Fig. 7. Make sure that you have selected the correct input data and variables. After you have selected the entries, click on “Run workflow” in the upper right corner. This will start the workflow.
-
-The workflow should be started with the following parameter settings:
+On the next screen, select the input variables and input datasets as listed in Fig. 7. Make sure that you have selected the correct input data and variables. 
 
 ![mtbls520_workflow_settings](../galaxy/mtbls520_workflow_settings.jpg)
 Fig. 7: Parameter settings for starting the entire workflow
 
+After you have selected the entries, click on “Run workflow” in the upper right corner (Fig. 7). This will start the computational workflow.
+
 Optional: In case you have selected "negative" mode when extracting the data in step 2 (module "mtbls520_02_extract", see Fig. 2), please make sure that you also select the corresponding "negative" mode in the modules "mtbls520_04_preparations" and "mtbls520_03_quality_control" (Fig. 8).
 
 ![mtbls520_workflow](mtbls520_instructions_07.jpg)
@@ -102,6 +102,8 @@ Fig. 9: Overview of the entire workflow
 
 The processing of the entire workflow will take about 30 minutes, depending on load and the number of CPU cores of the workstation Galaxy is running.
 
+When the entries in the right pane have become green, you can click on them to see details. A click on the small “eye” icon will open a particular plot or text file of the module.
+
 
 
 ## Publications