From 65529d132c789b2385639d422f3b38e3123785ca Mon Sep 17 00:00:00 2001
From: Ubuntu <19364610+tuncK@users.noreply.github.com>
Date: Fri, 6 Oct 2023 14:10:38 +0000
Subject: [PATCH 01/10] ilastik wrapper added

---
 tools/interactive/interactivetool_ilastik.xml | 44 +++++++++++++++++++
 1 file changed, 44 insertions(+)
 create mode 100644 tools/interactive/interactivetool_ilastik.xml

diff --git a/tools/interactive/interactivetool_ilastik.xml b/tools/interactive/interactivetool_ilastik.xml
new file mode 100644
index 000000000000..934f643b9c95
--- /dev/null
+++ b/tools/interactive/interactivetool_ilastik.xml
@@ -0,0 +1,44 @@
+<tool id="interactive_tool_ilastik" tool_type="interactive" name="Ilastik" version="@VERSION@" profile="23.0">
+    <description>interactive learning and segmentation toolkit</description>
+    <macros>
+        <token name="@VERSION@">1.4.0</token>
+    </macros>
+    <requirements>
+        <container type="docker">quay.io/galaxy/ilastik:@VERSION@</container>
+    </requirements>
+    <entry_points>
+        <entry_point name="Ilastik on $infile.display_name" requires_domain="True">
+            <port>5800</port>
+        </entry_point>
+    </entry_points>
+    <command detect_errors="exit_code">
+    <![CDATA[
+        ## export HOME=\$PWD &&
+        mkdir -p ./galaxy_outputs ./galaxy_inputs &&
+        #for input in $infile:
+            ln -s '$input' ./galaxy_inputs/'$input.name' &&
+        #end for
+        /init
+    ]]>
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="tiff" multiple="true" label="Input files in TIFF format"/>
+    </inputs>
+    
+    <outputs>
+        <data name="ilastik_project" format="h5" label="Ilastik project file">
+            <discover_datasets pattern=".*.ilp" directory="galaxy_outputs" visible="true" assign_primary_output="true"/>
+        </data>
+    </outputs>
+    
+    <tests>
+    </tests>
+    
+    <help><![CDATA[
+        Leverage machine learning algorithms to easily segment, classify, track and count your cells or other experimental data. Most operations are interactive, even on large datasets: you just draw the labels and immediately see the result. No machine learning expertise required.
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1038/s41592-019-0582-9</citation>
+    </citations>
+</tool>

From ada2dd8015bfed5bb8a5ff660f3f9bd0bebb21cd Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Fri, 6 Oct 2023 17:55:11 +0200
Subject: [PATCH 02/10] use available arguments

---
 tools/interactive/interactivetool_ilastik.xml | 53 ++++++++++++++++---
 1 file changed, 46 insertions(+), 7 deletions(-)

diff --git a/tools/interactive/interactivetool_ilastik.xml b/tools/interactive/interactivetool_ilastik.xml
index 934f643b9c95..6812f9c725d3 100644
--- a/tools/interactive/interactivetool_ilastik.xml
+++ b/tools/interactive/interactivetool_ilastik.xml
@@ -14,21 +14,58 @@
     <command detect_errors="exit_code">
     <![CDATA[
         ## export HOME=\$PWD &&
-        mkdir -p ./galaxy_outputs ./galaxy_inputs &&
-        #for input in $infile:
+        ## Make a copy of the existing project if exists
+        #if str($input_type.existing) == "existing":
+            cp $input_type.project ./MyProject.ilp &&
+        #end if
+
+        mkdir -p ./galaxy_inputs &&
+        #for input in $infiles:
             ln -s '$input' ./galaxy_inputs/'$input.name' &&
         #end for
-        /init
+        ilastik
+        #if str($input_type.existing) == "new":
+            --new_project ./MyProject.ilp --workflow '$input_type.Workflow'
+        #else:
+            --project ./MyProject.ilp
+        #end if
     ]]>
     </command>
     <inputs>
-        <param name="infile" type="data" format="tiff" multiple="true" label="Input files in TIFF format"/>
+        <conditional name="input_type">
+            <param name="existing" type="select" label="Which project you want to work on?">
+                <option value="new">Start a new project</option>
+                <option value="existing">Modify an existing project</option>
+            </param>
+            <when value="new">
+                <param name="Workflow" type="select" label="Type of Workflow" >
+                    <option value="PixelClassificationWorkflow">Pixel Classification</option>
+                    <option value="AutocontextTwoStage">Autocontext (2-stage)</option>
+                    <option value="ObjectClassificationWorkflowPixel">Pixel Classification + Object Classification</option>
+                    <option value="ObjectClassificationWorkflowPrediction">Object Classification [Inputs: Raw Data, Pixel Prediction Map]</option>
+                    <option value="ObjectClassificationWorkflowBinary">Object Classification [Inputs: Raw Data, Segmentation]</option>
+                    <option value="ConservationTrackingWorkflowFromBinary">Tracking [Inputs: Raw Data, Segmentation Image]</option>
+                    <option value="ConservationTrackingWorkflowFromPrediction">Tracking [Inputs: Raw Data, Pixel Prediction Map]</option>
+                    <option value="AnimalConservationTrackingWorkflowFromBinary">Animal Tracking [Inputs: Raw Data, Segmentation Image]</option>
+                    <option value="AnimalConservationTrackingWorkflowFromPrediction">Animal Tracking [Inputs: Raw Data, Pixel Prediction Map]</option>
+                    <option value="StructuredTrackingWorkflowFromBinary">Tracking with Learning [Inputs: Raw Data, Segmentation Image]</option>
+                    <option value="StructuredTrackingWorkflowFromPrediction">Tracking with Learning [Inputs: Raw Data, Pixel Prediction Map]</option>
+                    <option value="EdgeTrainingWithMulticutWorkflow">Bounary-based Segmentation with Multicut</option>
+                    <option value="CountingWorkflow">Cell Density Counting</option>
+                    <option value="DataConversionWorkflow">Data Conversion</option>
+                    <option value="neuralNetwork.RemoteWorkflow">Neural Network Classification (Remote)</option>
+                    <option value="neuralNetwork.LocalWorkflow">Neural Network Classification (Local)</option>
+                </param>
+            </when>
+            <when value="existing">
+                <param argument="--project" type="data" format="h5" label="Existing ilastik project" />
+            </when>
+        </conditional>
+        <param name="infiles" type="data" format="tiff" multiple="true" label="Input files in TIFF format"/>
     </inputs>
     
     <outputs>
-        <data name="ilastik_project" format="h5" label="Ilastik project file">
-            <discover_datasets pattern=".*.ilp" directory="galaxy_outputs" visible="true" assign_primary_output="true"/>
-        </data>
+        <data name="ilastik_project" format="h5" label="Ilastik project file" from_work_dir="./MyProject.ilp"/>
     </outputs>
     
     <tests>
@@ -36,6 +73,8 @@
     
     <help><![CDATA[
         Leverage machine learning algorithms to easily segment, classify, track and count your cells or other experimental data. Most operations are interactive, even on large datasets: you just draw the labels and immediately see the result. No machine learning expertise required.
+
+        Please, check the documentation at https://www.ilastik.org/documentation/.
 ]]>
     </help>
     <citations>

From 57c1c65cfbc7581818bd0c1c04c60540a1ee4826 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Mon, 9 Oct 2023 14:20:22 +0200
Subject: [PATCH 03/10] fix entry_point

---
 tools/interactive/interactivetool_ilastik.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/interactive/interactivetool_ilastik.xml b/tools/interactive/interactivetool_ilastik.xml
index 6812f9c725d3..78a8778a6f23 100644
--- a/tools/interactive/interactivetool_ilastik.xml
+++ b/tools/interactive/interactivetool_ilastik.xml
@@ -7,7 +7,7 @@
         <container type="docker">quay.io/galaxy/ilastik:@VERSION@</container>
     </requirements>
     <entry_points>
-        <entry_point name="Ilastik on $infile.display_name" requires_domain="True">
+        <entry_point name="Ilastik" requires_domain="True">
             <port>5800</port>
         </entry_point>
     </entry_points>

From aa947abe85e3405b1cf05aa6eab1a976b3f25d42 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Tue, 10 Oct 2023 14:19:10 +0200
Subject: [PATCH 04/10] change command and output to make it work

---
 tools/interactive/interactivetool_ilastik.xml | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/tools/interactive/interactivetool_ilastik.xml b/tools/interactive/interactivetool_ilastik.xml
index 78a8778a6f23..c9ff3590a08e 100644
--- a/tools/interactive/interactivetool_ilastik.xml
+++ b/tools/interactive/interactivetool_ilastik.xml
@@ -13,7 +13,7 @@
     </entry_points>
     <command detect_errors="exit_code">
     <![CDATA[
-        ## export HOME=\$PWD &&
+        export HOME=\$PWD &&
         ## Make a copy of the existing project if exists
         #if str($input_type.existing) == "existing":
             cp $input_type.project ./MyProject.ilp &&
@@ -23,12 +23,14 @@
         #for input in $infiles:
             ln -s '$input' ./galaxy_inputs/'$input.name' &&
         #end for
-        ilastik
         #if str($input_type.existing) == "new":
-            --new_project ./MyProject.ilp --workflow '$input_type.Workflow'
+            echo "ilastik --new_project \$HOME/MyProject.ilp --workflow '$input_type.Workflow'" > run_ilastik &&
         #else:
-            --project ./MyProject.ilp
+            echo "ilastik --project \$HOME/MyProject.ilp" > run_ilastik &&
         #end if
+        chmod +x run_ilastik &&
+        cp run_ilastik '/bin/' &&
+        /init
     ]]>
     </command>
     <inputs>
@@ -65,7 +67,7 @@
     </inputs>
     
     <outputs>
-        <data name="ilastik_project" format="h5" label="Ilastik project file" from_work_dir="./MyProject.ilp"/>
+        <data name="ilastik_project" format="h5" label="Ilastik project file" from_work_dir="MyProject.ilp"/>
     </outputs>
     
     <tests>

From 8aac1ccf6239ef821726cfc97883f0eaa5d3e2fc Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Thu, 12 Oct 2023 08:57:12 +0200
Subject: [PATCH 05/10] change run_ilastik to ilastik_with_args to fit the
 docker image + put images in working directory.

---
 tools/interactive/interactivetool_ilastik.xml | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/tools/interactive/interactivetool_ilastik.xml b/tools/interactive/interactivetool_ilastik.xml
index c9ff3590a08e..8120663d3885 100644
--- a/tools/interactive/interactivetool_ilastik.xml
+++ b/tools/interactive/interactivetool_ilastik.xml
@@ -19,17 +19,19 @@
             cp $input_type.project ./MyProject.ilp &&
         #end if
 
-        mkdir -p ./galaxy_inputs &&
+        ## Link input images to current working directory
         #for input in $infiles:
-            ln -s '$input' ./galaxy_inputs/'$input.name' &&
+            ln -s '$input' ./'$input.name' &&
         #end for
+        ## Write the bash script to run:
         #if str($input_type.existing) == "new":
-            echo "ilastik --new_project \$HOME/MyProject.ilp --workflow '$input_type.Workflow'" > run_ilastik &&
+            echo "ilastik --new_project \$HOME/MyProject.ilp --workflow '$input_type.Workflow'" > ilastik_with_args &&
         #else:
-            echo "ilastik --project \$HOME/MyProject.ilp" > run_ilastik &&
+            echo "ilastik --project \$HOME/MyProject.ilp" > ilastik_with_args &&
         #end if
-        chmod +x run_ilastik &&
-        cp run_ilastik '/bin/' &&
+        ## Copy it to /bin/ so it will be used by the container:
+        chmod +x ilastik_with_args &&
+        cp ilastik_with_args '/bin/' &&
         /init
     ]]>
     </command>

From 4110a93cbf2472edd20592212fad9f22d788ace9 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Thu, 12 Oct 2023 08:57:35 +0200
Subject: [PATCH 06/10] add more info in help section

---
 tools/interactive/interactivetool_ilastik.xml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/tools/interactive/interactivetool_ilastik.xml b/tools/interactive/interactivetool_ilastik.xml
index 8120663d3885..9af710b5f330 100644
--- a/tools/interactive/interactivetool_ilastik.xml
+++ b/tools/interactive/interactivetool_ilastik.xml
@@ -78,6 +78,11 @@
     <help><![CDATA[
         Leverage machine learning algorithms to easily segment, classify, track and count your cells or other experimental data. Most operations are interactive, even on large datasets: you just draw the labels and immediately see the result. No machine learning expertise required.
 
+        This tool has been designed uniquely to make/modify a project.
+        
+        - When you have trained your project, save it and quit the application. The project called 'MyProject.ilp' will be imported into your history.
+        - If you want to modify a project, make sure you use at least the same images as the first time (but you can add more).
+
         Please, check the documentation at https://www.ilastik.org/documentation/.
 ]]>
     </help>

From 8092aba68e568e350e5f83ed1852b97c8743d528 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Thu, 12 Oct 2023 14:11:55 +0200
Subject: [PATCH 07/10] add some quotes

---
 tools/interactive/interactivetool_ilastik.xml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/interactive/interactivetool_ilastik.xml b/tools/interactive/interactivetool_ilastik.xml
index 9af710b5f330..07e60a060398 100644
--- a/tools/interactive/interactivetool_ilastik.xml
+++ b/tools/interactive/interactivetool_ilastik.xml
@@ -16,7 +16,7 @@
         export HOME=\$PWD &&
         ## Make a copy of the existing project if exists
         #if str($input_type.existing) == "existing":
-            cp $input_type.project ./MyProject.ilp &&
+            cp '$input_type.project' ./MyProject.ilp &&
         #end if
 
         ## Link input images to current working directory
@@ -25,13 +25,13 @@
         #end for
         ## Write the bash script to run:
         #if str($input_type.existing) == "new":
-            echo "ilastik --new_project \$HOME/MyProject.ilp --workflow '$input_type.Workflow'" > ilastik_with_args &&
+            echo "ilastik --new_project \$HOME/MyProject.ilp --workflow '$input_type.Workflow'" > ./ilastik_with_args &&
         #else:
             echo "ilastik --project \$HOME/MyProject.ilp" > ilastik_with_args &&
         #end if
         ## Copy it to /bin/ so it will be used by the container:
-        chmod +x ilastik_with_args &&
-        cp ilastik_with_args '/bin/' &&
+        chmod +x ./ilastik_with_args &&
+        cp ./ilastik_with_args '/bin/' &&
         /init
     ]]>
     </command>

From 9a1cc32e341422fd5711f5e2bdb362456601755c Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Thu, 12 Oct 2023 15:10:37 +0200
Subject: [PATCH 08/10] add ./

---
 tools/interactive/interactivetool_ilastik.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/interactive/interactivetool_ilastik.xml b/tools/interactive/interactivetool_ilastik.xml
index 07e60a060398..b7976c7ab72d 100644
--- a/tools/interactive/interactivetool_ilastik.xml
+++ b/tools/interactive/interactivetool_ilastik.xml
@@ -27,7 +27,7 @@
         #if str($input_type.existing) == "new":
             echo "ilastik --new_project \$HOME/MyProject.ilp --workflow '$input_type.Workflow'" > ./ilastik_with_args &&
         #else:
-            echo "ilastik --project \$HOME/MyProject.ilp" > ilastik_with_args &&
+            echo "ilastik --project \$HOME/MyProject.ilp" > ./ilastik_with_args &&
         #end if
         ## Copy it to /bin/ so it will be used by the container:
         chmod +x ./ilastik_with_args &&

From ce82be8f448492e66b27a7d900eb45465fc3db9b Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Thu, 12 Oct 2023 15:31:46 +0200
Subject: [PATCH 09/10] raise error when identical identifiers

---
 tools/interactive/interactivetool_ilastik.xml | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/tools/interactive/interactivetool_ilastik.xml b/tools/interactive/interactivetool_ilastik.xml
index b7976c7ab72d..3c037ac1f387 100644
--- a/tools/interactive/interactivetool_ilastik.xml
+++ b/tools/interactive/interactivetool_ilastik.xml
@@ -13,6 +13,17 @@
     </entry_points>
     <command detect_errors="exit_code">
     <![CDATA[
+        ## Check inputs have no duplicated element_identifier:
+        #set labels = [input.element_identifier for input in $infiles]
+        #set duplicates = [label for label in labels if labels.count(label) > 1]
+        #if len(duplicates) > 0:
+            #set unique_duplicates = list(set(duplicates))
+            echo "Cannot run ilastik because these identifiers are present more than once:" &&
+            #for label in $unique_duplicates:
+                echo $label &&
+            #end for
+            exit 1 &&
+        #end if
         export HOME=\$PWD &&
         ## Make a copy of the existing project if exists
         #if str($input_type.existing) == "existing":
@@ -21,7 +32,7 @@
 
         ## Link input images to current working directory
         #for input in $infiles:
-            ln -s '$input' ./'$input.name' &&
+            ln -s '$input' ./'$input.element_identifier'.tif &&
         #end for
         ## Write the bash script to run:
         #if str($input_type.existing) == "new":
@@ -80,8 +91,9 @@
 
         This tool has been designed uniquely to make/modify a project.
         
+        - It requires that input images have unique identifiers.
         - When you have trained your project, save it and quit the application. The project called 'MyProject.ilp' will be imported into your history.
-        - If you want to modify a project, make sure you use at least the same images as the first time (but you can add more).
+        - If you want to modify a project, make sure you use at least the same images (with the same identifiers) as the first time (but you can add more).
 
         Please, check the documentation at https://www.ilastik.org/documentation/.
 ]]>

From 822f4c5927a7bcdb8f3eec6bd7b22b55ffdffdc6 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Fri, 13 Oct 2023 14:05:05 +0200
Subject: [PATCH 10/10] use directory where app user has rw access

---
 tools/interactive/interactivetool_ilastik.xml | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/tools/interactive/interactivetool_ilastik.xml b/tools/interactive/interactivetool_ilastik.xml
index 3c037ac1f387..8f52af0b7b7b 100644
--- a/tools/interactive/interactivetool_ilastik.xml
+++ b/tools/interactive/interactivetool_ilastik.xml
@@ -25,9 +25,12 @@
             exit 1 &&
         #end if
         export HOME=\$PWD &&
+        ## Create a directory where the app user has access
+        mkdir -p ./output &&
+        chown 1000:1000 ./output/ &&
         ## Make a copy of the existing project if exists
         #if str($input_type.existing) == "existing":
-            cp '$input_type.project' ./MyProject.ilp &&
+            cp '$input_type.project' ./output/MyProject.ilp &&
         #end if
 
         ## Link input images to current working directory
@@ -36,9 +39,9 @@
         #end for
         ## Write the bash script to run:
         #if str($input_type.existing) == "new":
-            echo "ilastik --new_project \$HOME/MyProject.ilp --workflow '$input_type.Workflow'" > ./ilastik_with_args &&
+            echo "ilastik --new_project \$HOME/output/MyProject.ilp --workflow '$input_type.Workflow'" > ./ilastik_with_args &&
         #else:
-            echo "ilastik --project \$HOME/MyProject.ilp" > ./ilastik_with_args &&
+            echo "ilastik --project \$HOME/output/MyProject.ilp" > ./ilastik_with_args &&
         #end if
         ## Copy it to /bin/ so it will be used by the container:
         chmod +x ./ilastik_with_args &&
@@ -80,7 +83,7 @@
     </inputs>
     
     <outputs>
-        <data name="ilastik_project" format="h5" label="Ilastik project file" from_work_dir="MyProject.ilp"/>
+        <data name="ilastik_project" format="h5" label="Ilastik project file" from_work_dir="output/MyProject.ilp"/>
     </outputs>
     
     <tests>