--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cellprofiler.xml	Mon Apr 25 18:30:59 2022 +0000
@@ -0,0 +1,245 @@
+<tool id="cp_cellprofiler4" name="CellProfiler" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
+    <description>run a CellProfiler pipeline</description>
+    <macros>
+        <import>macros.xml</import>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <xml name="test_assert_content" token_n="291">
+            <assert_contents>
+                <has_n_lines n="@N@" />
+            </assert_contents>
+        </xml>
+    </macros>
+    <expand macro="cp_requirements" />
+    <command detect_errors="aggressive"><![CDATA[
+        export MPLCONFIGDIR=\$TEMP &&
+        bash '$script_file' &&
+        cellprofiler -c -r --file-list list.txt -o ./output -p '$pipeline' 
+        #if $detailed_output
+            -L 10 > ./cp.log 2>&1
+        #end if 
+    ]]></command>
+    <configfiles>
+        <configfile name="script_file">
+mkdir ./input
+mkdir ./output
+
+#if $con_input_type.input_type =="yes"
+    tar -C ./input -xvf $con_input_type.input_images
+#else
+    #for $i, $filename in enumerate($con_input_type.input_images):
+        ln -s '$filename' './input/${filename.element_identifier}.${filename.ext}'
+    #end for
+#end if
+
+find `pwd`/input -name "*.*" > list.txt
+        </configfile>
+    </configfiles>
+  
+    <inputs>
+        <param name="pipeline" type="data" format="txt" label="Pipeline file" help="A ready-to-run .cppipe file. It can be created with various CellProfiler modules." />
+        <conditional name="con_input_type">
+            <param name="input_type" type="select" label="Are the input images packed into a tar archive?">
+                <option value="yes">Yes</option>
+                <option value="no">No</option>
+            </param> 
+            <when value="no">
+                <param name="input_images" type="data" multiple="true" format="@FORMATS@" label="Images" />
+            </when>
+            <when value="yes">
+                <param name="input_images" type="data" format="tar" label="A tarball of images" />
+            </when>
+        </conditional>
+       
+        <param name="detailed_output" type="boolean" label="Detailed logging file?" help="If set, a detailed CellProfiler log file will be generated." />
+    </inputs>
+
+    <outputs>
+        <collection name="pipeline_output" type="list" label="CellProfiler pipeline output files">
+            <discover_datasets pattern="__designation_and_ext__" visible="false" directory="output"/>
+        </collection>
+        <data format="txt" name="logs" from_work_dir="cp.log" label="CellProfiler log">
+            <filter>detailed_output</filter>
+        </data>
+    </outputs>
+
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="pipeline" value="ExampleHuman.cppipe" />
+            <conditional name="con_input_type">
+                <param name="input_type" value="no" />
+                <param name="input_images" value="images/AS_09125_050116030001_D03f00d0.tif,images/AS_09125_050116030001_D03f00d1.tif,images/AS_09125_050116030001_D03f00d2.tif" />
+            </conditional>
+            <param name="detailed_output" value="False" />
+            <output_collection name="pipeline_output" type="list" count="7">
+                <element name="AS_09125_050116030001_D03f00d0.tif_Overlay">
+                    <assert_contents>
+                      <has_size value="168221"/>
+                    </assert_contents>
+                </element>
+                <element name="Cells">
+                    <expand macro="test_assert_content" n="290" />
+                </element>
+                <element name="Cytoplasm">
+                  <expand macro="test_assert_content" n="290" />
+                </element>
+                <element name="Experiment">
+                  <expand macro="test_assert_content" n="261" />
+                </element>
+                <element name="Image">
+                  <expand macro="test_assert_content" n="2" />
+                </element>
+                <element name="Nuclei">
+                  <expand macro="test_assert_content" n="290" />
+                </element>
+                <element name="PH3">
+                  <expand macro="test_assert_content" n="23" />
+                </element>
+            </output_collection>
+        </test>
+        <test expect_num_outputs="2">
+            <param name="pipeline" value="ExampleHuman.cppipe" />
+            <conditional name="con_input_type">
+                <param name="input_type" value="no" />
+                <param name="input_images" value="images/AS_09125_050116030001_D03f00d0.tif,images/AS_09125_050116030001_D03f00d1.tif,images/AS_09125_050116030001_D03f00d2.tif" />
+            </conditional>
+            <param name="detailed_output" value="True" />
+            <output_collection name="pipeline_output" type="list" count="7">
+                <element name="AS_09125_050116030001_D03f00d0.tif_Overlay">
+                    <assert_contents>
+                      <has_size value="168221"/>
+                    </assert_contents>
+                </element>
+                <element name="Cells">
+                    <expand macro="test_assert_content" n="290" />
+                </element>
+                <element name="Cytoplasm">
+                  <expand macro="test_assert_content" n="290" />
+                </element>
+                <element name="Experiment">
+                  <expand macro="test_assert_content" n="261" />
+                </element>
+                <element name="Image">
+                  <expand macro="test_assert_content" n="2" />
+                </element>
+                <element name="Nuclei">
+                  <expand macro="test_assert_content" n="290" />
+                </element>
+                <element name="PH3">
+                  <expand macro="test_assert_content" n="23" />
+                </element>
+            </output_collection>
+            <output name="logs" ftype='txt'>
+                <assert_contents>
+                    <has_text_matching expression="JVM will be started with AWT in headless mode" />
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Repeat tests for tarball input -->
+        <test expect_num_outputs="1">
+            <param name="pipeline" value="ExampleHuman.cppipe" />
+            <conditional name="con_input_type">
+                <param name="input_type" value="yes" />
+                <param name="input_images" value="images.tar" />
+            </conditional>
+            <param name="detailed_output" value="False" />
+            <output_collection name="pipeline_output" type="list" count="7">
+                <element name="AS_09125_050116030001_D03f00d0_Overlay">
+                    <assert_contents>
+                      <has_size value="168221"/>
+                    </assert_contents>
+                </element>
+                <element name="Cells">
+                    <expand macro="test_assert_content" n="290" />
+                </element>
+                <element name="Cytoplasm">
+                  <expand macro="test_assert_content" n="290" />
+                </element>
+                <element name="Experiment">
+                  <expand macro="test_assert_content" n="261" />
+                </element>
+                <element name="Image">
+                  <expand macro="test_assert_content" n="2" />
+                </element>
+                <element name="Nuclei">
+                  <expand macro="test_assert_content" n="290" />
+                </element>
+                <element name="PH3">
+                  <expand macro="test_assert_content" n="23" />
+                </element>
+            </output_collection>
+        </test>
+        <test expect_num_outputs="2">
+            <param name="pipeline" value="ExampleHuman.cppipe" />
+            <conditional name="con_input_type">
+                <param name="input_type" value="yes" />
+                <param name="input_images" value="images.tar" />
+            </conditional>
+            <param name="detailed_output" value="True" />
+            <output_collection name="pipeline_output" type="list" count="7">
+                <element name="AS_09125_050116030001_D03f00d0_Overlay">
+                    <assert_contents>
+                      <has_size value="168221"/>
+                    </assert_contents>
+                </element>
+                <element name="Cells">
+                    <expand macro="test_assert_content" n="290" />
+                </element>
+                <element name="Cytoplasm">
+                  <expand macro="test_assert_content" n="290" />
+                </element>
+                <element name="Experiment">
+                  <expand macro="test_assert_content" n="261" />
+                </element>
+                <element name="Image">
+                  <expand macro="test_assert_content" n="2" />
+                </element>
+                <element name="Nuclei">
+                  <expand macro="test_assert_content" n="290" />
+                </element>
+                <element name="PH3">
+                  <expand macro="test_assert_content" n="23" />
+                </element>
+            </output_collection>
+            <output name="logs" ftype='txt'>
+                <assert_contents>
+                    <has_text_matching expression="JVM will be started with AWT in headless mode" />
+                </assert_contents>
+            </output>
+        </test>        
+
+    </tests>
+    
+    <help>
+    <![CDATA[
+
+      .. class:: infomark
+
+      **What it does**
+
+      This is the last tool in a CellProfiler workflow and runs a CellProfiler @TOOL_VERSION@ pipeline file on a collection of images.
+
+
+      .. class:: infomark
+
+      **Input**
+
+      - Collection of images.
+
+      - Existing CellProfiler pipeline file *(.cppipe)* or generated by linking CellProfiler tools.
+
+      .. class:: infomark
+
+      **Output**
+
+      - Images if the tool *SaveImages* was included in the workflow.
+      - The features selected if the tool *ExportToSpreadsheet* was included in the workflow.
+
+      .. class:: warningmark
+
+      **IMPORTANT**
+
+      Only the pipelines generated with the version @TOOL_VERSION@ of CellProfiler can be run, other versions may cause problems.
+      ]]>
+    </help>
+    <expand macro="citations" />
+</tool>