Mercurial > repos > bgruening > cp_cellprofiler4
diff cellprofiler.xml @ 0:b333df978624 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4cb71c4badd30480d67860ff614410f37f2cc8d0"
| author | bgruening |
|---|---|
| date | Mon, 25 Apr 2022 18:30:59 +0000 |
| parents | |
| children | 5a810dc963f4 |
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--- /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>