Mercurial > repos > bgruening > cp_cellprofiler
diff cellprofiler.xml @ 3:a98608f3abc5 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
| author | bgruening |
|---|---|
| date | Mon, 11 May 2020 07:50:04 -0400 |
| parents | 78a16d8c8d5e |
| children | fca368c99299 |
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--- a/cellprofiler.xml Thu Apr 16 05:40:08 2020 -0400 +++ b/cellprofiler.xml Mon May 11 07:50:04 2020 -0400 @@ -20,9 +20,14 @@ <configfile name="script_file"> mkdir ./input mkdir ./output -#for $i, $filename in enumerate($input_images): - ln -s '$filename' './input/${filename.element_identifier}.${filename.ext}' -#end for + +#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> @@ -30,7 +35,19 @@ <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." /> - <param name="input_images" type="data" multiple="true" format="@FORMATS@" label="Images" /> + <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> @@ -46,7 +63,10 @@ <tests> <test expect_num_outputs="1"> <param name="pipeline" value="ExampleHuman.cppipe" /> - <param name="input_images" value="images/AS_09125_050116030001_D03f00d0.tif,images/AS_09125_050116030001_D03f00d1.tif,images/AS_09125_050116030001_D03f00d2.tif" /> + <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"> @@ -76,7 +96,10 @@ </test> <test expect_num_outputs="2"> <param name="pipeline" value="ExampleHuman.cppipe" /> - <param name="input_images" value="images/AS_09125_050116030001_D03f00d0.tif,images/AS_09125_050116030001_D03f00d1.tif,images/AS_09125_050116030001_D03f00d2.tif" /> + <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"> @@ -109,6 +132,79 @@ </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="183808"/> + </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="259" /> + </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="21" /> + </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="183808"/> + </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="259" /> + </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="21" /> + </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>