Mercurial > repos > galaxyp > cardinal_single_ion_segmentation
diff spatial_DGMM.xml @ 2:db423b7bce78 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c
author | galaxyp |
---|---|
date | Thu, 04 Jul 2024 13:43:40 +0000 |
parents | 4cb6c83d3777 |
children |
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--- a/spatial_DGMM.xml Wed Apr 19 22:40:35 2023 +0000 +++ b/spatial_DGMM.xml Thu Jul 04 13:43:40 2024 +0000 @@ -1,11 +1,9 @@ -<tool id="cardinal_single_ion_segmentation" name="MSI single ion segmentation" version="@VERSION@.0"> +<tool id="cardinal_single_ion_segmentation" name="MSI single ion segmentation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> <description>mass spectrometry imaging spatial DGMM</description> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"> - <requirement type="package" version="2.3">r-gridextra</requirement> - </expand> + <expand macro="requirements"/> <command detect_errors="exit_code"> <![CDATA[ @@ -66,7 +64,6 @@ ## set seed to make analysis reproducible set.seed($setseed) - ## single ion segmentation dgmm <- spatialDGMM(msidata, @@ -156,7 +153,7 @@ <expand macro="reading_pixel_annotations"/> </when> </conditional> - <param name="r" type="text" value="2" + <param name="r" type="text" value="2" label="r" help="The spatial neighborhood radius of nearby pixels to consider. Only a single value is allowed"> <expand macro="sanitizer_multiple_digits"/> </param> @@ -213,56 +210,82 @@ </collection> </outputs> <tests> - <test> - <param name="infile" value="" ftype="imzml"> - <composite_data value="spatial_DGMM_input.imzML"/> - <composite_data value="spatial_DGMM_input.ibd"/> - </param> - <param name="r" value="1"/> - <param name="k" value="6"/> - <param name="method" value="adaptive"/> - <param name="dist" value="radial"/> - <param name="annealing" value="TRUE"/> + <test expect_num_outputs="4"> + <param name="infile" value="" ftype="imzml"> + <composite_data value="spatial_DGMM_input.imzML"/> + <composite_data value="spatial_DGMM_input.ibd"/> + </param> + <param name="r" value="1"/> + <param name="k" value="6"/> + <param name="method" value="adaptive"/> + <param name="dist" value="radial"/> + <param name="annealing" value="TRUE"/> + <param name="setseed" value="7353"/> <param name="output_estimates" value="True"/> <param name="output_probability" value="True"/> - <output name="file_info" file="dgmm_test1.pdf" compare="sim_size"/> - <output name="dgmm_summary" file="dgmm_summary1.tabular"/> - <output_collection name="estimates_output" type="list" count="10"> - <element name="estimates_r1_k6_mz1135.93347167969" file="estimates_r1_k6_mz1135.93347167969.tabular"/> + <output name="file_info" file="dgmm_test1.pdf" compare="sim_size"/> + <output name="dgmm_summary" file="dgmm_summary1.tabular"/> + <output_collection name="estimates_output" type="list" count="10"> + <element name="estimates_r1_k6_mz1135.93347167969"> + <assert_contents> + <has_text text="files_"/> + <has_text text="3"/> + <has_text_matching expression="0\.\d+"/> + </assert_contents> + </element> </output_collection> <output_collection name="probability_output" type="list" count="10"> - <element name="probability_r1_k6_mz1023.70806884766" file="probability_r1_k6_mz1023.70806884766.tabular"/> + <element name="probability_r1_k6_mz1023.70806884766"> + <assert_contents> + <has_text text="xy_16_1"/> + <has_text text="3"/> + <has_text_matching expression="0\.\d+"/> + </assert_contents> + </element> </output_collection> </test> - <test> - <param name="infile" value="" ftype="imzml"> - <composite_data value="spatial_DGMM_input.imzML"/> - <composite_data value="spatial_DGMM_input.ibd"/> - </param> - <conditional name="sample_groups"> - <param name="group" value="multiple_groups"/> - <param name="annotation_file" value="DGMM_annotations.tabular"/> - <param name="column_x" value="1"/> - <param name="column_y" value="2"/> - <param name="column_names" value="3"/> - <param name="tabular_header" value="True"/> - </conditional> - <param name="r" value="2"/> - <param name="k" value="10"/> - <param name="annealing" value="TRUE"/> - <param name="output_estimates" value="True"/> - <param name="output_probability" value="True"/> - <param name="output_plots" value="True"/> - <param name="output_rdata" value="True"/> - <output name="file_info" file="dgmm_test2.pdf" compare="sim_size"/> - <output name="dgmm_summary" file="dgmm_summary2.tabular"/> - <output name="dgmm_rdata" file="dgmm_test2.RData" compare="sim_size"/> - <output_collection name="estimates_output" type="list" count="10"> - <element name="estimates_r2_k10_mz1200.46533203125" file="estimates_r2_k10_mz1200.46533203125.tabular"/> - </output_collection> - <output_collection name="probability_output" type="list" count="10"> - <element name="probability_r2_k10_mz1135.93347167969" file="probability_r2_k10_mz1135.93347167969.tabular"/> - </output_collection> + <test expect_num_outputs="6"> + <param name="infile" value="" ftype="imzml"> + <composite_data value="spatial_DGMM_input.imzML"/> + <composite_data value="spatial_DGMM_input.ibd"/> + </param> + <conditional name="sample_groups"> + <param name="group" value="multiple_groups"/> + <param name="annotation_file" value="DGMM_annotations.tabular"/> + <param name="column_x" value="1"/> + <param name="column_y" value="2"/> + <param name="column_names" value="3"/> + <param name="tabular_header" value="True"/> + </conditional> + <param name="r" value="2"/> + <param name="k" value="10"/> + <param name="annealing" value="TRUE"/> + <param name="setseed" value="7353"/> + <param name="output_estimates" value="True"/> + <param name="output_probability" value="True"/> + <param name="output_plots" value="True"/> + <param name="output_rdata" value="True"/> + <output name="file_info" file="dgmm_test2.pdf" compare="sim_size"/> + <output name="dgmm_summary" file="dgmm_summary2.tabular"/> + <output name="dgmm_rdata" file="dgmm_test2.RData" compare="sim_size"/> + <output_collection name="estimates_output" type="list" count="10"> + <element name="estimates_r2_k10_mz1200.46533203125"> + <assert_contents> + <has_text text="circle"/> + <has_text text="3"/> + <has_text_matching expression="0\.\d+"/> + </assert_contents> + </element> + </output_collection> + <output_collection name="probability_output" type="list" count="10"> + <element name="probability_r2_k10_mz1135.93347167969"> + <assert_contents> + <has_text text="xy_9_1"/> + <has_text text="3"/> + <has_text_matching expression="0\.\d+"/> + </assert_contents> + </element> + </output_collection> </test> </tests> <help>