comparison spatial_DGMM.xml @ 2:db423b7bce78 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 91e77c139cb3b7c6d67727dc39140dd79355fa0c

1:53a2f4fa6cd2

<tool id="cardinal_single_ion_segmentation" name="MSI single ion segmentation" version="@VERSION@.0">
    <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>
    <command detect_errors="exit_code">
    <![CDATA[

        @INPUT_LINKING@
        cat '${MSI_spatial_DGMM}' &&

if (npeaks > 0)
{
        
    ## set seed to make analysis reproducible
    set.seed($setseed)
    

    ## single ion segmentation
    dgmm <- spatialDGMM(msidata, 
            r = c($r),
            k = c($k), 

                <when value="single_group"/>
                <when value="multiple_groups">
                    <expand macro="reading_pixel_annotations"/>
                </when>
            </conditional>
	    <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>
            <param name="k" type="text" value="5"
                   label="k" help="The maximum number of segments (clusters). The final number of segments may differ. Only a single value is allowed.">

            <filter>output_plots</filter>
            <discover_datasets pattern="__designation_and_ext__" directory="DGMM_plots" format="tabular"/>
        </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"/>
            <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_collection>
            <output_collection name="probability_output" type="list" count="10">
                <element name="probability_r1_k6_mz1023.70806884766" file="probability_r1_k6_mz1023.70806884766.tabular"/>
            </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>         
    </tests>
    <help>
        <![CDATA[

2:db423b7bce78

<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"/>
    <command detect_errors="exit_code">
    <![CDATA[

        @INPUT_LINKING@
        cat '${MSI_spatial_DGMM}' &&

if (npeaks > 0)
{
        
    ## set seed to make analysis reproducible
    set.seed($setseed)

    ## single ion segmentation
    dgmm <- spatialDGMM(msidata, 
            r = c($r),
            k = c($k), 

                <when value="single_group"/>
                <when value="multiple_groups">
                    <expand macro="reading_pixel_annotations"/>
                </when>
            </conditional>
	        <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>
            <param name="k" type="text" value="5"
                   label="k" help="The maximum number of segments (clusters). The final number of segments may differ. Only a single value is allowed.">

            <filter>output_plots</filter>
            <discover_datasets pattern="__designation_and_ext__" directory="DGMM_plots" format="tabular"/>
        </collection>
    </outputs>
    <tests>
        <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">
                    <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">
                    <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 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>
        <![CDATA[