comparison process_intensities.xml @ 2:7f93f472a242 draft

planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 130ef7e8ae6cab35866b72617e53d35acc11475a

1:7a77ed0e579a

<tool id="cell_intensity_processing" name="Process single-cell intensities" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Options to correct for exposure time, autofluorescence subtraction, or compute signal-to-background ratio.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="aggressive"><![CDATA[
        
        ln -s '$quant_table' ./quant.csv &&

1. Exposure correction - Divide single-cell intensities by respective exposure time in channel metadata
2. Background subtraction - Subtract single-cell mmean marker intensities by respective AF/bg channel mean intensity specified in channel metadata
3. Signal-to-background ratio - Divide single-cell mmean marker intensities by respective AF/bg channel mean intensity specified in channel metadata

**Outputs**
1. Feature observation matrix with processed intensities for all markers in channel metadata file. 
   CellIDs, centroids, and morphological data remain unchanged.
    ]]></help>
    <expand macro="citations" />
</tool>

2:7f93f472a242

<tool id="cell_intensity_processing" name="Process single-cell intensities" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <expand macro="requirements" />
    <command detect_errors="aggressive"><![CDATA[
        
        ln -s '$quant_table' ./quant.csv &&

1. Exposure correction - Divide single-cell intensities by respective exposure time in channel metadata
2. Background subtraction - Subtract single-cell mmean marker intensities by respective AF/bg channel mean intensity specified in channel metadata
3. Signal-to-background ratio - Divide single-cell mmean marker intensities by respective AF/bg channel mean intensity specified in channel metadata

**Outputs**
1. Feature observation matrix with processed intensities for all markers in channel metadata file. CellIDs, centroids, and morphological data remain unchanged.
    ]]></help>
    <expand macro="citations" />
</tool>