diff process_intensities.xml @ 0:34bb79f271fc draft

planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/process_intensities.xml	Thu Sep 29 16:53:01 2022 +0000
@@ -0,0 +1,116 @@
+<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 '$quant_table' ./quant.csv &&
+
+        python '$script'
+
+    ]]></command>
+    <configfiles>
+        <configfile name = "script">
+import os
+import numpy as np
+import pandas as pd
+
+cwd = os.getcwd()
+quant = pd.read_csv(os.path.join(cwd, 'quant.csv'), index_col = 0)
+marker_df = pd.read_csv('$channel_csv')
+
+markers_to_normalize = marker_df['marker_name'].to_list()
+
+for marker in markers_to_normalize:
+
+#if $exp.exposure == 'correct_exposure':
+    exp_time = marker_df.loc[marker_df['marker_name'] == marker, '${exp.exp_col}'].values[0]
+    quant[marker] = quant[marker] / exp_time
+#end if
+
+#if $AF_method.select_method == 'dont_adjust':
+    pass
+#elif $AF_method.select_method == 'subtract':
+    current_AF_channel = marker_df.loc[marker_df['marker_name'] == marker, '${AF_method.AF_col}'].values[0]
+    if current_AF_channel in markers_to_normalize:
+        quant[marker] = quant[marker] - quant[current_AF_channel]
+        quant[marker] = np.where(quant[marker] &lt; 0, 0, quant[marker])
+#elif $AF_method.select_method == 'SBR':
+    current_AF_channel = marker_df.loc[marker_df['marker_name'] == marker, '${AF_method.AF_col}'].values[0]
+    if current_AF_channel in markers_to_normalize:
+        quant[marker] = quant[marker] / quant[current_AF_channel]
+#end if
+
+quant.to_csv(os.path.join(cwd, 'processed_quant.csv'))
+        </configfile>
+    </configfiles>
+    <inputs>
+        <param name="quant_table" type="data" format="csv" label="Input quantification table (csv)" />
+        <param name="channel_csv" type="data" format="csv" label="Channel Metadata (csv)" />
+        <conditional name="exp">
+            <param name="exposure" type="select" label="Select whether to divide intensities by exposure times">
+                <option value="dont_correct_exposure">No exposure correction</option>
+                <option value="correct_exposure">Exposure correction</option>
+            </param>
+            <when value="dont_correct_exposure" />
+            <when value="correct_exposure">
+                <param name="exp_col" type="text" value="exposure_time" label="Name of column in markers file containing exposure times" />
+            </when>
+        </conditional>
+        <conditional name="AF_method">
+            <param name="select_method" type="select" label="Select method of autofluorescence/background adjustment">
+                <option value="dont_adjust">No AF/background adjustment</option>
+                <option value="subtract">Autofluorescence subtraction</option>
+                <option value="SBR">Signal-to-background ratio</option>
+            </param>
+            <when value="dont_adjust" />
+            <when value="subtract">
+                <param name="AF_col" type="text" value="AF_channel" label="Name of column in markers file containing respective AF channel for each marker" />
+            </when>
+            <when value="SBR">
+                <param name="AF_col" type="text" value="AF_channel" label="Name of column in markers file containing respective AF channel for each marker" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="processed_quant" from_work_dir="processed_quant.csv" format="csv"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="quant_table" value="intensities.csv" />
+            <param name="channel_csv" value="intensity_channels.csv" />
+            <conditional name="exp">
+                <param name="exposure" value="correct_exposure" />
+            </conditional>
+            <conditional name="AF_method">
+                <param name="select_method" value="SBR" />
+            </conditional>
+            <output name="processed_quant" ftype="csv">
+                <assert_contents>
+                    <has_n_columns n="15" sep="," />
+                    <has_n_lines n="15" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+This tool can be used to perform several different common signal processing operations for single-cell mean marker intensities from multiplex
+tissue imaging data.
+
+**Inputs**
+1. Comma-separated feature observation matrix that is generated by **MCQuant**
+2. Comma-separated channel metadata file that maps marker names to exposure times (optional) and respective AF/bg channels (optional)
+
+**Options**
+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>
\ No newline at end of file