Mercurial > repos > goeckslab > cell_intensity_processing

annotate process_intensities.xml @ 2:7f93f472a242 draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 130ef7e8ae6cab35866b72617e53d35acc11475a
author goeckslab
date Wed, 28 Feb 2024 20:52:16 +0000
parents 34bb79f271fc
children 4f5abe01531c
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1 <tool id="cell_intensity_processing" name="Process single-cell intensities" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
2
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6 <edam_operations>
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7 <edam_operation>operation_3443</edam_operation>
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8 </edam_operations>
0
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9 <expand macro="requirements" />
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10 <command detect_errors="aggressive"><![CDATA[
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12 ln -s '$quant_table' ./quant.csv &&
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14 python '$script'
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16 ]]></command>
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17 <configfiles>
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18 <configfile name = "script">
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19 import os
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20 import numpy as np
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21 import pandas as pd
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23 cwd = os.getcwd()
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24 quant = pd.read_csv(os.path.join(cwd, 'quant.csv'), index_col = 0)
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25 marker_df = pd.read_csv('$channel_csv')
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27 markers_to_normalize = marker_df['marker_name'].to_list()
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29 for marker in markers_to_normalize:
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31 #if $exp.exposure == 'correct_exposure':
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32 exp_time = marker_df.loc[marker_df['marker_name'] == marker, '${exp.exp_col}'].values[0]
34bb79f271fc planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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33 quant[marker] = quant[marker] / exp_time
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34 #end if
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36 #if $AF_method.select_method == 'dont_adjust':
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37 pass
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38 #elif $AF_method.select_method == 'subtract':
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39 current_AF_channel = marker_df.loc[marker_df['marker_name'] == marker, '${AF_method.AF_col}'].values[0]
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40 if current_AF_channel in markers_to_normalize:
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41 quant[marker] = quant[marker] - quant[current_AF_channel]
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42 quant[marker] = np.where(quant[marker] &lt; 0, 0, quant[marker])
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43 #elif $AF_method.select_method == 'SBR':
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44 current_AF_channel = marker_df.loc[marker_df['marker_name'] == marker, '${AF_method.AF_col}'].values[0]
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45 if current_AF_channel in markers_to_normalize:
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46 quant[marker] = quant[marker] / quant[current_AF_channel]
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47 #end if
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48
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49 quant.to_csv(os.path.join(cwd, 'processed_quant.csv'))
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50 </configfile>
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51 </configfiles>
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52 <inputs>
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53 <param name="quant_table" type="data" format="csv" label="Input quantification table (csv)" />
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54 <param name="channel_csv" type="data" format="csv" label="Channel Metadata (csv)" />
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55 <conditional name="exp">
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56 <param name="exposure" type="select" label="Select whether to divide intensities by exposure times">
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57 <option value="dont_correct_exposure">No exposure correction</option>
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58 <option value="correct_exposure">Exposure correction</option>
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59 </param>
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60 <when value="dont_correct_exposure" />
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61 <when value="correct_exposure">
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62 <param name="exp_col" type="text" value="exposure_time" label="Name of column in markers file containing exposure times" />
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63 </when>
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64 </conditional>
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65 <conditional name="AF_method">
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66 <param name="select_method" type="select" label="Select method of autofluorescence/background adjustment">
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67 <option value="dont_adjust">No AF/background adjustment</option>
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68 <option value="subtract">Autofluorescence subtraction</option>
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69 <option value="SBR">Signal-to-background ratio</option>
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70 </param>
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71 <when value="dont_adjust" />
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72 <when value="subtract">
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73 <param name="AF_col" type="text" value="AF_channel" label="Name of column in markers file containing respective AF channel for each marker" />
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74 </when>
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75 <when value="SBR">
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76 <param name="AF_col" type="text" value="AF_channel" label="Name of column in markers file containing respective AF channel for each marker" />
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77 </when>
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78 </conditional>
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79 </inputs>
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80 <outputs>
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81 <data name="processed_quant" from_work_dir="processed_quant.csv" format="csv"/>
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82 </outputs>
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83 <tests>
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84 <test>
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85 <param name="quant_table" value="intensities.csv" />
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86 <param name="channel_csv" value="intensity_channels.csv" />
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87 <conditional name="exp">
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88 <param name="exposure" value="correct_exposure" />
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89 </conditional>
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90 <conditional name="AF_method">
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91 <param name="select_method" value="SBR" />
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92 </conditional>
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93 <output name="processed_quant" ftype="csv">
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94 <assert_contents>
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95 <has_n_columns n="15" sep="," />
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96 <has_n_lines n="15" />
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97 </assert_contents>
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98 </output>
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99 </test>
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100 </tests>
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101 <help><![CDATA[
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102 This tool can be used to perform several different common signal processing operations for single-cell mean marker intensities from multiplex
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103 tissue imaging data.
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104
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105 **Inputs**
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106 1. Comma-separated feature observation matrix that is generated by **MCQuant**
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107 2. Comma-separated channel metadata file that maps marker names to exposure times (optional) and respective AF/bg channels (optional)
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108
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109 **Options**
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110 1. Exposure correction - Divide single-cell intensities by respective exposure time in channel metadata
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111 2. Background subtraction - Subtract single-cell mmean marker intensities by respective AF/bg channel mean intensity specified in channel metadata
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112 3. Signal-to-background ratio - Divide single-cell mmean marker intensities by respective AF/bg channel mean intensity specified in channel metadata
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113
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114 **Outputs**
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115 1. Feature observation matrix with processed intensities for all markers in channel metadata file. CellIDs, centroids, and morphological data remain unchanged.
0
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116 ]]></help>
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117 <expand macro="citations" />
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118 </tool>