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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/quantification commit 4a521310a7989b781380c20e1aab3ac13ca86dff
author goeckslab
date Tue, 02 Jul 2024 17:48:30 +0000
parents 3a916c4e9f5f
children
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1 <tool id="quantification" name="MCQUANT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01">
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2 <description>a module for single-cell data extraction</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version_cmd"/>
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9 <command detect_errors="aggressive"><![CDATA[
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10 ln -s '$image' 'input.ome.tiff' &&
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11 ln -s '$primary_mask' 'primary_mask.tiff' &&
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12 #if $supp_mask
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13 ln -s '$supp_mask' 'supp_mask.tiff' &&
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14 #end if
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16 mkdir './tool_out' &&
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18 @CMD_BEGIN@
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20 --masks 'primary_mask.tiff'
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21 #if $supp_mask
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22 'supp_mask.tiff'
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23 #end if
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25 --image 'input.ome.tiff'
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26 --output './tool_out'
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28 #if str($mask_props).strip()
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29 --mask_props '$mask_props'
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30 #end if
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31 #if str($intensity_props).strip()
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32 --intensity_props '$intensity_props'
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33 #end if
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34
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35 --channel_names '$channel_names' &&
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37 #if $supp_mask
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38 mv tool_out/*supp_mask.csv supp_mask.csv &&
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39 #end if
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41 mv tool_out/*primary_mask.csv primary_mask.csv
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42 ]]></command>
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44 <inputs>
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45 <param name="image" type="data" format="tiff" label="Registered TIFF"/>
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46 <param name="primary_mask" type="data" format="tiff" label="Primary Mask"/>
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47 <param name="supp_mask" type="data" optional="true" format="tiff" label="Additional Mask"/>
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48 <param name="channel_names" type="data" format="csv" label="Marker Channels"/>
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49 <param name="mask_props" type="text" label="Mask Metrics" help="Space separated list of additional metrics to be calculated for every mask."/>
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50 <param name="intensity_props" type="text" label="Intensity Metrics" help="Space separated list of additional metrics to be calculated for every marker separately."/>
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51 </inputs>
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52
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53 <outputs>
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54 <data format="csv" name="cellmask" from_work_dir="primary_mask.csv" label="Primary Mask Quantification"/>
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55 <data format="csv" name="suppmask" from_work_dir="supp_mask.csv" label="Supplemental Mask Quantification">
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56 <filter>supp_mask</filter>
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57 </data>
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58 </outputs>
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59 <tests>
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60 <test expect_num_outputs="2">
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61 <param name="image" value="test.tiff" />
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62 <param name="primary_mask" value="mask.tiff" />
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63 <param name="supp_mask" value="supp_mask.tiff" />
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64 <param name="channel_names" value="channels.csv" />
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65 <output name="cellmask" ftype="csv">
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66 <assert_contents>
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67 <has_n_lines n="264" delta="1" />
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68 </assert_contents>
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69 </output>
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70 <output name="suppmask" ftype="csv">
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71 <assert_contents>
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72 <has_n_lines n="264" delta="1" />
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73 </assert_contents>
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74 </output>
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75 </test>
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76 </tests>
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77 <help><![CDATA[
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78
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79 --------
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80 MCQUANT
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81 --------
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82 **MCQUANT** module for single cell quantification given a segmentation mask and multi-channel image. The CSV structure is aligned with histoCAT output.
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83
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84 **Inputs**
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85 1. A fully stitched and registered image in .ome.tif format. Nextflow will use images in the registration/ and dearray/ subfolders as appropriate.
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86 2. One or more segmentation masks in .tif format. Nextflow will use files in the segmentation/ subfolder within the project.
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87 3. A .csv file containing a marker_name column specifying names of individual channels. Nextflow will look for this file in the project directory.
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88
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89 **Outputs**
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90 A cell-by-feature table mapping Cell IDs to marker expression and morphological features (including x,y coordinates).
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92 ]]></help>
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93 <expand macro="citations" />
928db0f952e3 "planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
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94 </tool>