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"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 897a7dc7cb43e45d6f0fdfe2b2970e59f20f8853"
author watsocam
date Fri, 11 Mar 2022 23:35:52 +0000
parents 928db0f952e3
children 46b897eb2c8e
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1 <tool id="quantification" name="Quantification" version="@VERSION@.5" profile="17.09">
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2 <description>Single cell quantification, a module for single-cell data extraction given a segmentation mask and multi-channel image.</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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7 <expand macro="requirements"/>
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8 @VERSION_CMD@
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10 <command detect_errors="exit_code"><![CDATA[
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11 ln -s '$image' '${image.name}'.ome.tiff;
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12 ln -s '$primary_mask' '${primary_mask.name}'.ome.tiff;
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13 #for $mask in $supp_masks:
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14 ln -s '$mask' '${mask.name}'.ome.tiff;
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15 #end for
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17 mkdir ./tool_out;
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19 @CMD_BEGIN@
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21 python \$QUANT_PATH
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22 --masks
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23 '${primary_mask.name}'.ome.tiff
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24 #if $supp_masks
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25 #for $mask in $supp_masks:
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26 '${mask.name}'.ome.tiff
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27 #end for
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28 #end if
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30 --image '${image.name}'.ome.tiff
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31 --output ./tool_out
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33 #if $mask_props
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34 --mask_props $mask_props
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35 #end if
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36 #if $intensity_props
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37 --intensity_props $intensity_props
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38 #end if
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39
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40 --channel_names '$channel_names';
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41
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42 cp tool_out/*cellMasks.csv cellMasks.csv
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43 ]]></command>
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44
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45 <inputs>
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46 <param name="image" type="data" format="tiff" label="Registered TIFF"/>
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47 <param name="primary_mask" type="data" format="tiff" label="Primary Cell Mask"/>
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48 <param name="supp_masks" type="data" multiple="true" optional="true" format="tiff" label="Additional Cell Masks"/>
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49 <param name="channel_names" type="data" format="csv" label="Marker Channels"/>
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50 <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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51 <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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52 </inputs>
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53
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54 <outputs>
1
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55 <data format="csv" name="cellmask" from_work_dir="cellMasks.csv" label="CellMaskQuant"/>
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56 <collection type="list" name="quantification" label="${tool.name} on ${on_string}">
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57 <discover_datasets pattern="__designation_and_ext__" format="csv" directory="tool_out/" visible="true"/>
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58 </collection>
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59 </outputs>
0
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60 <help><![CDATA[
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61 # Single cell quantification
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62 Module for single-cell data extraction given a segmentation mask and multi-channel image. The CSV structure is aligned with histoCAT output.
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63
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64 **CommandSingleCellExtraction.py**:
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65
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66 * `--masks` Paths to where masks are stored (Ex: ./segmentation/cellMask.tif) -> If multiple masks are selected the first mask will be used for spatial feature extraction but all will be quantified
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67
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68 * `--image` Path to image(s) for quantification. (Ex: ./registration/*.h5) -> works with .h(df)5 or .tif(f)
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69
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70 * `--output` Path to output directory. (Ex: ./feature_extraction)
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71
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72 * `--channel_names` csv file containing the channel names for the z-stack (Ex: ./my_channels.csv)
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73
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74 # Run script
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75 `python CommandSingleCellExtraction.py --masks ./segmentation/cellMask.tif ./segmentation/membraneMask.tif --image ./registration/Exemplar_001.h5 --output ./feature_extraction --channel_names ./my_channels.csv`
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76
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77 # Main developer
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78 Denis Schapiro (https://github.com/DenisSch)
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79
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80 Joshua Hess (https://github.com/JoshuaHess12)
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81
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82 Jeremy Muhlich (https://github.com/jmuhlich)
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83 ]]></help>
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84 <expand macro="citations" />
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85 </tool>