Mercurial > repos > perssond > quantification
annotate quantification.xml @ 3:c09e444635d9 draft
"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 98cddbe59b6834a2368a0085b3938d5058f6d10b"
author | watsocam |
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date | Thu, 07 Apr 2022 16:54:04 +0000 |
parents | 46b897eb2c8e |
children | 261464223fa3 |
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3
c09e444635d9
"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 98cddbe59b6834a2368a0085b3938d5058f6d10b"
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1 <tool id="quantification" name="Quantification" version="@VERSION@.7" 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> |
928db0f952e3
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3 <macros> |
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4 <import>macros.xml</import> |
928db0f952e3
"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
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5 </macros> |
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6 |
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7 <expand macro="requirements"/> |
928db0f952e3
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8 @VERSION_CMD@ |
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9 |
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10 <command detect_errors="exit_code"><![CDATA[ |
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11 ln -s $image input.ome.tiff; |
46b897eb2c8e
"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 150f21e52974f99ec39bf92d9e7e611861860d0f"
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12 ln -s $primary_mask primary_mask.tiff; |
46b897eb2c8e
"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 150f21e52974f99ec39bf92d9e7e611861860d0f"
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13 #if $supp_masks |
46b897eb2c8e
"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 150f21e52974f99ec39bf92d9e7e611861860d0f"
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14 ln -s $supp_masks supp_mask.tiff; |
46b897eb2c8e
"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 150f21e52974f99ec39bf92d9e7e611861860d0f"
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15 #end if |
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16 |
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17 mkdir ./tool_out; |
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"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
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18 |
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19 @CMD_BEGIN@ |
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20 |
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21 python \$QUANT_PATH |
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22 --masks |
46b897eb2c8e
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23 primary_mask.tiff |
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24 #if $supp_masks |
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25 supp_mask.tiff |
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26 #end if |
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27 |
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28 --image input.ome.tiff |
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29 --output ./tool_out |
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"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 150f21e52974f99ec39bf92d9e7e611861860d0f"
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30 |
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31 #if $mask_props |
aba3655fdef0
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32 --mask_props $mask_props |
aba3655fdef0
"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 897a7dc7cb43e45d6f0fdfe2b2970e59f20f8853"
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33 #end if |
aba3655fdef0
"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 897a7dc7cb43e45d6f0fdfe2b2970e59f20f8853"
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34 #if $intensity_props |
aba3655fdef0
"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 897a7dc7cb43e45d6f0fdfe2b2970e59f20f8853"
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35 --intensity_props $intensity_props |
aba3655fdef0
"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 897a7dc7cb43e45d6f0fdfe2b2970e59f20f8853"
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36 #end if |
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"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 897a7dc7cb43e45d6f0fdfe2b2970e59f20f8853"
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37 |
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38 --channel_names '$channel_names'; |
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"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
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39 |
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40 cp tool_out/*primary_mask.csv primary_mask.csv |
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41 ]]></command> |
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42 |
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43 <inputs> |
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44 <param name="image" type="data" format="tiff" label="Registered TIFF"/> |
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"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
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45 <param name="primary_mask" type="data" format="tiff" label="Primary Cell Mask"/> |
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"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 150f21e52974f99ec39bf92d9e7e611861860d0f"
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46 <param name="supp_masks" type="data" optional="true" format="tiff" label="Additional Cell Masks"/> |
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47 <param name="channel_names" type="data" format="csv" label="Marker Channels"/> |
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48 <param name="mask_props" type="text" label="Mask Metrics" help="Space separated list of additional metrics to be calculated for every mask."/> |
aba3655fdef0
"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 897a7dc7cb43e45d6f0fdfe2b2970e59f20f8853"
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49 <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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50 </inputs> |
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51 |
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52 <outputs> |
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53 <data format="csv" name="cellmask" from_work_dir="primary_mask.csv" label="CellMaskQuant"/> |
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54 <collection type="list" name="quantification" label="${tool.name} on ${on_string}"> |
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55 <discover_datasets pattern="__designation_and_ext__" format="csv" directory="tool_out/" visible="false"/> |
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56 </collection> |
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57 </outputs> |
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58 <help><![CDATA[ |
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59 # Single cell quantification |
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60 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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"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
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61 |
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62 **CommandSingleCellExtraction.py**: |
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63 |
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64 * `--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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"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
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65 |
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66 * `--image` Path to image(s) for quantification. (Ex: ./registration/*.h5) -> works with .h(df)5 or .tif(f) |
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67 |
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68 * `--output` Path to output directory. (Ex: ./feature_extraction) |
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69 |
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70 * `--channel_names` csv file containing the channel names for the z-stack (Ex: ./my_channels.csv) |
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71 |
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72 # Run script |
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73 `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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74 |
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75 # Main developer |
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76 Denis Schapiro (https://github.com/DenisSch) |
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77 |
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78 Joshua Hess (https://github.com/JoshuaHess12) |
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79 |
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80 Jeremy Muhlich (https://github.com/jmuhlich) |
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81 ]]></help> |
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82 <expand macro="citations" /> |
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83 </tool> |