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annotate quantification.xml @ 0:928db0f952e3 draft

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"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit a4349062e9177b5e60fb7c49115c57299e0d648d-dirty"
author perssond
date Fri, 12 Mar 2021 00:19:24 +0000
parents
children aba3655fdef0
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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' '${mask.name}'.ome.tiff;
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15 #end for
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17 mkdir ./tool_out;
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19 @CMD_BEGIN@
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21 --masks
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22 '${primary_mask.name}'.ome.tiff
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23 #if $supp_masks
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24 #for $mask in $supp_masks:
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25 '${mask.name}'.ome.tiff
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26 #end for
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27 #end if
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28
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29 --image '${image.name}'.ome.tiff
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30 --output ./tool_out
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31 --channel_names '$channel_names';
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32
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33 mv ./tool_out/*.csv ./tool_out/quantified.csv;
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34 ]]></command>
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35
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36 <inputs>
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37 <param name="image" type="data" format="tiff" label="Registered TIFF"/>
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38 <param name="primary_mask" type="data" format="tiff" label="Primary Cell Mask"/>
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39 <param name="supp_masks" type="data" multiple="true" optional="true" format="tiff" label="Additional Cell Masks"/>
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40 <param name="channel_names" type="data" format="csv" label="Marker Channels"/>
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41 </inputs>
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42
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43 <outputs>
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44 <data format="csv" name="quant_out" from_work_dir="./tool_out/quantified.csv" label="${tool.name} on ${on_string}"/>
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45 </outputs>
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46 <help><![CDATA[
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47 # Single cell quantification
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48 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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49
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50 **CommandSingleCellExtraction.py**:
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51
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52 * `--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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53
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54 * `--image` Path to image(s) for quantification. (Ex: ./registration/*.h5) -> works with .h(df)5 or .tif(f)
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55
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56 * `--output` Path to output directory. (Ex: ./feature_extraction)
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57
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58 * `--channel_names` csv file containing the channel names for the z-stack (Ex: ./my_channels.csv)
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59
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60 # Run script
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61 `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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62
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63 # Main developer
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64 Denis Schapiro (https://github.com/DenisSch)
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65
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66 Joshua Hess (https://github.com/JoshuaHess12)
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67
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68 Jeremy Muhlich (https://github.com/jmuhlich)
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69 ]]></help>
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70 <expand macro="citations" />
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71 </tool>