Mercurial > repos > perssond > quantification
view quantification.xml @ 1:aba3655fdef0 draft
"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 897a7dc7cb43e45d6f0fdfe2b2970e59f20f8853"
author | watsocam |
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date | Fri, 11 Mar 2022 23:35:52 +0000 |
parents | 928db0f952e3 |
children | 46b897eb2c8e |
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<tool id="quantification" name="Quantification" version="@VERSION@.5" profile="17.09"> <description>Single cell quantification, a module for single-cell data extraction given a segmentation mask and multi-channel image.</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> @VERSION_CMD@ <command detect_errors="exit_code"><![CDATA[ ln -s '$image' '${image.name}'.ome.tiff; ln -s '$primary_mask' '${primary_mask.name}'.ome.tiff; #for $mask in $supp_masks: ln -s '$mask' '${mask.name}'.ome.tiff; #end for mkdir ./tool_out; @CMD_BEGIN@ python \$QUANT_PATH --masks '${primary_mask.name}'.ome.tiff #if $supp_masks #for $mask in $supp_masks: '${mask.name}'.ome.tiff #end for #end if --image '${image.name}'.ome.tiff --output ./tool_out #if $mask_props --mask_props $mask_props #end if #if $intensity_props --intensity_props $intensity_props #end if --channel_names '$channel_names'; cp tool_out/*cellMasks.csv cellMasks.csv ]]></command> <inputs> <param name="image" type="data" format="tiff" label="Registered TIFF"/> <param name="primary_mask" type="data" format="tiff" label="Primary Cell Mask"/> <param name="supp_masks" type="data" multiple="true" optional="true" format="tiff" label="Additional Cell Masks"/> <param name="channel_names" type="data" format="csv" label="Marker Channels"/> <param name="mask_props" type="text" label="Mask Metrics" help="Space separated list of additional metrics to be calculated for every mask."/> <param name="intensity_props" type="text" label="Intensity Metrics" help="Space separated list of additional metrics to be calculated for every marker separately."/> </inputs> <outputs> <data format="csv" name="cellmask" from_work_dir="cellMasks.csv" label="CellMaskQuant"/> <collection type="list" name="quantification" label="${tool.name} on ${on_string}"> <discover_datasets pattern="__designation_and_ext__" format="csv" directory="tool_out/" visible="true"/> </collection> </outputs> <help><![CDATA[ # Single cell quantification Module for single-cell data extraction given a segmentation mask and multi-channel image. The CSV structure is aligned with histoCAT output. **CommandSingleCellExtraction.py**: * `--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 * `--image` Path to image(s) for quantification. (Ex: ./registration/*.h5) -> works with .h(df)5 or .tif(f) * `--output` Path to output directory. (Ex: ./feature_extraction) * `--channel_names` csv file containing the channel names for the z-stack (Ex: ./my_channels.csv) # Run script `python CommandSingleCellExtraction.py --masks ./segmentation/cellMask.tif ./segmentation/membraneMask.tif --image ./registration/Exemplar_001.h5 --output ./feature_extraction --channel_names ./my_channels.csv` # Main developer Denis Schapiro (https://github.com/DenisSch) Joshua Hess (https://github.com/JoshuaHess12) Jeremy Muhlich (https://github.com/jmuhlich) ]]></help> <expand macro="citations" /> </tool>