| Previous changeset 1:aba3655fdef0 (2022-03-11) Next changeset 3:c09e444635d9 (2022-04-07) |
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Commit message:
"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 150f21e52974f99ec39bf92d9e7e611861860d0f" |
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modified:
quantification.xml |
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| diff -r aba3655fdef0 -r 46b897eb2c8e quantification.xml --- a/quantification.xml Fri Mar 11 23:35:52 2022 +0000 +++ b/quantification.xml Wed Mar 30 16:56:29 2022 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="quantification" name="Quantification" version="@VERSION@.5" profile="17.09"> +<tool id="quantification" name="Quantification" version="@VERSION@.6" 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> @@ -8,28 +8,26 @@ @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 + ln -s $image input.ome.tiff; + ln -s $primary_mask primary_mask.tiff; + #if $supp_masks + ln -s $supp_masks supp_mask.tiff; + #end if mkdir ./tool_out; @CMD_BEGIN@ - + python \$QUANT_PATH - --masks - '${primary_mask.name}'.ome.tiff + --masks + primary_mask.tiff #if $supp_masks - #for $mask in $supp_masks: - '${mask.name}'.ome.tiff - #end for + supp_mask.tiff #end if - --image '${image.name}'.ome.tiff + --image input.ome.tiff --output ./tool_out - + #if $mask_props --mask_props $mask_props #end if @@ -39,22 +37,22 @@ --channel_names '$channel_names'; - cp tool_out/*cellMasks.csv cellMasks.csv + cp tool_out/*primary_mask.csv primary_mask.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="supp_masks" type="data" 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"/> + <data format="csv" name="cellmask" from_work_dir="primary_mask.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"/> + <discover_datasets pattern="__designation_and_ext__" format="csv" directory="tool_out/" visible="true"/> </collection> </outputs> <help><![CDATA[ |