Mercurial > repos > lldelisle > incucyte_stack_and_upload_omero
diff incucyte_stack_and_upload_omero.xml @ 0:e1cba36becb2 draft
planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero commit 4ac9b1d66ba6857357867c8eccb6c9d1ad603364
| author | lldelisle |
|---|---|
| date | Tue, 19 Dec 2023 15:02:41 +0000 |
| parents | |
| children | 3c942429f610 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/incucyte_stack_and_upload_omero.xml Tue Dec 19 15:02:41 2023 +0000 @@ -0,0 +1,303 @@ +<tool id="incucyte_stack_and_upload_omero" name="Stack Incucyte Plate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="BSD-3"> + <description>And upload to omero</description> + <macros> + <token name="@TOOL_VERSION@">20231219</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + <requirements> + <requirement type="package" version="20220414">Fiji</requirement> + <requirement type="package" version="5.13.1">omero-py</requirement> + <requirement type="package" version="5.1.0">gawk</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #import os + ## the user wants to use a non-public OMERO instance + ## check if credentials are set in the user-preferences, if not warn the user and exit + #set $username = $__user__.extra_preferences.get('omero_account|username', "") + #set $password = $__user__.extra_preferences.get('omero_account|password', "") + + #if str($upload_omero.upload_omero_select) == "yes": + #if ($username == "" or $password ==""): + echo "OMERO connection credentials are empty. Set your credentials via: User -> Preferences -> Manage Information" 1>&2 && + exit 1 && + #end if + #set $incucyteXMLFile = str($upload_omero.incucyteXMLFile) + #set $objectiveChoice = str($upload_omero.objectiveChoice) + #set $startStage = str($upload_omero.startStage) + #set $plateName = str($upload_omero.plateName) + #set $ignoreConcentration = str($upload_omero.ignoreConcentration) + #set $ignorePassage = str($upload_omero.ignorePassage) + #set $ignoreSeeding = str($upload_omero.ignoreSeeding) + #else + #set $incucyteXMLFile = "inexisting.plateMap" + #set $objectiveChoice = "4x" + #set $startStage = "72" + #set $plateName = "Experiment:0" + #set $ignoreConcentration = "true" + #set $ignorePassage = "true" + #set $ignoreSeeding = "true" + #end if + + ## Prefix to directories provided by users + #set $prefix = "/data/mount_s3/image_storage/" + ## Prepare input and output directories to match groovy expectations + mkdir input && + mkdir output && + #if str($structure.structure_type) == "directory": + #set $original_file = "" + #if str($structure.phase_dir_s3) != "": + #if not os.path.isdir($prefix + "/" + str($structure.phase_dir_s3)): + echo "'${prefix}/${structure.phase_dir_s3}'" && + echo "Phase dir $structure.phase_dir_s3 does not exists" && + exit 1 && + #end if + mkdir input/Phase/ && + ln -s '${prefix}/${structure.phase_dir_s3}/'*'${structure.pattern}'* input/Phase/ && + #set $original_file = str($structure.phase_dir_s3) + #end if + #if str($structure.green_dir_s3) != "": + #if not os.path.isdir($prefix + "/" + str($structure.green_dir_s3)): + echo "Green dir $structure.green_dir_s3 does not exists" && + exit 1 && + #end if + mkdir input/Green/ && + ln -s '${prefix}/${structure.green_dir_s3}/'*'${structure.pattern}'* input/Green/ && + #set $original_file = $original_file + "," + str($structure.green_dir_s3) + #end if + #if str($structure.red_dir_s3) != "": + #if not os.path.isdir($prefix + "/" + str($structure.red_dir_s3)): + echo "Red dir $structure.red_dir_s3 does not exists" && + exit 1 && + #end if + mkdir input/Red/ && + ln -s '${prefix}/${structure.red_dir_s3}/'*'${structure.pattern}'* input/Red/ && + #set $original_file = $original_file + "," + str($structure.red_dir_s3) + #end if + #else: + #if not os.path.isdir($prefix + "/" + str($structure.base_dir)): + echo "Base dir $structure.base_dir does not exists" && + exit 1 && + #end if + #set $original_file = str($structure.base_dir) + #if str($structure.phase_key) != "": + mkdir input/Phase/ && + ln -s '${prefix}/${structure.base_dir}/'*'${structure.phase_key}'* input/Phase/ && + #end if + #if str($structure.green_key) != "": + mkdir input/Green/ && + ln -s '${prefix}/${structure.base_dir}/'*'${structure.green_key}'* input/Green/ && + #end if + #if str($structure.red_key) != "": + mkdir input/Red/ && + ln -s '${prefix}/${structure.base_dir}/'*'${structure.red_key}'* input/Red/ && + #end if + #end if + ## Run the groovy + ImageJ --ij2 --headless --console --run '$__tool_directory__/'stack_buildXml.groovy + 'base_dir="input/",output_dir="output/",incucyteXMLFile="$incucyteXMLFile",objectiveChoice="$objectiveChoice",nWells="${nWells}",n_images_per_well="${n_images_per_well}",plateName="$plateName",commonKeyValues="original_file=${original_file};start_stage=$startStage",xmlName="$plateName",ignoreConcentration="$ignoreConcentration",ignorePassage="$ignorePassage",ignoreSeeding="$ignoreSeeding"' > output.log + ## Upload to omero + #if str($upload_omero.upload_omero_select) == "yes": + && bash '$__tool_directory__/'upload_omero.sh '$upload_omero.omero_host' '$credentials' '$upload_omero.screen.screen_create' '$upload_omero.screen.screenNameOrID' >> output.log + ## Copy the companion.ome + && cp output/*.companion.ome output.companion.ome + #end if + ]]></command> + <configfiles> + <configfile name="credentials"><![CDATA[ + #set $username = $__user__.extra_preferences.get('omero_account|username', "") + #set $password = $__user__.extra_preferences.get('omero_account|password', "") +$username +$password + ]]></configfile> + </configfiles> + <inputs> + <conditional name="structure"> + <param name="structure_type" type="select" label="How are your data organized?" > + <option value="directory">One directory per channel</option> + <option value="keyword">All channels into the same directory</option> + </param> + <when value="directory"> + <param name="phase_dir_s3" type="text" value="" label="Directory on s3 with Phase images (leave empty if no)" help="For example Pierre/EXP001/My_expe_Phase"/> + <param name="green_dir_s3" type="text" value="" label="Directory on s3 with Green images (leave empty if no)" help="For example Pierre/EXP001/My_expe_Green"/> + <param name="red_dir_s3" type="text" value="" label="Directory on s3 with Red images (leave empty if no)" help="For example Pierre/EXP001/My_expe_Red"/> + <param name="pattern" type="text" value="" label="Pattern to restrict to only some wells" help="For example A2"/> + </when> + <when value="keyword"> + <param name="base_dir" type="text" value="" label="Directory on s3 with all images" help="For example Lucille/MyIncucyte/20230213/"/> + <param name="phase_key" type="text" value="" label="Word that can identify all Phase images (leave empty if no)" help="For example Phase or Brightfield"/> + <param name="green_key" type="text" value="" label="Word that can identify all Green images (leave empty if no)" help="For example Green or green or GFP"/> + <param name="red_key" type="text" value="" label="Word that can identify all Red images (leave empty if no)" help="For example Red or red"/> + </when> + </conditional> + <param name="nWells" type="select" label="Number of wells into your plate" > + <option value="96">96</option> + <option value="384">384</option> + </param> + <param name="n_images_per_well" type="integer" min="1" value="1" label="Maximum number of images per well" /> + <conditional name="upload_omero"> + <param name="upload_omero_select" type="select" label="Upload your images to omero?" > + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <when value="yes"> + <param name="incucyteXMLFile" type="data" format="xml" label="Incucyte PlateMap" /> + <param name="objectiveChoice" type="select" label="Select the objective used"> + <option value="4x">4x</option> + <option value="10x">10x</option> + <option value="20x">20x</option> + </param> + <param name="startStage" type="integer" min="0" value="72" label="Stage in hour at first acquisition"/> + <param name="omero_host" type="text" label="OMERO host URL"> + <validator type="regex" message="Enter a valid host location, for example, your.omero.server">^[a-zA-Z0-9._-]*$</validator> + <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator> + </param> + <param name="plateName" type="text" value="Experiment:0" label="Name of the plate (on omero)" /> + <conditional name="screen"> + <param name="screen_create" type="select" label="Create the screen on OMERO or use existing one"> + <option value="create">Create a new one</option> + <option value="exists">Use an existing one</option> + </param> + <when value="create"> + <param name="screenNameOrID" type="text" value="MyNewScreen" label="Name of the screen (on omero)" /> + </when> + <when value="exists"> + <param name="screenNameOrID" type="integer" min="0" value="605" label="ID of the screen (on omero)" /> + </when> + </conditional> + <param name="get_stacks_in_galaxy" type="boolean" checked="false" label="Get stacks in galaxy" /> + <param name="ignoreConcentration" type="boolean" checked="true" label="Ignore the concentration of compounds from the plateMap" /> + <param name="ignorePassage" type="boolean" checked="true" label="Ignore the passage number of Cells from the plateMap" /> + <param name="ignoreSeeding" type="boolean" checked="true" label="Ignore the seeding concentration of Cells from the plateMap" /> + </when> + <when value="no"> + <param name="get_stacks_in_galaxy" type="hidden" value="true"/> + </when> + </conditional> + </inputs> + <outputs> + <data name="logfile" format="txt" from_work_dir="output.log" label="${tool.name} on ${on_string}: logfile" /> + <collection name="list_output" type="list" label="${tool.name} on ${on_string}: Stacks"> + <discover_datasets pattern="(?P<designation>.+)\.tif" directory="output/" ext="tiff" /> + <filter>upload_omero['get_stacks_in_galaxy']</filter> + </collection> + <data format="xml" name="companion_ome" from_work_dir="output.companion.ome" label="${tool.name} on ${on_string}: companion.ome" > + <filter>upload_omero['get_stacks_in_galaxy'] and upload_omero['upload_omero_select'] == "yes"</filter> + </data> + </outputs> + <tests> + <test> + <conditional name="structure"> + <param name="structure_type" value="directory"/> + <param name="phase_dir_s3" value="tutu_Phase"/> + <param name="green_dir_s3" value="toto_Green"/> + </conditional> + <conditional name="upload_omero"> + <param name="upload_omero_select" value="no"/> + </conditional> + <output name="logfile"> + <assert_contents> + <has_line line="No match for B1"/> + </assert_contents> + </output> + <output_collection name="list_output" type="list" count="1"> + <element name="A1_1_merge" ftype="tiff"> + <assert_contents> + <has_size value="17574881" delta="1500000"/> + </assert_contents> + </element> + </output_collection> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What it does** + +It will use images coming from the Incucyte which are on the s3 server to make a "T-stack" per well and upload it to omero with key values in the plateMap. +This wrapper uses ImageJ to combine images (with a groovy) and omero-py to import the images. + +Usage +..... + + +**Input** + +- 3 paths of directories (some can be empty of phase, green and red) or one path of directory and 3 keywords (some of them can be empty) +- plateMap generated with the software coming with Incucyte +- objective used (to correctly set the pixel size) +- number of well in your plate (96 or 384), they don't need to be all in your input directories. +- maximum number of images per well +- URL of omero +- Name of the Plate in omero +- Whether the Screen should be created or use an existing one +- Name of the new screen or id of the existing screen +- Whether the concentration of the compounds, the passage and the seeding concentration should be ignored from the plateMap. + +**Output** + +- A log file with info +- Optionally all images as T-stack and the xml to upload to omero +- On OMERO your images all channels combined and all time points combined into a plate. + +**License** + +License text:: + + ************************************************* + Relative to the generation of the .companion.ome * + ************************************************** + #%L + BSD implementations of Bio-Formats readers and writers + %% + The functions buildXML, makeImage, makePlate, postProcess and asString has been modified and adapted from + https://github.com/ome/bioformats/blob/master/components/formats-bsd/test/loci/formats/utests/SPWModelMock.java + + Copyright (C) 2005 - 2015 Open Microscopy Environment: + - Board of Regents of the University of Wisconsin-Madison + - Glencoe Software, Inc. + - University of Dundee + + @author Chris Allan <callan at blackcat dot ca> + %% + + ************************************************** + Relative to the rest of the script * + ************************************************** + + * = AUTHOR INFORMATION = + Code written by Rémy Dornier, EPFL - SV - PTECH - BIOP + and Romain Guiet, EPFL - SV - PTECH - BIOP + and Lucille Delisle, EPFL - SV - UPDUB + and Pierre Osteil, EPFL - SV - UPDUB + + Last modification: 2023-08-24 + + = COPYRIGHT = + © All rights reserved. ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE, Switzerland, BioImaging And Optics Platform (BIOP), 2023 + + Licensed under the BSD-3-Clause License: + Redistribution and use in source and binary forms, with or without modification, are permitted provided + that the following conditions are met: + 1. Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. + 2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer + in the documentation and/or other materials provided with the distribution. + 3. Neither the name of the copyright holder nor the names of its contributors + may be used to endorse or promote products + derived from this software without specific prior written permission. + + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" + AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE + LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR + CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF + SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS + INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN + CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) + ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE + POSSIBILITY OF SUCH DAMAGE. + ]]></help> +</tool> \ No newline at end of file