annotate uploadROIandMeasuresToOMERO.xml @ 0:d507ce86f0d0 draft default tip

planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero commit 68de74426a3f93a240d64cb416f608ba7caca6eb

<tool id="uploadROIandMeasuresToOMERO" name="uploadROIandMeasuresToOMERO" version="0.0.5">
    <description>Designed to work after measureGastruloids</description>
    <requirements>
        <requirement type="package" version="5.10.1">omero-py</requirement>
        <requirement type="package" version="1.3.4">pandas</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #import re
        #if $omero_instance_type.omero_instance == "priv":
            ## 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 $omero_instance_type.galaxy_test_param != 'true' and ($username == "" or $password ==""):
                echo "OMERO connection credentials are empty. Set your credentials via: User -> Preferences -> Manage Information" 1>&2 &&
                exit 1 &&
            #end if
        #end if
        
        mkdir rois &&
        #for file in $rois
            #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
            ln -s '$file' rois/${identifier}.txt &&
        #end for
        python '$__tool_directory__/upload_omero_roi_results.py'
        #if $omero_instance_type.omero_instance =='priv':
            -oh '$omero_instance_type.omero_host'
            $omero_instance_type.omero_secured
            -cf '$credentials'
        #end if
        --rois rois
        --summaryResults $summary_results
        --verbose
        > output.log
        ]]>
    </command>
    <configfiles>
        <configfile name="credentials"><![CDATA[
#if $omero_instance_type.omero_instance =='priv' and $omero_instance_type.galaxy_test_param == 'true':
    ## as a test for a private instance we actually use a public instance, but with credentials
    #set $username = 'public'
    #set $password = 'public'
#else:
    #set $username = $__user__.extra_preferences.get('omero_account|username', "")
    #set $password = $__user__.extra_preferences.get('omero_account|password', "")
#end if
{
    "username": "$username",
    "password": "$password"
}
        ]]></configfile>
    </configfiles>
    <inputs>
        <conditional name="omero_instance_type">
            <param name="omero_instance" type="select" label="Which OMERO instance to connect?"
                   help="By default, the tool will download a tarball containing individual images from IDR into your Galaxy history. If you 
                   need to connect to your own instance, set your connection username and password from User->Preference->Manage Information" >
                <option value="idr">IDR</option>
                <option value="priv">other OMERO instance</option>
            </param>
            <when value="priv">
                <param name="omero_host" type="text" label="OMERO host URL">
                    <validator type="regex" message="Enter a valid host location, for example, your.omero.server">^[a-zA-Z0-9._-]*$</validator>
                    <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator>
                </param>
                <param name="omero_secured" type="boolean" label="Secured connection?" checked="true" truevalue="--omero-secured" falsevalue=""
                        help="Select Yes if your OMERO instance is running with SSL, otherwise select No">
                </param>
                <param name="galaxy_test_param" type="hidden" value="false" />
            </when>
            <when value="idr" />
        </conditional>
        <param name="rois" type="data_collection" format="tabular" label="Select ROIs." collection_type="list"/>
        <param name="summary_results" type="data" format="csv" label="Select the all results csv."/>
    </inputs>

    <outputs>
        <data name="logfile" format="txt" from_work_dir="output.log" label="${tool.name} on ${on_string}: logfile">
        </data>
    </outputs>
    <help>
    <![CDATA[
**Overview**

This tool will upload to OMERO the ROIs and the Results as table.

The expected workflow is: idr_download_by_ids > measureGastruloids > uploadROIandMeasuresToOMERO
]]>
    </help>
</tool>