annotate aarnet_filesender.xml @ 3:8a4b0f14aa4e draft default tip

planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit 62cfda2672d51d769c18c633cb57a7a71dd5d226

<tool id="aarnet_filesender" name="AARNet FileSender" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>transfer files with AARNet's FileSender Service</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
#if $test != "":
    filesender -h &&
    exit 0;
#end if

#set $apiuser = $__user__.extra_preferences.get('aarnet_filesender_account|username', "").strip()
#set $apikey = $__user__.extra_preferences.get('aarnet_filesender_account|apikey', "").strip()

#if $apiuser == "" or $apikey == "":
    echo "ERROR: Please enter your FileSender Username in your user preferences under the AARNet FileSender Account Info section" >&2 &&
    exit 1;
#end if

#if $to == "":
    echo "WARNING: recipent email not set, setting to $__user_email__" &&
    #set $to = $__user_email__
#end if

mkdir filestosend &&

#for $file in $data
    if [ -f "filestosend/${file.element_identifier}" ]; then
        echo "ERROR: two datasets have the same name (${file.element_identifier})" &&
        exit 1;
    fi &&
    ln -s "$file" "filestosend/${file.element_identifier}" &&
#end for

filesender -p -u '$apiuser' -a '$apikey' -b https://filesender.aarnet.edu.au/rest.php -f '$__user_email__' -r '$to' -s 'Data sent from Galaxy' filestosend >$output 2>&1
    ]]></command>
    <inputs>
        <param name="data" type="data" format="data" multiple="true" optional="false" label="Datasets to be sent:"/>
        <param name="to" type="text" optional="true" label="Email address of recipent:">
            <sanitizer sanitize="False"/>
        </param>
        <param name="test" type="hidden" value=""/>
    </inputs>
    <outputs>
        <data name="output" format="txt" hidden="false"/>
    </outputs>
    <tests>
        <test expect_exit_code="1" expect_failure="true">
            <param name="data" value="summary_statistics.txt"/>
            <assert_stderr>
                <has_text text="ERROR: Please enter your FileSender Username in your user preferences under the AARNet FileSender Account Info section"/>
            </assert_stderr>
        </test>
        <test>
            <param name="data" value="summary_statistics.txt"/>
            <param name="test" value="true"/>
            <assert_stdout>
                <has_text text="File Sender CLI client"/>
            </assert_stdout>
        </test>
    </tests>
    <help>
        **What it does**

        Uses `AARNet’s FileSender service`_ to send dataset(s) from Galaxy. The
        recipient will receive an email with a link to download the files.
        
        **Who can use it**
        
        AARNet FileSender is available to all institutions affiliated with the
        `Australian Access Federation (AAF)`_. You can use your institution
        login details to access and use FileSender.
        
        **How to connect your Galaxy account to FileSender**
        
        To send files from Galaxy you will need to connect your Galaxy account
        to FileSender. This is done by entering your FileSender API key into your
        Galaxy user preferences.
        
        1. Log in to FileSender, and copy your API key from the “API Secret” section on the FileSender “My
           Profile” page. See the `AARNet Knowledge Base`_ for more information.
        2. In Galaxy, add your API key to the “AARNet FileSender API Key” field
           in User &gt; Preferences &gt; Manage Information. Your AARNet FileSender
           Username is the email address you used to log in to FileSender.
        
        .. _AARNet’s FileSender service: https://filesender.aarnet.edu.au
        .. _Australian Access Federation (AAF): https://aaf.edu.au/subscribers/
        .. _AARNet Knowledge Base: https://support.aarnet.edu.au/hc/en-us/articles/235972948-FileSender-API
    </help>
    <citations>
        <citation type="bibtex">
           @misc{FileSenderCLI_github,
           title={FileSenderCLI Github page},
           url = {https://github.com/madsi1m/FileSenderCLI},}
        </citation>
    </citations>
</tool>