view get_projects.xml @ 0:713502c9a98f draft default tip

planemo upload for repository https://github.com/jw44lavo/galaxy-tools/blob/bgo/tools/lambdaminer/ commit 3f45cd07445498cefa73931cadf3d1115245ca1e

<tool id="lm_get_projects" name="Get LMDB Projects" version="0.1.0+galaxy0" profile="21.05">
    <requirements>
        <requirement type="package" version="2.2.2">pandas</requirement>
        <requirement type="package" version="2.9.9">psycopg2</requirement>
        <requirement type="package" version="2.0.37">sqlalchemy</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if $test != ""
            export LAMBDAMINER_CREDENTIALS="$__tool_directory__/test-data/$test";
        #end if
        python '$__tool_directory__/get_projects.py'
        --login-name '$__user_name__'
        --output-file '$projects'
    ]]></command>
    <inputs>
        <param name="test" type="hidden"/>
    </inputs>
    <outputs>
        <data name="projects" format="csv"/>
    </outputs>
    <tests>
        <test>
            <param name="test" value="test_credentials.json"/>
            <output name="projects" value="test_projects.csv" compare="contains"/>
        </test>
        <test expect_failure="true">
            <param name="test" value="test_credentials_false.json"/>
        </test>
        <test expect_failure="true">
            <param name="test" value="test_credentials_nonexistent.json"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

This tool queries the Lambda-Miner database for the users projects.

**Input**

There is no input necessary from the user. The tool connects to the Lambda-Miner database and uses the users login name to query it.

**Output**

CSV file containing the projects (id, name, sample count) corresponding to the user.]]>
    </help>
    <citations>
        <citation type="doi">10.5194/egusphere-egu24-15782</citation>
    </citations>
</tool>