comparison trinotate.xml @ 1:9e61bc67866f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate commit 910addf8de57fa9fa678c8a69c558390f5a16601

0:499d87c45612

        ]]>
    </version_command>
    <command><![CDATA[

#if str($cond_download.select_download) == "yes":
    wget --no-verbose 'https://data.broadinstitute.org/Trinity/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz' -O Trinotate.sqlite.gz &&
    gunzip Trinotate.sqlite.gz &&
#else:
    ln -s '$cond_download.trinotate_sqlite_in' Trinotate.sqlite
#end if

            <param name="select_download" type="select" label="Let Galaxy downloading the Trinotate Pre-generated Resource SQLite database">
                <option value="yes" selected="True">Yes</option>
                <option value="no">No, I will provide it</option>
            </param>
            <when value="no">
                <param name="trinotate_sqlite_in" type="data" format="sqlite" optional="false" label="Trinotate Pre-generated Resource SQLite database" help="https://data.broadinstitute.org/Trinity/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz" />
            </when>
            <when value="yes" />
        </conditional>
        
        <section name="report_option" title="Report options" expanded="False">

.. _tmhmm_and_signalp: https://toolshed.g2.bx.psu.edu/repository?repository_id=292389a45f1a238a


Trinotate Pre-generated Resource SQLite database

- You can provide the SQLite database yourself, if Galaxy have trouble to download it : https://data.broadinstitute.org/Trinity/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz

--------

**Output**

1:9e61bc67866f

        ]]>
    </version_command>
    <command><![CDATA[

#if str($cond_download.select_download) == "yes":
    wget --no-verbose 'https://data.broadinstitute.org/Trinity/__deprecated_trinotate_resources/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz' -O Trinotate.sqlite.gz &&
    gunzip Trinotate.sqlite.gz &&
#else:
    ln -s '$cond_download.trinotate_sqlite_in' Trinotate.sqlite
#end if

            <param name="select_download" type="select" label="Let Galaxy downloading the Trinotate Pre-generated Resource SQLite database">
                <option value="yes" selected="True">Yes</option>
                <option value="no">No, I will provide it</option>
            </param>
            <when value="no">
                <param name="trinotate_sqlite_in" type="data" format="sqlite" optional="false" label="Trinotate Pre-generated Resource SQLite database" help="https://data.broadinstitute.org/Trinity/__deprecated_trinotate_resources/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz" />
            </when>
            <when value="yes" />
        </conditional>
        
        <section name="report_option" title="Report options" expanded="False">

.. _tmhmm_and_signalp: https://toolshed.g2.bx.psu.edu/repository?repository_id=292389a45f1a238a


Trinotate Pre-generated Resource SQLite database

- You can provide the SQLite database yourself, if Galaxy have trouble to download it : https://data.broadinstitute.org/Trinity/__deprecated_trinotate_resources/Trinotate_v3_RESOURCES/Trinotate_v3.sqlite.gz

--------

**Output**