comparison rpviz.xml @ 2:751dfcc6f663 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690

1:1c8a408bd3fb

<tool id="rptools_rpviz" name="Visualize pathways" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
    <description>Visualize pathways from the RetroPath Suite</description>
    <macros>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@TOOL_VERSION@">5.13.1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #set input_folder="input_folder"
        mkdir -p '$input_folder' &&
        #if str($input_type_conditional.input_type) == "sbml":
            #for $input in $input_type_conditional.input_sbml.keys():

    <outputs>
        <data name="html_file" format="html" label="Rpviz: Pathways Visualization"/>
    </outputs>
    <tests>
        <test>
        <!-- test 1: check if identical html output is produced (single sbml input) --> 
            <conditional name="input_type_conditional">
                <param name="input_type" value="single_sbml"/>
                <param name="input_single_sbml" value="lycopene_CrtEBI_from_selenzy.xml" />
            </conditional>
            <output name="html_file" >
                <assert_contents>
                    <has_size value="1296252" delta="100" />
                </assert_contents>
            </output>
        </test>
        <test>
        <!-- test 2: check if identical html output is produced (tar input) --> 
            <conditional name="input_type_conditional">
                <param name="input_type" value="tar"/>
                <param name="input_tar" value="as_tar_inputs.tgz" />
            </conditional>
            <output name="html_file" >
                <assert_contents>
                    <has_size value="1604488" delta="100" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
RPVIZ
================

Visualize pathways from the `RetroPath Suite <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_.

Input
-----

Output
------

* **Pathways Visualization**\ : HTML output for pathway's visualization.

Project Links
------------------

* `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rpviz>`_

License
-------

* `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_

    ]]></help>
    <creator>
        <person givenName="Thomas" familyName="Duigou" email="[e-mail]" identifier="https://orcid.org/0000-0002-2649-2950" />
    </creator>
</tool>

2:751dfcc6f663

<tool id="rptools_rpviz" name="Visualize pathways" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
    <description>Visualize pathways from the RetroPath Suite</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        #set input_folder="input_folder"
        mkdir -p '$input_folder' &&
        #if str($input_type_conditional.input_type) == "sbml":
            #for $input in $input_type_conditional.input_sbml.keys():

    <outputs>
        <data name="html_file" format="html" label="Rpviz: Pathways Visualization"/>
    </outputs>
    <tests>
        <test>
        <!-- test 1: check if identical html output is produced (single sbml input) -->
            <conditional name="input_type_conditional">
                <param name="input_type" value="single_sbml"/>
                <param name="input_single_sbml" value="lycopene_CrtEBI_from_selenzy.xml" />
            </conditional>
            <output name="html_file" >
                <assert_contents>
                    <has_size value="1296252" delta="1000" />
                </assert_contents>
            </output>
        </test>
        <test>
        <!-- test 2: check if identical html output is produced (tar input) -->
            <conditional name="input_type_conditional">
                <param name="input_type" value="tar"/>
                <param name="input_tar" value="as_tar_inputs.tgz" />
            </conditional>
            <output name="html_file" >
                <assert_contents>
                    <has_size value="1604488" delta="1000" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
RPVIZ
=====

Visualize pathways from the `RetroPath Suite <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_.

Input
-----

Output
------

* **Pathways Visualization**\ : HTML output for pathway's visualization.
    ]]></help>
    <expand macro="creator"/>
    <citations>
        <citation type="doi">10.1038/s41467-022-32661-x</citation>
    </citations>
</tool>