view inchi_to_sink.xml @ 3:47f49582d8db draft

planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6

<tool id="inchi_to_sink" name="Inchi to sink" version="@TOOL_VERSION@" profile="19.09" license="MIT">
    <description>Convert InChI input to CSV sink</description>
    <macros>
        <token name="@TOOL_VERSION@">1.0.1</token>
    </macros>
    <command detect_errors="exit_code"><![CDATA[
        #set inchi=$source_inchi.rstrip()
        echo -e '"name","inchi"\n"$source_name","$inchi"' > '$sink'
    ]]></command>
    <inputs>
        <param name="source_inchi" type="text" label="Source InChI" optional="false">
            <validator type="empty_field" message="InChI string is required"/>
        </param>
        <param name="source_name" type="text" value="Biosensor" label="Source name">
            <validator type="empty_field" message="Source name is required"/>
        </param>
    </inputs>
    <outputs>
        <data name="sink" format="csv" label="${tool.name} - ${source_name}" />
    </outputs>
    <tests>
        <test>
        <!-- test 1: check if identical outputs are produced -->
            <param name="source_inchi" value="InChI=1S/C5H14NO/c1-6(2,3)4-5-7/h7H,4-5H2,1-3H3/q+1" />
            <param name="source_name" value="Choline" />
            <output name="sink" file="sink_to-detect_choline.csv" ftype="csv" compare="diff"/>
        </test>
    </tests>
    <help><![CDATA[
Inchi to sink
===============

Convert Inchi string to CSV sink file for Retropath2.0 Input.

Input
-----

Required:

* **source_inchi**\ : (string) Inchi string

Optional:

* **source_name**\ : (string) Inchi name (Default=Biosensor)
    ]]></help>
    <creator>
        <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
    </creator>
    <citations>
        <citation type="bibtex">
            @unpublished{inchi_to_sink
                title = {{inchi_to_sink}},
                url = {https://github.com/brsynth/},
            }
        </citation>
    </citations>
</tool>