PingPong.xml

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    Copyright (C) 2015 Laurent Modolo

    This file is part of TEtools suite for galaxy.

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-->

<tool id="PingPong" name="PingPong" version="1.0.0" hidden="false">
    <description>PingPong signal analysis</description>
    <version_command interpreter="python3">PingPong.py -v</version_command>
    <command interpreter="python3">${__root_dir__}/tools/pi_galaxy/PingPong.py
        -fastq=$fastq_files
        -fasta=
        #for $fastq_file in $fastq_files:
            $fastq_file
        #end for
        -TE_names=$TE_names
    </command>

    <inputs>
        <param name="fasta_file" type="data" format="fasta" label="fasta file that contain the sequence(s) of the transposable element(s) to analyse" />
        <param name="TE_names" size="30x10" type="text" value="" label="space sperated list of TE sequences names to analyse"/>
        <repeat name="fastq_files" title="fastq file">
             <param name="fastq_file" type="data" format="fastq" label="fastq file"/>
        </repeat>
    </inputs>

    <outputs>
        <data label="${tool.name} on ${on_string}">
            <discover_datasets pattern="__designation_and_ext__" directory="pingpong_working_directory" visible="true" />
        </data>
    </outputs>

    <requirements>
        <requirement type="package">Rscript</requirement>
    </requirements>

    <help>
PingPong documentation:
=======================


    </help>
</tool>