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<tool id="giveinfofasta" name="GiveInfoFasta" version="1.0.0">
    <description>Give informations about your Fasta File</description>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        GiveInfoFasta.py -i ${input} ${stat}
        && 
        cp ${input}.stats ${output_stats}
    ]]></command>
    <inputs>
        <param name="input" type="data" format="fasta" label="Input file" help="Genome file in fasta format."/>
        <param name="stat" type="boolean" checked="false" truevalue="-l" falsevalue="" label="Give stats for each input sequence" help="Default=No"/>
        <param name="label" type="text" label="Output name" help="[Optional] Specify the project label for your outputs. By default it will be the name of your input fasta file."/>
    </inputs>
    <outputs>
        <data name="output_stats" format="txt" label="#if str($label)=='' then os.path.splitext(str($input.name))[0] else $label #.stats"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="input"/>
            <param name="stat" value="-l"/>
            <output name="output_stats" file="output"/>
        </test>
    </tests>

   <help><![CDATA[
.. class:: infomark

**Author**
Valentin Marcon

---------------------------------------------------

.. class:: infomark

**Please cite** If you use this tool, please cite : 
"This work was performed using the facilities of the URGI platform (https://urgi.versailles.inra.fr/) and the IFB project 'Galaxy For Life Sciences' (http://www.france-bioinformatique.fr/fr/projets2015/gfls)".

---------------------------------------------------

===============
GiveInfoFasta
===============

-----------
Description
-----------

GiveInfoFasta is a tool from the REPET package ("https://urgi.versailles.inra.fr/Tools/REPET").

It gives informations about your Fasta File:
Number of bp;
Number and stats of sequences;
GC content;
Number of each base and 'N';
MD5 of the file;


-----------
Input files
-----------

Fasta file 
        Genome file in fasta format.

----------
Settings
----------

Give stats for each input sequence
        Previously described informations for each sequences.

Output Name [optional]
        Specify the project label for your outputs. By default it will be the name of your input fasta file.

------------
Output files
------------

Output_name.stats
        Stats file for the input file. 


    ]]></help>
</tool>