<tool id="Fasta_to_Contig2Bin" name="Converts genome bins in fasta format" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>
        to scaffolds-to-bin table
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
#import re
mkdir "inputs" &&
#for $i in $inputs
    #set file_name = $i.file_name
    #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
    ln -s '$file_name' 'inputs/${identifier}.fasta' &&
#end for
Fasta_to_Contig2Bin.sh
    --extension fasta
    --input_folder 'inputs'
    > '$contigs2bin'
    ]]></command>
    <inputs>
        <param name="inputs" type="data_collection" collection_type="list"  format="fasta" label="Bin sequences"/>
    </inputs>
    <outputs>
        <data name="contigs2bin" format="tabular"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="inputs">
                <collection type="list">
                    <element name="001" value="maxbin2.001.fasta" ftype="fasta"/>
                    <element name="002" value="maxbin2.002.fasta" ftype="fasta"/>
                </collection>
            </param>
            <output name="contigs2bin" ftype="tabular">
                <assert_contents>
                    <has_text text="contig-201_2"/>
                    <has_text text="001"/>
                    <has_text text="contig-201_798"/>
                    <has_text text="002"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@
    ]]></help>
    <expand macro="citations"/>
</tool>