<?xml version="1.0"?>
<tool id="describe_samples" name="Describe samples" version="@WRAPPER_VERSION@">
    <description>and replicates</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <command detect_errors="aggressive"><![CDATA[
        cp $sample_list $output
      ]]></command>
    <configfiles>
        <configfile name="sample_list"><![CDATA[#for $sample in $samples:
$sample.condition	$sample.name
#end for]]></configfile>
    </configfiles>
    <inputs>
        <repeat name="samples" title="Samples">
            <param name="name" type="text" label="Full sample name" help="e.g. CondA_replicate1" optional="False" />
            <param name="condition" type="text" label="Condition" help="e.g. ConditionA" optional="False" />
        </repeat>
    </inputs>
    <outputs>
        <data format="tabular" name="output"/>
    </outputs>
    <tests>
        <test>
            <repeat name="samples">
                <param name="condition" value="ConditionA" />
                <param name="name" value="CondA_replicate1" />
            </repeat>
            <repeat name="samples">
                <param name="condition" value="ConditionA" />
                <param name="name" value="CondA_replicate2" />
            </repeat>
            <repeat name="samples">
                <param name="condition" value="ConditionB" />
                <param name="name" value="CondB_replicate1" />
            </repeat>
            <repeat name="samples">
                <param name="condition" value="ConditionB" />
                <param name="name" value="CondB_replicate2" />
            </repeat>
            <output name="output" file="samples.tsv"/>
        </test>
    </tests>
    <help><![CDATA[
        This tools allows to describe your samples and replicates, producing a tabular file looking like this:

        =========== ================
        ConditionA  CondA_replicate1
        ----------- ----------------
        ConditionA  CondA_replicate2
        ----------- ----------------
        ConditionB  CondB_replicate1
        ----------- ----------------
        ConditionB  CondB_replicate2
        ----------- ----------------
        ConditionC  CondC_replicate1
        ----------- ----------------
        ConditionC  CondC_replicate2
        ----------- ----------------
        ConditionC  CondC_replicate3
        =========== ================

        IThe output file can be used in the tools 'RNASeq samples quality check for transcript quantification' and 'Differential expression analysis'.
        The names in column 2 must match the names given to the datasets in your history.
    ]]></help>
    <expand macro="citation"/>
</tool>