<tool id="chira_quantify" name="ChiRA qauntify" version="@TOOL_VERSION@0">
    <description>quantify aligned loci to score the alignments</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements" />
    <command><![CDATA[
        chira_quantify.py
        -b '$segments'
        -m '$merged'
        -cs '$crl_share'
        -ls '$min_locus_size'
        -e '$em_threshold'
        $crl
        -o ./
    ]]></command>

    <inputs>
        <param format="bed" name="segments" type="data" label="BED file of aligned segments"/>
        <param format="tabular" name="merged" type="data" label="Tabular file of merged alignments"/>
        <param name="crl_share" type="float" value="0.7" label="CRL locus fraction" min="0" max="1"
            help="Minimum fraction of reads of a locus that must overlap with all CRL loci inorder to merge itinto that CRL."/>
        <param name="min_locus_size" type="integer" value="10" label="Minimum locus size" min="1"
            help="Minimum number of reads a locus should have in order to participate in CRL creation.
                 Always set this value relative to your sequencing depth. Setting this to lower leads
                 CRLs of random multimappings Also consider setting the --crl_share option
                 along with this"/>
       <param name="em_threshold" type="float" value="0.00001" label="EM threshold"
              help="The maximum difference of transcripts expression between two consecutive iterations of EM algorithm to converge."/>
       <param name="crl" type="boolean" truevalue="-crl" falsevalue="" checked="true"
              label="Create CRLs" help="Create CRLs and qunatify them or use the loci further without creating the CRLs" />
    </inputs>
    <outputs>
        <data format="tabular" name="loci" from_work_dir="loci.counts" label="ChiRA quantified loci on ${on_string}"/>
    </outputs>

    <tests>
        <test expect_num_outputs="1">
            <param name="segments" value="segments.bed"/>
            <param name="em_threshold" value="1"/>
            <param name="merged" value="merged.bed"/>
            <param name="min_locus_size" value="5"/>
            <output name="loci" file="loci.counts"/>
        </test>
    </tests>

    <help>

.. class:: infomark

**What it does**

This tool first creates CRLS from merged BED file and quantifies them based on the mapped reads.

**Inputs**

  * A BED file containing alignment segments
  * A BED file containing merged alignments

**Output**

  * Tabular file containing the reads and their CRLs with TPM values.

    </help>
    <expand macro="citations" />
  </tool>