<tool id="express" name="eXpress" version="1.1.1">
	<description>Quantify the abundances of a set of target sequences from sampled subsequences</description>
	<requirements>
		<requirement type="package" version="1.1.1">eXpress</requirement>
	</requirements>
	<command>
		express --no-update-check
		## Additional parameters.
		#if $additional_params.use_additional == "yes":
            -B $additional_params.additional_batch
            -O $additional_params.additional_online
			
	    	#if str( $additional_params.calc_covar ) == 'yes':
	    		--calc-covar
	    	#end if

	        -m $additional_params.mean_fragment_length

	        -s $additional_params.fragment_length_deviation
        #end if

        ## Input files
		$multiFasta 
		$bamOrSamFile
	</command>
	<inputs>
		<param format="fasta" name="multiFasta" type="data" label="A set of target references (annotation) in multi-FASTA format" help="The multi-FASTA file can also be a fasta file." />
		<param format="sam,bam" name="bamOrSamFile" type="data" label="Alignments in the BAM or SAM format" help="The set of aligned reads." />
		<conditional name="additional_params">
            <param name="use_additional" type="select" label="Use Additional Parameters?">
                <option value="no">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no">
            </when>
            <when value="yes">            
                <param name="additional_batch" type="integer" label="Additional batch EM rounds" value="0" help="0 is default. Can improve accuracy at the cost of time."/>
                <param name="additional_online" type="integer" label="Additional online EM rounds" value="0" help="0 is default. Can improve accuracy at the cost of time."/>
		        <param name="calc_covar" type="select" label="Calculate the covariance between targets and outputs?" help="This calculation requires slightly more time and memory.">
		            <option value="no">No</option>
		            <option value="yes">Yes</option>
		        </param>
		        <param name="mean_fragment_length" type="integer" label="Specifies the mean fragment length" value="200" help="200 is default. While the empirical distribution is estimated from paired-end reads on-the-fly, this value paramaterizes the prior distribution."/>
		        <param name="fragment_length_deviation" type="integer" label="Specified the fragment length standard deviation" value="60" help="60 is default. While the empirical distribution is estimated from paired-end reads on-the-fly, this value paramaterizes the prior distribution."/>
			</when>
        </conditional>
	</inputs>
	<outputs>  
       <data format="txt" name="params" from_work_dir="params.xprs"/>
       <data format="txt" name="results" from_work_dir="results.xprs"/>
       <data format="txt" name="varcov" from_work_dir="varcov.xprs">
       		<filter>additional_params[ 'use_additional' ] == "yes" and additional_params[ 'calc_covar' ] == "yes"</filter>
       </data>
   </outputs>

   <tests>
        <!-- Test for the most simple case : Running eXpress with a .bam file and a .fasta file -->
        <test>
            <!-- TopHat commands:
            eXpress Trinity.fasta hits.bam
            -->
            <param name="bamOrSamFile" ftype="bam" value="eXpress_hits.bam"/>
            <param name="multiFasta" ftype="fasta" value="eXpress_Trinity.fasta"/>
            <param name="use_additional" value="no"/>

            <output name="params" file="eXpress_params.xprs" lines_diff="300"/>
            <output name="results" file="eXpress_results.xprs" lines_diff="10"/>
        </test>
        <!-- Test for an other simple case : Running eXpress with a .sam file and a .fasta file -->
        <test>
            <!-- TopHat commands:
            eXpress Trinity.fasta hits.sam
            -->
            <param name="bamOrSamFile" ftype="sam" value="eXpress_hits.sam"/>
            <param name="multiFasta" ftype="fasta" value="eXpress_Trinity.fasta"/>
            <param name="use_additional" value="no"/>

            <output name="params" file="eXpress_params_sam.xprs" lines_diff="300"/>
            <output name="results" file="eXpress_results_sam.xprs" lines_diff="10"/>
        </test>
        <!-- Test for a complex case : All the parameters has been activated and modified -->
        <test>
            <!-- TopHat commands: eXpress -B 1 -O 1 ++calc-covar -m 300 -s 85 Trinity.fasta hits.sam -->
            <param name="bamOrSamFile" ftype="sam" value="eXpress_hits_all_params.bam"/>
            <param name="multiFasta" ftype="fasta" value="eXpress_Trinity_all_params.fasta"/>
            
            <param name="use_additional" value="yes"/>
            <param name="additional_batch" value="1"/>
            <param name="additional_online" value="1" />
            <param name="calc_covar" value="yes"/>
            <param name="mean_fragment_length" value="300"/>
            <param name="fragment_length_deviation" value="85"/>

            <output name="params" file="eXpress_params_all_params.xprs" lines_diff="300"/>
            <output name="results" file="eXpress_results_all_params.xprs" lines_diff="10"/>
            <output name="varcov" file="eXpress_varcov_all_params.xprs"/>
        </test>
    </tests>
    <help>
**eXpress Overview**

eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. Example applications include transcript-level RNA-Seq quantification, allele-specific/haplotype expression analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data.

.. _Ensembl: http://bio.math.berkeley.edu/eXpress/

-----

**Input format**

eXpress requires two input files:

- A multi-FASTA file containing the transcript sequences.
- Read alignments to the multi-FASTA file in BAM or SAM format.

------

**Outputs**

- The output for eXpress is saved in a file called results.xprs in an easy-to-parse tab-delimited format.

- Also, params.xprs contains the values of the other parameters (besides abundances and counts) estimated by eXpress.

- If you choose to use to calculate the covariance between targets and outputs, an other output would be : varcov.xprs.
    </help>
</tool>