<tool id='align_and_estimate_abundance' name='Align and Estimate Abundance' version='r20140717'>

<description> using utility align_and_estimate_abundance.pl</description>

<requirements>
	<requirement type="package" version="r20140717">trinityrnaseq</requirement>
	<requirement type="package" version="0.12.7">bowtie</requirement>
	<requirement type="package" version="2.1">samtools</requirement>
	<requirement type="package" version="1.5.1">eXpress</requirement>
</requirements>

<command> \$TRINITY_HOME/util/align_and_estimate_abundance.pl
        --transcripts $transcripts
        --est_method $est_method
        --aln_method $aln_method
        --prep_reference

        ## Inputs.
        #if str($reads.paired_or_single) == "paired":

                --left $reads.left_input --right $reads.right_input

                #if  $reads.left_input.ext == 'fa':
                        --seqType fa
                #else:
                        --seqType fq
                #end if

                ## Additional parameters.
                #if str($reads.optional.use_options) == "yes":

                        #if str($reads.optional.library_type) != "None":
                                --SS_lib_type $reads.optional.library_type
                        #end if



                #end if

        #else:
                --single $reads.input

                #if  str($reads.input.ext) == 'fa':
                     --seqType fa
                #else:
                     --seqType fq
                #end if

                ## Additional parameters.
                #if str($reads.optional.use_option) == "yes":

                        #if str($reads.additional_params.library_type) != "None":
                                --SS_lib_type $reads.optional.library_type
                        #end if

                #end if
        #end if

## direct to output
&gt; $align_and_estimate_abundance_log 2&gt;&amp;1

</command>