annotate align_and_estimate_abundance.xml @ 1:16aaa05e7d67 draft

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<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>

<inputs>

<!-- Required -->
	<param name="transcripts" type="data" format="fasta" label="Transcripts [ in fasta format ]" help="--transcripts &lt; string &gt; ; transcript fasta file"/>

	<param name="est_method" type="select" display="radio" label="Choose abundance estimation method" help="">
        	<option value="RSEM" selected="True">RSEM</option>
	        <option value="eXpress">eXpress</option>
	</param>

	<param name="aln_method" type="select" display="radio" label="Choose alignment method" help="">
	        <option value="bowtie" selected="True">bowtie</option>
	        <option value="bowtie2">bowtie2</option>
	</param>

<conditional name="reads">
        <param name="paired_or_single" type="select" label="Paired or Single-end reads?">
                <option value="paired">Paired</option>
                <option value="single">Single</option>
        </param>


        <when value="paired">
                <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
                <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>

                <param name="seqtype" type="select" label="--seqType" help="">
                        <option value='fq' selected='true'>fastq</option>
                        <option value='fa'>fasta</option>
                </param>

                <conditional name='optional'>
                        <param name='use_options' type='select' label='Use Optional parameters?'>
                                <option value='no'>NO</option>
                                <option value='yes'>YES</option>
                        </param>
                        <when value='no'/>
                        <when value='yes'>
                                <param name="library_type" type="select" label="Strand-specific Library Type">
                                        <option value="None">None</option>
                                        <option value="FR">FR</option>
                                        <option value="RF">RF</option>
                                </param>



                        </when>
                </conditional>
        </when>
        <when value="single">
                <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
                <param name="seqtype" type="select" label="--seqType" help="">
                        <option value='fq' selected='true'>fastq</option>
                        <option value='fa'>fasta</option>
                </param>

                <conditional name='optional'>
                        <param name='use_options' type='select' label='Use Optional parameters?'>
                                <option value='no'>NO</option>
                                <option value='yes'>YES</option>
                        </param>
                        <when value='no'/>
                        <when value='yes'>
                                <param name="library_type" type="select" label="Strand-specific Library Type">
                                        <option value="None">None</option>
                                        <option value="F">F</option>
                                        <option value="R">R</option>
                                </param>
                        </when>
                </conditional>
        </when>
</conditional>

</inputs>

<outputs>
        <data format="txt" name="align_and_estimate_abundance_log" label="${tool.name} on ${on_string}: log" />
        <data format="bam" name="bowtie_bam" label="${tool.name} on ${on_string}: bam" from_work_dir="bowtie.bam" />
        <data format="tabular"  name="rsem_isoforms"  label="${tool.name} on ${on_string}: isoforms" from_work_dir="RSEM.isoforms.results"/>
        <data format="tabular"  name="rsem_genes" label="${tool.name} on ${on_string}: genes" from_work_dir="RSEM.genes.results"/>
</outputs>
</tool>