view align_and_estimate_abundance.xml @ 0:d4c781f09244 draft default tip

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<tool id='id_align_and_estimate_abundance' name='align_and_estimate_abundance' version='1.0'>

<description>align_and_estimate_abundance</description>

<requirements>
        <requirement type="package" version="2013_08_14">trinityrnaseq</requirement>
        <requirement type="package" version="1.1.17">rsem</requirement>
        <requirement type="package" version="1.5.1">eXpress</requirement>
        <requirement type="package" version="2.1.0">bowtie2</requirement>
        <requirement type="package" version="0.12.7">bowtie</requirement>
        <requirement type="package" version="0.1.18">samtools</requirement>
        <requirement type="set_environment">TRINITY_HOME</requirement>

</requirements>
<command >perl \$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="fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
		<param format="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="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>