diff testing6/align_and_estimate_abundance.xml @ 0:fbafdad29706 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/testing6/align_and_estimate_abundance.xml	Fri Jul 31 03:25:28 2015 -0400
@@ -0,0 +1,150 @@
+<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>
+