diff transDecoder.xml @ 0:cc71440b759f draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/transDecoder.xml	Tue Sep 22 01:58:00 2015 -0400
@@ -0,0 +1,120 @@
+<tool id='id_transDecoder' name='transDecoder' version='1.0'>
+<description> coding region </description>
+<!--requirement></requirement-->
+<requirements>
+        <requirement type="package" version="2013_08_14">trinityrnaseq</requirement>
+        <requirement type="set_environment">TRINITY_HOME</requirement>
+
+</requirements>
+<command>perl \$TRINITY_HOME/trinity-plugins/transdecoder/TransDecoder
+	
+	-t $transcript
+	
+	#if str($optional.parameters) == 'yes':
+		#if ($train):
+			--train $train
+		#end if
+
+		#if ($min_protein_length):
+			-m $min_protein_length
+		#end if
+
+		#if ($genetic_code):
+			-G $genetic_code
+		#end if
+
+		#if ($strand-specific):
+			$strand-specific	
+		#end if
+
+		#if ($lottmn):
+			-T $lottmm	
+		#end if
+
+		#if ($retain_long_orfs):
+			--retain_long_orfs $retain_long_orfs
+		#end if
+	#end if
+
+	#if str($pfam.options) == 'yes':
+		#if ($pfam_db):
+			--search_pfam $pfam_db
+		#end if
+
+		#if ($CPU):
+			--CPU $CPU
+		#end if
+	#end if	
+	
+	##log file
+	&gt; $transdecoder_log 2&gt;&amp;1;
+
+
+	## output renaming
+
+	cp -s dataset_*.dat.transdecoder.pep transcript.transdecoder.pep;
+	cp -s dataset_*.dat.transdecoder.cds transcript.transdecoder.cds;
+	cp -s dataset_*.dat.transdecoder.bed transcript.transdecoder.bed;
+	cp -s dataset_*.dat.transdecoder.gff3 transcript.transdecoder.gff3;
+	cp -s dataset_*.dat.transdecoder.mRNA transcript.transdecoder.mRNA;
+</command>
+
+<inputs>
+ <!-- Required -->
+
+  <param name='transcript' type='data' label='Transcripts [ in fasta format ]' help=' -t &lt; string &gt; ; Assembled reads in fasta file format'/>
+
+ <!-- Optional -->
+
+ <conditional name='optional'>
+ 	<param name='parameters' 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='train' type='data' optional='true' label='FASTA file with ORFs to train Markov Mod for protein identification' help='--train &lt; string &gt; ; FASTA file with ORFs to train Markov Mod for protein identification; otherwise longest non-redundant ORFs used' />
+		<param name='min_protein_length' type='integer' optional='true' value='100' label='Minimum Protein Length' help='-m &lt; int &gt; ;minimum protein length (default: 100)'/>
+		<param name='genetic_code' type='select' optional='true' label='Select Genetic Code' help=' -G &lt; string &gt; ; genetic code (default is "universal")'>
+			<option value='universal' selected='true'>Universal</option>
+			<option value='Euplotes'>Euplotes</option>
+			<option value='Tetrahymena'>Tetrahymena</option>
+			<option value='Candida'>Candida</option>
+			<option value='Acetabularia'>Acetabularia</option>
+  		</param>
+  		<param name='strand-specific' type='boolean' truevalue='-S' falsevalue='' optional='true' label='Strand-Specific [ -S ]' help='strand-specific (only analyzes top strand)'/> 
+  		<param name='lottmm' type='integer' optional='true' value='500' label=' -T ; Needs a label ??? ' help='-T &lt; int &gt; ; If no --train, top longest ORFs to train Markov Model (hexamer stats) (default: 500)'/>	
+  		<param name='retain_long_orfs' type="integer" optional='true' value="900" label=' --retain_long_orfs ; Needs a label ??? ' help='--retain_long_orfs &lt; int &gt; ; Retain all ORFs found that are equal or longer than these many nucleotides even if no other evidence marks it as coding (default: 900 bp => 300aa)' />
+	 </when>
+ </conditional>
+
+
+ <!-- Pfam Options -->
+
+ <conditional name='pfam'>
+	<param name='options' type='select' label='Use Pfam Options [ Optional ]'>
+		<option value='no'>NO</option>
+		<option value='yes'>YES</option>	
+	</param>
+	<when value='no'/>
+	<when value='yes'>
+		<param name='pfam_db' type='select' label='Search pfam database' help=' --search_pfam  &lt; pfam_db.hmm &gt; ; /path/to/pfam_db.hmm to search using hmmscan'>
+    			<options from_file="pfam_db.loc">
+				<column name="name" index="0"/>
+		       	 	<column name="value" index="2"/>
+			</options>
+		</param>
+		<param name='CPU' type='integer' value='2'  label='CPU' help='--CPU &lt; int &gt; Number of CPU for the job'/>
+	</when>
+  </conditional>
+
+</inputs>
+<outputs>
+	<data name='transdecoder_pep' format='fasta' label="${tool.name} on ${on_string}: pep" from_work_dir="transcript.transdecoder.pep"/>
+	<data name='transdecoder_cds' format='fasta' label="${tool.name} on ${on_string}: cds" from_work_dir="transcript.transdecoder.cds"/>
+	<data name='transdecoder_bed' format='bed' label="${tool.name} on ${on_string}: bed" from_work_dir="transcript.transdecoder.bed"/>
+	<data name='transdecoder_gff3' format='tabular' label="${tool.name} on ${on_string}: gff3" from_work_dir="transcript.transdecoder.gff3"/>
+	<data name='transdecoder_mRNA' format='fasta' label="${tool.name} on ${on_string}: mRNA" from_work_dir="transcript.transdecoder.mRNA"/>
+	<data name='transdecoder_log' format='txt' label="${tool.name} on ${on_string}: log" />
+</outputs>
+</tool>