# HG changeset patch
# User gkumar09
# Date 1443036328 14400
# Node ID 8061878519dc83b3bc316875df40cc03d6e8f804
# Parent  6b72a97471c656cca627328cd29d4cee2c55bdd2
Deleted selected files

diff -r 6b72a97471c6 -r 8061878519dc transcriptsToOrfs.xml
--- a/transcriptsToOrfs.xml	Wed Sep 23 15:25:19 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,53 +0,0 @@
-<tool id="transcriptsToOrfs" name="transcriptsToOrfs" version="0.0.1">
-	
-    <description>Trinity Transcripts to Candidate Peptides</description>
-    <requirements>
-        <requirement type="package">trinity</requirement>
-    </requirements>
-    <command interpreter="python">
-        trinityToolWrapper.py Analysis/Coding/transcripts_to_best_scoring_ORFs.pl 
-
-		-t $transcripts 
-		-m $min_prot_length 
-		--CPU $CPU
-		--search_pfam "${ filter( lambda x: str( x[0] ) == str( $pfam_db ), $__app__.tool_data_tables[ 'pfam_databases' ].get_fields() )[0][-1] }"
-
-		#if str($strand_specificity) == 'SS':
-			-S
-		#end if
-		                
-        ## direct to output
-        > output 
- 
-    </command>
-    <inputs>
-
-		<param format="fasta" name="transcripts" type="data" label="Transcripts sequences in fastA format" help="" />
-
-		<param name="min_prot_length"  type="integer" label="Minimum peptide length (in amino acids)" value="100" min="50" help="" />
-		
-		<param name="strand_specificity" type="select" label="Strand specificity type">
-			<option value="DS">NOT strand specific, examine both strands</option>
-			<option value="SS">Strand specific, examine only top strand</option>
-		</param>
-	
-    	<param name="pfam_db" type="select" label="Pfam database">
-            <options from_data_table="pfam_databases" />
-		</param>
-	
-		<param name="CPU" type="integer" value="2" min="1" label="CPU" help="Number of CPUs to use by hmmscan" />
-
-    </inputs>
-    <outputs>
-        <data format="txt" name="trinity_pep_pfam" label="${tool.name} on ${on_string}: Pfam matches to Candidate Peptide Sequences" from_work_dir="longest_orfs.pep.pfam.dat"/>
-        <data format="fasta" name="trinity_pep_seqs" label="${tool.name} on ${on_string}: Candidate Peptide Sequences" from_work_dir="best_candidates.eclipsed_orfs_removed.pep"/>
-		<data format="bed" name="trinity_pep_coords" label = "${tool.name} on ${on_string} Candidate Peptide Coordinates" from_work_dir="best_candidates.eclipsed_orfs_removed.bed" />
-    </outputs>
-    <tests>
-    </tests>
-    <help>
-        Trinity is a de novo transcript assembler that uses RNA-seq data as input. This tool runs all Trinity_ commands--Inchworm, Chrysalis, and Butterfly--in a single pass.
-        
-        .. _Trinity: http://trinityrnaseq.sourceforge.net
-    </help>
-</tool>