# HG changeset patch
# User greg
# Date 1486064519 18000
# Node ID 6b547036c627dd2cf5de792555de3ceb772879be
# Parent  0bf214a0646a4148e145e19756ae1db464bf95c8
Uploaded

diff -r 0bf214a0646a -r 6b547036c627 phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml	Thu Feb 02 11:38:52 2017 -0500
+++ b/phylogenomics_analysis.xml	Thu Feb 02 14:41:59 2017 -0500
@@ -20,7 +20,11 @@
         	#set scaffold_dir = $os.path.split($scaffold_path)[0]
         	#set scaffold_selection = $os.path.split($scaffold_path)[1]
             #set src_fasta_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_fasta')
-            #set dest_fasta_dir = $output_fasta.extra_files_path
+            #if str($input.ext) == 'ptcgf':
+            	#set dest_fasta_dir = $output_fasta_ptcgf.extra_files_path
+            else:
+            	#set dest_fasta_dir =$output_fasta_ptcgfcs.extra_files_path
+           	#end if
 
             #if str($options_type.options_type_selector) == 'advanced' and str($options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments) == 'yes':
                 #set generate_output_aln = True
@@ -91,7 +95,7 @@
                         #if str($multiple_codon_alignments) == 'yes':
                             --codon_alignments
                             #if str($use_corresponding_coding_sequences) == 'yes':
-                            	#if str($input.ext) == 'pgfccs):
+                            	#if str($input.ext) == 'ptcgfcs):
                                 	--orthogroup_fna
                               	#else:
                               		raise Exception("Selected input does not include corresponding coding sequences")
@@ -133,8 +137,13 @@
                 #end if
             #end if
 
-            && echo "Sequence alignments and corresponding phylogenies: `ls $src_fasta_dir | grep f | wc -l` files" > $output_fasta
-            && ls -al $src_fasta_dir | grep f >> $output_fasta
+			#if str($input.ext) == 'ptcgf':
+            	&& echo "Sequence alignments and corresponding phylogenies: `ls $src_fasta_dir | grep f | wc -l` files" > $output_fasta_ptcgf
+            	&& ls -al $src_fasta_dir | grep f >> $output_fasta_ptcgf
+           	#else:
+            	&& echo "Sequence alignments and corresponding phylogenies: `ls $src_fasta_dir | grep f | wc -l` files" > $output_fasta_ptcgfcs
+            	&& ls -al $src_fasta_dir | grep f >> $output_fasta_ptcgfcs
+           	#end if
             && mv $src_fasta_dir/* $dest_fasta_dir || true
 
             #if $generate_output_aln:
@@ -151,7 +160,7 @@
         ]]>
     </command>
     <inputs>
-        <param name="input" format="pgfc,pgfccs" type="data" label="Select gene family clusters" help="Selection may optionally include corresponding coding sequences"/>
+        <param name="input" format="ptcgf,ptcgfcs" type="data" label="Select gene family clusters" help="Selection may optionally include corresponding coding sequences"/>
         <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
             <options from_data_table="plant_tribes_scaffolds" />
             <validator type="no_options" message="No PlantTribes scaffolds are available.  Use the PlantTribes Scaffolds Download Data Manager tool to install and populate the PlantTribes scaffolds data table."/>
@@ -283,11 +292,16 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="output_fasta" format="txt" label="Sequence alignments and corresponding phylogenies on ${on_string}"/>
+        <data name="output_fasta_ptcgf" format="ptcgf" label="Sequence alignments and corresponding phylogenies on ${on_string}">
+        	<filter>input.ext == 'ptcgf'</filter>
+        </data>
+        <data name="output_fasta_ptcgfcs" format="ptcgfcs" label="Sequence alignments and corresponding phylogenies on ${on_string}">
+        	<filter>input.ext == 'ptcgfcs'</filter>
+        </data>
         <data name="output_aln" format="txt" label="Multiple alignments on ${on_string}">
             <filter>options_type['options_type_selector'] == 'advanced' and options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments'] == 'yes'</filter>
         </data>
-        <data name="output_tree" format="txt" label="Phylogenetic trees on ${on_string}">
+        <data name="output_tree" format="ptpt" label="Phylogenetic trees on ${on_string}">
             <filter>options_type['options_type_selector'] == 'advanced' and options_type['phylogenetic_trees_cond']['phylogenetic_trees'] == 'yes'</filter>
         </data>
     </outputs>
@@ -314,10 +328,10 @@
 * **Multiple sequence alignments options**
 
  - **Select method for multiple sequence alignments** - Method used for setting multiple sequence alignments.
- - **Input sequences include corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'pgfccs'.
+ - **Input sequences include corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'ptcgfcs'.
  - **Construct orthogroup multiple codon alignments?** - Construct orthogroup multiple codon alignments.
  - **Sequence type used in the phylogenetic inference** - Sequence type (dna or amino acid) used in the phylogenetic inference.
- - **Use corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'pgfccs' or this tool will produce an error.
+ - **Use corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'ptcgfcs' or this tool will produce an error.
 
 * **Phylogenetic trees options**