# HG changeset patch
# User greg
# Date 1483646213 18000
# Node ID b3712c598290821994d38061cdfc9e5770b71b87
# Parent  0ca4bba49038fa16a8ada58ea4c05392ee636b5a
Uploaded

diff -r 0ca4bba49038 -r b3712c598290 phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml	Thu Jan 05 14:38:49 2017 -0500
+++ b/phylogenomics_analysis.xml	Thu Jan 05 14:56:53 2017 -0500
@@ -14,10 +14,18 @@
         <![CDATA[
             #import os
             #import sys
-            #if not os.exists($orthogroup_faa.extra_files_path):
-                print > sys.stderr("The select input is not a valid list of sequences classified into gene family clusters, select another input.")
+            #set invalid_input = "The selected input is not a valid list of sequences classified into gene family clusters, select another input."
+            #if not $os.path.exists($orthogroup_faa.extra_files_path):
+                print > $sys.stderr($invalid_input)
+                $sys.exit(1)
             #end if
             #set src_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_fasta')
+            #set num_orthogroup_faa = `ls $src_dir/*.faa | wc -l`
+            #if $num_orthogroup_faa == 0:
+                print > $sys.stderr($invalid_input)
+                $sys.exit(1)
+            #end if
+            #set num_orthogroup_fna = `ls $src_dir/*.fna | wc -l`
             #set dest_dir = $output.extra_files_path
             mkdir -p $dest_dir &&
             PhylogenomicsAnalysis
@@ -43,6 +51,10 @@
                     #if str($multiple_codon_alignments) == 'yes':
                         --codon_alignments
                         #if str($use_corresponding_coding_sequences) == 'yes':
+                            #if $num_orthogroup_fna == 0:
+                                print > $sys.stderr("No corresponding coding sequences were generated for the selected input.  You must not have selected 'Yes' for the 'Create corresponding coding sequences?' option in the GeneFamilyClassifier tool for the selected input.")
+                                $sys.exit(1)
+                            #end if
                             --orthogroup_fna
                         #end if
                         --sequence_type $multiple_codon_alignments_cond.sequence_type
@@ -128,7 +140,7 @@
                                     <option value="dna">Nucleotide based</option>
                                 </param>
                                 <conditional name="use_corresponding_coding_sequences_cond">
-                                    <param name="use_corresponding_coding_sequences" type="select" label="Use corresponding coding sequences if available?" help="Ignored if 'No' was selected for the 'Create corresponding coding sequences?' option in the GeneFamilyClassifier tool for the selected 'sequences classified into gene family clusters' input above">
+                                    <param name="use_corresponding_coding_sequences" type="select" label="Use corresponding coding sequences if available?" help="Must have selected 'Yes' for the 'Create corresponding coding sequences?' option in the GeneFamilyClassifier tool for the selected input above">
                                         <option value="no" selected="true">No</option>
                                         <option value="yes">Yes</option>
                                     </param>