Mercurial > repos > greg > gene_family_classifier

changeset 85:97f9b65d8e44 draft

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Uploaded
author greg
date Thu, 23 Feb 2017 09:35:18 -0500
parents 2b9ceaf853cf
children 9548303eec2f
files gene_family_classifier.xml
diffstat 1 files changed, 5 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/gene_family_classifier.xml	Thu Feb 23 09:23:05 2017 -0500
+++ b/gene_family_classifier.xml	Thu Feb 23 09:35:18 2017 -0500
@@ -37,10 +37,10 @@
 
                     #if str($create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences) == 'yes':
                         #set create_corresponding_coding_sequences = True
-                        #set orthogroups_fasta_dest_dir = $output_ptorthocs.extra_files_path
+                        #set orthogroups_fasta_dest_dir = $output_ptorthocs.files_path
                     #else:
                         #set create_corresponding_coding_sequences = False
-                        #set orthogroups_fasta_dest_dir = $output_ptortho.extra_files_path
+                        #set orthogroups_fasta_dest_dir = $output_ptortho.files_path
                     #end if
                     mkdir -p $orthogroups_fasta_dest_dir &&
                 #else:
@@ -54,7 +54,7 @@
                     #set single_copy = $single_copy_cond.single_copy
                     #if $create_ortho_sequences:
                         #set single_copy_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'single_copy_fasta')
-                        #set single_copy_fasta_dest_dir = $output_ptsco.extra_files_path
+                        #set single_copy_fasta_dest_dir = $output_ptsco.files_path
                         mkdir -p $single_copy_fasta_dest_dir &&
                     #end if:
                 #else:
@@ -117,7 +117,7 @@
                     #set out_file = $output_ptortho
                 #end if
                 && echo -e '<html>\n<head>\n<title>Galaxy - GeneFamilyClassifier Output</title>\n</head>\n<body>\n<p/>\n<ul>\n' > $out_file
-                #for $fname in sorted($os.listdir($orthogroups_fasta_src_dir)):
+                #for $fname in $os.listdir($orthogroups_fasta_src_dir):
                     && echo -e '<li><a href="$fname">$fname</a></li>\n' >> $out_file
                 #end for
                 && echo -e '</ul>\n</body>\n</html>\n' >> $out_file
@@ -127,7 +127,7 @@
             #if $single_copy_orthogroup:
                 #if $create_ortho_sequences:
                     && echo -e '<html>\n<head>\n<title>Galaxy - GeneFamilyClassifier Output</title>\n</head>\n<body>\n<p/>\n<ul>\n' > $output_ptsco
-                    #for $fname in sorted($os.listdir($single_copy_fasta_src_dir)):
+                    #for $fname in $os.listdir($single_copy_fasta_src_dir):
                         && echo -e '<li><a href="$fname">$fname</a></li>\n' >> $output_ptsco
                     #end for
                     && echo -e '</ul>\n</body>\n</html>\n' >> $output_ptsco