Mercurial > repos > greg > gene_family_classifier

changeset 86:9548303eec2f draft

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Uploaded
author greg
date Thu, 23 Feb 2017 09:44:09 -0500
parents 97f9b65d8e44
children 2cb2c3349c57
files gene_family_classifier.xml
diffstat 1 files changed, 9 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- a/gene_family_classifier.xml	Thu Feb 23 09:35:18 2017 -0500
+++ b/gene_family_classifier.xml	Thu Feb 23 09:44:09 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.files_path
+                        #set orthogroups_fasta_dest_dir = $output_ptorthocs.extra_files_path
                     #else:
                         #set create_corresponding_coding_sequences = False
-                        #set orthogroups_fasta_dest_dir = $output_ptortho.files_path
+                        #set orthogroups_fasta_dest_dir = $output_ptortho.extra_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.files_path
+                        #set single_copy_fasta_dest_dir = $output_ptsco.extra_files_path
                         mkdir -p $single_copy_fasta_dest_dir &&
                     #end if:
                 #else:
@@ -112,25 +112,19 @@
 
             #if $create_ortho_sequences:
                 #if $create_corresponding_coding_sequences:
-                    #set out_file = $output_ptorthocs
+                    && echo -e "#Size\tName" > $output_ptorthocs
+                    && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptorthocs
                 #else:
-                    #set out_file = $output_ptortho
+                    && echo -e "#Size\tName" > $output_ptortho
+                    && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $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 $os.listdir($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
                 && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir || true
             #end if
 
             #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 $os.listdir($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
+                    && echo -e "#Size\tName" > $output_ptsco
+                    && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptsco
                     && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir || true
                 #end if
             #end if