# HG changeset patch # User greg # Date 1487857170 18000 # Node ID f71d34c9e6fcabd6a0b00bafe0191424f52fcc59 # Parent 887abff6ee2520b355b4652807301a94c7713091 Uploaded diff -r 887abff6ee25 -r f71d34c9e6fc gene_family_classifier.xml --- a/gene_family_classifier.xml Wed Feb 22 09:11:57 2017 -0500 +++ b/gene_family_classifier.xml Thu Feb 23 08:39:30 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: @@ -112,19 +112,25 @@ #if $create_ortho_sequences: #if $create_corresponding_coding_sequences: - && echo -e "#Size\tName" > $output_ptorthocs - && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptorthocs + # set out_file = $output_ptorthocs #else: - && echo -e "#Size\tName" > $output_ptortho - && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptortho + # set out_file = $output_ptortho #end if + && echo '\n\nGalaxy - GeneFamilyClassifier Output\n\n\n

\n

\n\n\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 "#Size\tName" > $output_ptsco - && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptsco + && echo '\n\nGalaxy - GeneFamilyClassifier Output\n\n\n

\n

\n\n\n' >> $output_ptsco && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir || true #end if #end if