Mercurial > repos > greg > gene_family_classifier
changeset 80:f71d34c9e6fc draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 23 Feb 2017 08:39:30 -0500 |
| parents | 887abff6ee25 |
| children | d8975fc916e0 |
| files | gene_family_classifier.xml |
| diffstat | 1 files changed, 14 insertions(+), 8 deletions(-) [+] |
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--- 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 '<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($orthogroups_fasta_src_dir)): + && echo '<li><a href="$fname">$fname</a></li>\n' >> $out_file + #end for + && echo '</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 "#Size\tName" > $output_ptsco - && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptsco + && echo '<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($orthogroups_fasta_src_dir)): + && echo '<li><a href="$fname">$fname</a></li>\n' >> $output_ptsco + #end for + && echo '</ul>\n</body>\n</html>\n' >> $output_ptsco && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir || true #end if #end if