# HG changeset patch
# User greg
# Date 1487861049 18000
# Node ID 9548303eec2f82af1f905a27cd1c1df273a02a5d
# Parent 97f9b65d8e445df3276ae87e5331a2a92f8a580d
Uploaded
diff -r 97f9b65d8e44 -r 9548303eec2f gene_family_classifier.xml
--- 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 '\n\nGalaxy - GeneFamilyClassifier Output\n\n\n\n\n' > $out_file
- #for $fname in $os.listdir($orthogroups_fasta_src_dir):
- && echo -e '- $fname
\n' >> $out_file
- #end for
- && echo -e '
\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 '\n\nGalaxy - GeneFamilyClassifier Output\n\n\n\n\n' > $output_ptsco
- #for $fname in $os.listdir($single_copy_fasta_src_dir):
- && echo -e '- $fname
\n' >> $output_ptsco
- #end for
- && echo -e '
\n\n\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