# HG changeset patch
# User greg
# Date 1487878496 18000
# Node ID 2cb2c3349c57f6fab050b2b3dfe669808e1c154f
# Parent 9548303eec2f82af1f905a27cd1c1df273a02a5d
Uploaded
diff -r 9548303eec2f -r 2cb2c3349c57 gene_family_classifier.xml
--- a/gene_family_classifier.xml Thu Feb 23 09:44:09 2017 -0500
+++ b/gene_family_classifier.xml Thu Feb 23 14:34:56 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:
@@ -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 -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 "#Size\tName" > $output_ptsco
- && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptsco
+ && 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
&& mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir || true
#end if
#end if