Mercurial > repos > greg > gene_family_classifier

changeset 97:484bedd86474 draft

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Uploaded
author greg
date Mon, 27 Feb 2017 10:48:07 -0500
parents ba924b724a8d
children e53492ae4ac0
files gene_family_classifier.xml
diffstat 1 files changed, 7 insertions(+), 34 deletions(-) [+]
line wrap: on
line diff
--- a/gene_family_classifier.xml	Mon Feb 27 10:48:00 2017 -0500
+++ b/gene_family_classifier.xml	Mon Feb 27 10:48:07 2017 -0500
@@ -22,45 +22,31 @@
                 #set create_orthogroup = $create_orthogroup_cond.create_orthogroup
                 #set specify_single_copy_cond = $options_type.specify_single_copy_cond
                 #set specify_single_copy = $specify_single_copy_cond.specify_single_copy
-
                 #if str($specify_super_orthogroups) == 'yes':
                     #set specify_super_orthos = True
                     #set super_orthogroups = $specify_super_orthogroups_cond.super_orthogroups
                 #else:
                     #set specify_super_orthos = False
                 #end if
-
                 #if str($create_orthogroup) == 'yes':
                     #set create_ortho_sequences = True
-                    #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
                     #set create_corresponding_coding_sequences_cond = $create_orthogroup_cond.create_corresponding_coding_sequences_cond
-
                     #if str($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
                     #else:
                         #set create_corresponding_coding_sequences = False
-                        #set orthogroups_fasta_dest_dir = $output_ptortho.files_path
                     #end if
-                    mkdir -p $orthogroups_fasta_dest_dir &&
                 #else:
                     #set create_ortho_sequences = False
                     #set create_corresponding_coding_sequences = False
                 #end if
-
                 #if str($specify_single_copy) == 'yes':
                     #set single_copy_orthogroup = True
                     #set single_copy_cond = $specify_single_copy_cond.single_copy_cond
                     #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
-                        mkdir -p $single_copy_fasta_dest_dir &&
-                    #end if:
                 #else:
                     #set single_copy_orthogroup = False
                 #end if
-
             #else:
                 #set single_copy_orthogroup = False
                 #set create_ortho_sequences = False
@@ -100,34 +86,21 @@
                     #end if
                 #end if
             #end if
-            >/dev/null
 
-            #if str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both':
-                #if str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes':
-                    && mv geneFamilyClassification_dir/hmmscan.log $hmmscan_log
-                #else:
-                    && rm geneFamilyClassification_dir/hmmscan.log
-                #end if
+            #if str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both' and str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes':
+                --save_hmmscan_log
+                --hmmscan_log '$hmmscan_log'
             #end if
-
             #if $create_ortho_sequences:
                 #if $create_corresponding_coding_sequences:
-                    #set out_file = $output_ptorthocs
+                    --output_ptorthocs '$output_ptorthocs'
                 #else:
-                    #set out_file = $output_ptortho
+                    --output_ptortho '$output_ptortho'
                 #end if
-                && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir || true
-                && echo -e "<html>\n<head>\n<title>orthogroups</title>\n</head>\n<body>\n<p/>\n<ul>\n" > $out_file
-                && for f in "$orthogroups_fasta_dest_dir"/*; do if [ -f "$f" ]; then echo -e "<li><a href=\"$f\">$f</a></li>\n" >> $out_file; fi; done
-                && echo -e "</ul>\n</body>\n</html>\n" >> $out_file
             #end if
-
             #if $single_copy_orthogroup:
                 #if $create_ortho_sequences:
-                    && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir || true
-                    && echo -e "<html>\n<head>\n<title>single copy orthogroups</title>\n</head>\n<body>\n<p/>\n<ul>\n" > $output_ptsco
-                    && for f in "$single_copy_fasta_dest_dir"/*; do if [ -f "$f" ]; then echo -e "<li><a href=\"$f\">$f</a></li>\n" >> $output_ptsco; fi; done
-                    && echo -e "</ul>\n</body>\n</html>\n" >> $output_ptsco
+                    --output_ptsco '$output_ptsco'
                 #end if
             #end if
         ]]>
@@ -177,7 +150,7 @@
                     </param>
                     <when value="no"/>
                     <when value="yes">
-                        <param name="super_orthogroups" type="select" label="Super Orthogroups">
+                        <param name="super_orthogroups" type="select" label="Super orthogroups clustering specification">
                             <option value="min_evalue" selected="true">Minimum e-value</option>
                             <option value="avg_evalue">Average e-value</option>
                         </param>