# HG changeset patch
# User greg
# Date 1490623074 14400
# Node ID de42cdf6e10b714023d3321040040da1269dee11
# Parent 56dbe45f4bfb8a0623ba5f3807fcd6dbc095063b
Uploaded
diff -r 56dbe45f4bfb -r de42cdf6e10b macros.xml
--- a/macros.xml Thu Mar 23 15:01:27 2017 -0400
+++ b/macros.xml Mon Mar 27 09:57:54 2017 -0400
@@ -13,7 +13,7 @@
-
+
#set remove_gappy_sequences_cond = $options_type_cond.remove_gappy_sequences_cond
#set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences
#if str($remove_gappy_sequences) == 'no':
@@ -53,18 +53,57 @@
#set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option
#if str($multiple_sequence_alignments_option) == 'pasta_alignments':
#set pasta_iter_limit = $multiple_sequence_alignments_option_cond.pasta_iter_limit
- #else if str($multiple_sequence_alignments_option) == 'iterative_realignments':
- #set iterative_realignments = $multiple_sequence_alignments_option_cond.iterative_realignments
+ #else if str($multiple_sequence_alignments_option) == 'iterative_realignment':
+ #set iterative_realignment = $multiple_sequence_alignments_option_cond.iterative_realignment
#end if
#end if
#end if
#end if
-
+
+ #if str($remove_gappy_sequences) == 'no':
+ #if str($multiple_sequence_alignments) == 'yes':
+ --alignments_method $multiple_sequence_alignments_option
+ #if str($multiple_sequence_alignments_option) == 'pasta_alignments':
+ --pasta_script_path '$__tool_directory__/run_pasta.py'
+ --pasta_iter_limit $pasta_iter_limit
+ #end if
+ #end if
+ #else:
+ ## str($remove_gappy_sequences) == 'yes':
+ --trim_type $trim_type
+ #if str($trim_type) == 'gap_trimming':
+ --gap_trimming $gap_trimming
+ #end if
+ #if str($remove_sequences_with_gaps) == 'no':
+ #if str($multiple_sequence_alignments) == 'yes':
+ --alignments_method $multiple_sequence_alignments_option
+ #if str($multiple_sequence_alignments_option) == 'pasta_alignments':
+ --pasta_script_path '$__tool_directory__/run_pasta.py'
+ --pasta_iter_limit $pasta_iter_limit
+ #end if
+ #end if
+ #else:
+ ## str($remove_sequences_with_gaps) == 'yes':
+ --remove_sequences $remove_sequences_with_gaps_of
+ #if str($multiple_sequence_alignments) == 'yes':
+ --alignments_method $multiple_sequence_alignments_option
+ #if str($multiple_sequence_alignments_option) == 'pasta_alignments':
+ #if str($multiple_sequence_alignments_option) == 'pasta_alignments':
+ --pasta_script_path '$__tool_directory__/run_pasta.py'
+ --pasta_iter_limit $pasta_iter_limit
+ #else:
+ --iterative_realignment $iterative_realignment
+ #end if
+ #end if
+ #end if
+ #end if
+
+
#set phylogenetic_trees_cond = $options_type_cond.phylogenetic_trees_cond
#set phylogenetic_trees = $phylogenetic_trees_cond.phylogenetic_trees
-
+
#set tree_inference_cond = $phylogenetic_trees_cond.tree_inference_cond
#set tree_inference = $tree_inference_cond.tree_inference
#if str($tree_inference) == 'raxml':
@@ -75,8 +114,21 @@
#end if
#set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates
#end if
+ #set min_orthogroup_size = $phylogenetic_trees_cond.min_orthogroup_size
#set max_orthogroup_size = $phylogenetic_trees_cond.max_orthogroup_size
- #set min_orthogroup_size = $phylogenetic_trees_cond.min_orthogroup_size
+
+
+ --tree_inference $tree_inference
+ #if str($tree_inference) == 'raxml':
+ #if str($rooting_order_file) == 'yes':
+ --rooting_order '$rooting_order'
+ ## No else block needed here because the default rooting_order
+ ## configuration will be used if the --rooting_order flag is missing.
+ #end if
+ --bootstrap_replicates $bootstrap_replicates
+ #end if
+ --min_orthogroup_size $min_orthogroup_size
+ --max_orthogroup_size $max_orthogroup_size
@@ -142,10 +194,10 @@
-
+
-
+
@@ -167,16 +219,16 @@
-
+
-
+
-
-
+
+
@@ -282,7 +334,7 @@
-
+
diff -r 56dbe45f4bfb -r de42cdf6e10b phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml Thu Mar 23 15:01:27 2017 -0400
+++ b/phylogenomics_analysis.xml Mon Mar 27 09:57:54 2017 -0400
@@ -22,11 +22,10 @@
#if str($options_type) == 'advanced':
#if str($input_format) == 'ptortho':
- @REMOVE_GAPPY_SEQUENCES_COND@
- @SET_PHYLOGENETIC_TREES@
+ @REMOVE_GAPPY_SEQUENCES_COND_PREP@
+ @SET_PHYLOGENETIC_TREES_PREP@
#if str($phylogenetic_trees) == 'yes':
- @TREE_INFERENCE_COND@
- #set sequence_type = 'protein'
+ @TREE_INFERENCE_COND_PREP@
#end if
#else:
## str($input_format) == 'ptorthocs'
@@ -36,20 +35,19 @@
#set options_type = $options_type_cond.options_type
#if str($orthogroup_fna) == 'yes':
#if str(options_type) == 'advanced':
- @REMOVE_GAPPY_SEQUENCES_COND@
+ @REMOVE_GAPPY_SEQUENCES_COND_PREP@
#set multiple_codon_alignments = $options_type_cond.multiple_codon_alignments
- @SET_PHYLOGENETIC_TREES@
+ @SET_PHYLOGENETIC_TREES_PREP@
#if str($phylogenetic_trees) == 'yes':
- @TREE_INFERENCE_COND@
- #set sequence_type = $phylogenetic_trees_cond.sequence_type
+ @TREE_INFERENCE_COND_PREP@
#end if
#end if
#else:
#if str(options_type) == 'advanced':
- @REMOVE_GAPPY_SEQUENCES_COND@
- @SET_PHYLOGENETIC_TREES@
+ @REMOVE_GAPPY_SEQUENCES_COND_PREP@
+ @SET_PHYLOGENETIC_TREES_PREP@
#if str($phylogenetic_trees) == 'yes':
- @TREE_INFERENCE_COND@
+ @TREE_INFERENCE_COND_PREP@
#set sequence_type = $phylogenetic_trees_cond.sequence_type
#end if
#end if
@@ -58,54 +56,42 @@
#end if
python $__tool_directory__/phylogenomics_analysis.py
- --num_threads \${GALAXY_SLOTS:-4}
- #if str($input_format) == 'ptortho':
- --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
- #else:
- --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
- #if str($orthogroup_fna) == 'yes':
- --orthogroup_fna 'true'
- #end if
- #set multiple_codon_alignments = $input_format_cond.multiple_codon_alignments
- #if str($multiple_codon_alignments) == 'yes':
- --codon_alignments 'true'
- #end if
- #end if
--config_dir '$scaffold.fields.path'
--scaffold '$scaffold.fields.path'
--method $method
+ --num_threads \${GALAXY_SLOTS:-4}
- #if str($options_type) == 'advanced':
- #if str($multiple_sequence_alignments) == 'yes':
- --alignments_method $multiple_sequence_alignments_option
- #if str($multiple_sequence_alignments_option) == 'pasta_alignments':
- --pasta_script_path '$__tool_directory__/run_pasta.py'
- --pasta_iter_limit $multiple_sequence_alignments_option_cond.pasta_iter_limit
+ #if str($input_format) == 'ptortho':
+ --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
+ #if str($options_type) == 'advanced':
+ @REMOVE_GAPPY_SEQUENCES_COND_CMD@
+ #if str($phylogenetic_trees) == 'yes':
+ @TREE_INFERENCE_COND_CMD@
+ --sequence_type 'protein'
#end if
#end if
-
- #if str($phylogenetic_trees) == 'yes':
- --tree_inference $tree_inference
- #if str($tree_inference) == 'raxml':
- #if str($rooting_order_file) == 'yes':
- --rooting_order '$rooting_order_file_cond.rooting_order'
- # No else block needed here because the default rooting_order
- # configuration will be used if the --rooting_order flag is missing.
+ #else:
+ ## str($input_format) == 'ptorthocs'
+ --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
+ #if str($orthogroup_fna) == 'yes':
+ --orthogroup_fna 'true'
+ #if str(options_type) == 'advanced':
+ @REMOVE_GAPPY_SEQUENCES_COND_CMD@
+ #if str($multiple_codon_alignments) == 'yes':
+ --codon_alignments 'true'
#end if
- --bootstrap_replicates $tree_inference_cond.bootstrap_replicates
+ #if str($phylogenetic_trees) == 'yes':
+ @TREE_INFERENCE_COND_CMD@
+ --sequence_type = $phylogenetic_trees_cond.sequence_type
+ #end if
#end if
- --max_orthogroup_size $options_type_cond.phylogenetic_trees_cond.max_orthogroup_size
- --min_orthogroup_size $options_type_cond.phylogenetic_trees_cond.min_orthogroup_size
- --sequence_type $sequence_type
- #end if
-
- #if str($remove_gappy_sequences) == 'yes':
- #if str($remove_sequences_with_gaps) == 'yes':
- --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of
- #end if
- --trim_type $trim_type_cond.trim_type
- #if str($trim_type_cond.trim_type) == 'gap_trimming':
- --gap_trimming $trim_type_cond.gap_trimming
+ #else:
+ #if str(options_type) == 'advanced':
+ @REMOVE_GAPPY_SEQUENCES_COND_CMD@
+ #if str($phylogenetic_trees) == 'yes':
+ @TREE_INFERENCE_COND_CMD@
+ --sequence_type = $phylogenetic_trees_cond.sequence_type
+ #end if
#end if
#end if
#end if