update PhlAnProf rules, add lines of code to strphlan_clade_profiling to...

update PhlAnProf rules, add lines of code to strphlan_clade_profiling to create additional figures with ggtree

config.yaml

@@ -48,3 +48,10 @@ preprocess:
     # http://seqanswers.com/forums/archive/index.php/t-42552.html
     bbmap_reference: '/home/mticlla/Documents/Git_repositories/metagenomicsnake/ref/hg19_main_mask_ribo_animal_allplant_allfungus.fa.gz'
     bbmap_ref_dir: '/home/mticlla/Documents/Git_repositories/metagenomicsnake/ref/ref_bbsplit'
+    
+phlanprof:
+    strphlan_clade_profiling:
+        metadatas:
+            - 'SubjectID'
+            - 'Group'
+        colorized_metadata: 'Group'

rules/phlanprof.smk

@@ -220,7 +220,9 @@ rule strphlan_clade_profiling:
         clade_results = OUT_DIR + '/{dataset}/PhlAnProf/logs/strphlan/clades_profiled/{clade}.log'
     params:
         mpa_pkl = METASNK_DB_DIR + '/metaphlan_databases/mpa_v20_m200.pkl',
-        strpa_dir = METASNK_DB_DIR+'/strainphlan_markers'
+        strpa_dir = METASNK_DB_DIR+'/strainphlan_markers',
+        metadatas = config['phlanprof']['strphlan_clade_profiling']['metadatas'],
+        colorized_metadata = config['phlanprof']['strphlan_clade_profiling']['colorized_metadata']
     threads: cpus_avail
     singularity:singularity_metaprof
     group: 'strphlan_clade_analysis'
@@ -239,12 +241,20 @@ rule strphlan_clade_profiling:
         add_metadata_tree.py \
         --ifn_trees {output.clade_result_dir}/RAxML_bestTree.{wildcards.clade}.tree \
         --ifn_metadatas {input.samples_metadata} \
-        --metadatas SubjectID; \
+        --metadatas {params.metadatas}; \
         plot_tree_graphlan.py \
         --ifn_tree {output.clade_result_dir}/RAxML_bestTree.{wildcards.clade}.tree.metadata \
-        --colorized_metadata SubjectID \
+        --colorized_metadata {params.colorized_metadata} \
         --leaf_marker_size 60 \
-        --legend_marker_size 60; fi') &>{log}
+        --legend_marker_size 60; \
+        deactivate; \
+        source activate py27breadcrumbs; \ 
+        strainphlan_ggtree.R \
+        {output.clade_result_dir}/RAxML_bestTree.{wildcards.clade}.tree \
+        {input.samples_metadata} \
+        {output.clade_result_dir}/{wildcards.clade}.fasta \
+        {output.clade_result_dir}/RAxML_bestTree.{wildcards.clade}.tree_1.png \
+        {output.clade_result_dir}/RAxML_bestTree.{wildcards.clade}.tree_2.png; fi') &>{log}
         '''
 
 def aggregate_clade_profiles(wildcards):