Merge pull request #210 from nicola-debernardini/pan-Draft

Add citation information

README.md

@@ -82,3 +82,7 @@ GNU General Public License version 3.0 ([GPLv3](https://www.gnu.org/licenses/gpl
   Licensed under the [GPL-3.0](https://www.gnu.org/licenses/gpl-3.0.en.html) license.
   Link to license: https://github.com/Ecogenomics/GTDBTk/blob/master/LICENSE
   Website: https://ecogenomics.github.io/GTDBTk/
+
+## Citation
+- Zimmermann, J., Kaleta, C. & Waschina, S. gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models. Genome Biol 22, 81 (2021). https://doi.org/10.1186/s13059-021-02295-1
+- De Bernardini, N., Zampieri, G., Campanaro, S., Zimmermann, J., Waschina, S. & Treu, L. pan-Draft: Automated reconstruction of species-representative metabolic models from multiple genomes. *Currently under revision*

docs/usage/panDraft.md

@@ -1,5 +1,7 @@
 # panDraft: species-level models
 
+*Details on performance of pan-Draft module are currently under evaluation for pubblication*
+
 When dealing with environmental samples, it's common for Metagenome-Assembled Genomes (MAGs) obtained from genome centric metagenomics to be incomplete and contaminated. Consequently, Genome-Scale Models (GEMs) derived from these incomplete MAGs lack a substantial portion of the metabolic potential of the corresponding species. In response, once a set of draft models is reconstructed, they can be conbined into a comprehensive model specific to the taxonomic group. This approach aims to fill the gaps present in individual models by combining homology-based searches and pan-reactome analysis.
 
 Using `gapseq pan`, draft species-level models can be generated to enhance the representativeness of the taxa (species) metabolism.

src/pan-draft.R

@@ -38,7 +38,6 @@ for(i in parm_idx){
 }
 opt <- getopt(spec, args_mod)
 
-
 # Help Screen
 if ( !is.null(opt$help) | is.null(opt$models_path)){
   cat(getopt(spec, usage=TRUE))
@@ -171,7 +170,7 @@ for (mod_idx in names(model_list)) {
     mod_ids <- c(mod_ids, n_name)
     model_list[[mod_idx]] <- mod
   } else {
-    mod_ids <- c(mod_ids, mod@mod_id)    
+    mod_ids <- c(mod_ids, mod@mod_id)
   }
   # Add annotation column to model attributes if not already there
   mod <- add_annotation_column_to_attributes(mod)