minor fixes

- more consistent macro names
- readme reformulation

tools/eggnog_mapper/eggnog_macros.xml

@@ -444,7 +444,7 @@ python '${__tool_directory__}/data_manager_eggnog.py' --config_file '$out_file'
 
     <token name="@SEED_ORTHOLOG_COLUMNS@">query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,query_start,query_end,seed_start,seed_end,pident,query_cov,seed_cov</token>
 
-    <xml name="ortho_search_outputs_macro">
+    <xml name="ortho_search_output_macro">
         <data name="seed_orthologs" format="tabular" label="${tool.name} on ${on_string}: seed_orthologs" from_work_dir="results.emapper.seed_orthologs">
             <filter>ortho_method['m'] not in ['no_search', 'cache']</filter>
             <actions>

tools/eggnog_mapper/eggnog_mapper/README

@@ -5,17 +5,17 @@ This folder contains three tools:
 3. eggnogg_mapper_annotate: which implements the annotation phase
 
 While the search phase of eggnog_mapper is very CPU intense and is efficient
-also for larger number of threads, the anotation phase is very IO intensive
+also for a larger number of threads, the annotation phase is very IO intensive
 and can be very inefficient (depending on the configuration, e.g. if the
 reference data is located on a slow partition).
 
-While for most applications eggnogg_mapper will be sufficient separating the
+While for most applications eggnogg_mapper will be sufficient to separate the
 two phases can be more efficient: 
 
 - sending eggnogg_mapper_search to a destination using many threads
-- and eggnogg_mapper_annotate to a destination using a small numbe of threads
+- and eggnogg_mapper_annotate to a destination using a small number of threads
 
-If eggnogg_mapper_annotate is send to a single core destination
+If eggnogg_mapper_annotate is sent to a single core destination
 the option `--dbmem` is activated which will copy the complete
 EggNOG annotation DB into memory which is usually much faster
 than using multiple cores (but needs approx. 37GB of RAM).

tools/eggnog_mapper/eggnog_mapper/eggnog_mapper.xml

@@ -41,7 +41,7 @@
         <expand macro="output_options_annotate_macro"/>
     </inputs>
     <outputs>
-        <expand macro="ortho_search_outputs_macro"/>
+        <expand macro="ortho_search_output_macro"/>
         <expand macro="annotation_output_macro">
             <filter>annotation_options['no_annot'] == ''</filter>
         </expand>

tools/eggnog_mapper/eggnog_mapper/eggnog_mapper_search.xml

@@ -22,7 +22,7 @@
         <expand macro="output_options_macro"/>
     </inputs>
     <outputs>
-        <expand macro="ortho_search_outputs_macro"/>
+        <expand macro="ortho_search_output_macro"/>
     </outputs>
     <tests>
         <!-- test producing only seed orthologs-->