fixed command line options

Author: Dom Laetsch

create.py

@@ -4,7 +4,7 @@
 """usage: blobtools create     -i FASTA [-y FASTATYPE] [-o OUTFILE] [--title TITLE]
                               [-b BAM...] [-s SAM...] [-a CAS...] [-c COV...]  
                               [--nodes <NODES>] [--names <NAMES>] [--db <NODESDB>] 
-                              [-t TAX...] [-r TAXRULE...]
+                              [-t TAX...] [-x TAXRULE...]
                               [-h|--help] 
     
     Options:
@@ -15,7 +15,7 @@
                                     (Parsing supported for 'spades', 'soap', 'velvet', 'abyss')
         -t, --taxfile TAX...        Taxonomy file in format (qseqid\\ttaxid\\tbitscore) 
                                     (e.g. BLAST output "--outfmt '6 qseqid staxids bitscore'")
-        -r, --taxrule <TAXRULE>...  Taxrule determines how taxonomy of blobs is computed [default: bestsum]
+        -x, --taxrule <TAXRULE>...  Taxrule determines how taxonomy of blobs is computed [default: bestsum]
                                     "bestsum"       : sum bitscore across all hits for each taxonomic rank
                                     "bestsumorder"  : sum bitscore across all hits for each taxonomic rank. 
                                                   - If first <TAX> file supplies hits, bestsum is calculated. 

view.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-"""usage: blobtools view    -i <BLOBDB> [-r <TAXRULE>] [--rank <TAXRANK>...] [--hits]
+"""usage: blobtools view    -i <BLOBDB> [-x <TAXRULE>] [--rank <TAXRANK>...] [--hits]
                             [--list <LIST>] [--out <OUT>]
                             [--h|--help] 
     
@@ -11,9 +11,9 @@
         -o, --out <OUT>             Output file [default: STDOUT]
         -l, --list <LIST>           List of sequence names (comma-separated or file). 
                                     If comma-separated, no whitespaces allowed.
-        -r, --taxrule <TAXRULE>     Taxrule used for computing taxonomy (supported: "bestsum", "bestsumorder")
+        -x, --taxrule <TAXRULE>     Taxrule used for computing taxonomy (supported: "bestsum", "bestsumorder")
                                     [default: bestsum]
-        --rank <TAXRANK>...         Taxonomic rank(s) at which output will be written. 
+        -r, --rank <TAXRANK>...         Taxonomic rank(s) at which output will be written. 
                                     (supported: 'species', 'genus', 'family', 'order', 
                                     'phylum', 'superkingdom', 'all') [default: phylum]
         -b, --hits                  Displays taxonomic hits from tax files