README.md edits

README.md

@@ -13,6 +13,7 @@ This CLI is actively being built so no guarantees are made for stability or bugs
 E.g. get from the releases page.
 
 ```bash
+# for mac
 curl -L "https://github.com/genomehubs/goat-cli/releases/download/0.1.1/goat_mac_0.1.1" > goat && chmod +x goat
 ```
 
@@ -45,70 +46,81 @@ USAGE:
     goat search [FLAGS] [OPTIONS] --file <file> --taxon <taxon>
 
 FLAGS:
-    -z, --all             This flag indicates all data should be printed.
-    -a, --assembly        This flag indicates assembly data should be printed.
-    -b, --busco           Include BUSCO estimates.
-    -c, --c-values        This flag indicates C-value data should be printed.
-    -g, --genome-size     This flag indicates genome size data should be printed.
-    -h, --help            Prints help information
-    -k, --karyotype       This flag indicates karyotype data should be printed.
-        --mitochondria    Include mitochondrial genome size & GC%.
-    -p, --phylogeny       Get information for all descendents of a common ancestor.
-        --plastid         Include plastid genome size & GC%.
-    -r, --raw             This flag indicates raw values should be all listed out. So you can do your own aggregations
-                          for example.
-    -u, --url             Print the underlying GoaT API URL(s). Useful for debugging.
-    -V, --version         Prints version information
+    -A, --all                  Print all currently implemented GoaT variables.
+    -a, --assembly             Print assembly data (span & level)
+    -B, --bioproject           Print the bioproject and biosample ID of records.
+    -b, --busco                Print BUSCO estimates.
+    -c, --c-values             Print c-value data.
+    -d, --date                 Print EBP & assembly dates.
+    -G, --gene-count           Print gene count data.
+    -g, --genome-size          Print genome size data.
+    -h, --help                 Prints help information
+    -i, --include-estimates    Include ancestral estimates. Omitting this flag includes only direct estimates from a
+                               taxon. Cannot be used with --raw.
+    -k, --karyotype            Print karyotype data (chromosome number & haploid number).
+    -l, --legislation          Print legislation data.
+    -m, --mitochondria         Print mitochondrial genome size & GC%.
+    -N, --n50                  Print the contig & scaffold n50 of assemblies.
+    -n, --names                Print all associated name data (synonyms, Tree of Life ID, and common names).
+    -p, --phylogeny            Get information for all descendents of a common ancestor.
+    -P, --plastid              Print plastid genome size & GC%.
+        --ploidy               Print ploidy estimates.
+    -r, --raw                  Print raw values (i.e. no aggregation/summary).
+    -S, --sex-determination    Print sex determination data.
+        --target-lists         Print target list data associated with each taxon.
+    -T, --tidy                 Print data in tidy format.
+    -u, --url                  Print the underlying GoaT API URL(s). Useful for debugging.
+    -V, --version              Prints version information
 
 OPTIONS:
     -f, --file <file>      A file of NCBI taxonomy ID's (tips) and/or binomial names.
                            Each line should contain a single entry.
         --ranks <ranks>    Choose a rank to display with the results. All ranks up to the given rank are displayed.
                            [default: none]  [possible values: none, subspecies, species, genus, family, order, class,
                            phylum, kingdom, superkingdom]
-        --size <size>      The number of results to return. [default: 50]
+    -s, --size <size>      The number of results to return. Max 10,000 currently. [default: 50]
     -t, --taxon <taxon>    The taxon to search. An NCBI taxon ID, or the name of a taxon at any rank.
 ```
 
 ### Flags
 
 There are a series of flags that can be added in any combination. For example:
 
-`goat search -abc -t "Arabidopsis thaliana"` (<- Note quotes needed when there are spaces in the query)
+`goat search -abct "Arabidopsis thaliana"` (<- Note quotes needed when there are spaces in the query)
 
-Will return TSV's for assembly statistics (`-a`, type & span), BUSCO completeness metrics (`-b`), and C-values (`-c`) for the taxon <i>Arabidopsis thaliana</i>.
+Will return a TSV for assembly statistics (`-a`, type & span), BUSCO completeness metrics (`-b`), and C-values (`-c`) for the taxon <i>Arabidopsis thaliana</i>. Add `--tidy` to format the results in tidy format (i.e. one observation per row).
 
 Two of the flags are different. `-p` (`--phylogeny`) will return a tax tree search. This means that a node on the tree and all of its descendents will be included in the query. For example:
 
-`goat search -pa -t Arabidopsis` 
+`goat search -pat Poaceae` 
 
-Will return aggregated results for every species in the genus <i>Arabidopsis</i>. If the default number of return hits is lower than the possible number of results, there will be a warning (in this case):
+Will return aggregated results for every species in the family <i>Poaceae</i>. If the default number of return hits is lower than the possible number of results, there will be a warning (in this case):
 
-`[-]     For search query Arabidopsis, size specified (50) was less than the number of results returned, (51).`
+`[-]     For search query Poaceae, size specified (50) was less than the number of results returned, (1116).`
 
-So up the `--size` option to `51`.
+So up the `--size` option to `1116`.
 
-You may not want aggregated results, instead requiring direct values. This is where the `-r --raw` flag is handy. Adding this flag will return all direct results. For example:
+You may not want aggregated results, instead requiring raw values. This is where the `-r --raw` flag is handy. Adding this flag will return all results for a taxon. For example:
 
-`goat search -pra -t Arabidopsis --size 51` 
+`goat search -part Poaceae --size 1116` 
 
-Will display each direct result in turn for the assembly statistics implemented so far.
+Will display each direct result in turn for the assembly statistics implemented so far. Note adding `raw` coerces results into tidy format.
 
 ### Options
 
 As for the options, we have already seen `size`. Next up is `--ranks`. Adding one of `subspecies, species, genus, family, order, class, phylum, kingdom, superkingdom` to this option will prepend a tab separated taxonomy for each record. Use it like this:
 
-`goat search -pa -t Arabidopsis --ranks genus` 
+`goat search -pat Arabidopsis --ranks genus` 
 
 Another way of searching for multiple species (related or not) is to use `-t` with quotes around a comma separated list. Like this:
 
-`goat search -ra -t "Arabidopsis thaliana, Zea mays, Solanum tuberosum"`
+`goat search -rat "Arabidopsis thaliana, Zea mays, Solanum tuberosum"`
 
 This search will return all the assembly spans and levels for the three taxa specified.
 
 Large numbers of requests are probably best submitted using a file, e.g:
 
-`goat search -k -f examples/brassicaceae.txt > brassicaceae_karyotype_data.tsv`
+`goat search -kf examples/taxids.txt > taxids_karyotype_data.tsv`
 
 ### Feedback, requests, etc