DOC: update docs

docs/evaluate.md

@@ -1 +1,20 @@
-# Evaluating binning results
+# Evaluating binning results
+
+Run `gbintk evaluate --help` or `gbintk evaluate -h` to list the help message for evaluation.
+
+```shell
+Usage: gbintk evaluate [OPTIONS]
+
+  Evaluate the binning results given a ground truth
+
+Options:
+  --binned PATH            path to the .csv file with the initial binning
+                           output from an existing tool  [required]
+  --groundtruth PATH       path to the .csv file with the ground truth
+                           [required]
+  --delimiter [,|;|     |" "]  delimiter for input/output results. Supports a
+                           comma (,), a semicolon (;), a tab ($'\t'), a space
+                           (" ") and a pipe (|)  [default: ,]
+  --output PATH            path to the output folder  [required]
+  -h, --help               Show this message and exit.
+```

docs/graphbin2_usage.md

@@ -1 +1,34 @@
-# Using GraphBin2
+# Using GraphBin2
+
+Run `gbintk graphbin2 --help` or `gbintk graphbin2 -h` to list the help message for GraphBin2.
+
+```shell
+Usage: gbintk graphbin2 [OPTIONS]
+
+  GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using
+  Assembly Graphs
+
+Options:
+  --assembler [spades|megahit|flye]
+                                  name of the assembler used (SPAdes, MEGAHIT
+                                  or Flye)  [required]
+  --graph PATH                    path to the assembly graph file  [required]
+  --contigs PATH                  path to the contigs file  [required]
+  --paths PATH                    path to the contigs.paths (metaSPAdes) or
+                                  assembly.info (metaFlye) file
+  --abundance PATH                path to the abundance file  [required]
+  --binned PATH                   path to the .csv file with the initial
+                                  binning output from an existing tool
+                                  [required]
+  --output PATH                   path to the output folder  [required]
+  --prefix TEXT                   prefix for the output file
+  --depthb INTEGER                maximum depth for the breadth-first-search.
+                                  [default: 5]
+  --threshold FLOAT               threshold for determining inconsistent
+                                  vertices.  [default: 1.5]
+  --delimiter [,|;|$'\t'|" "]     delimiter for input/output results. Supports
+                                  a comma (,), a semicolon (;), a tab ($'\t'),
+                                  a space (" ") and a pipe (|)  [default: ,]
+  --nthreads INTEGER              number of threads to use.  [default: 8]
+  -h, --help                      Show this message and exit.
+```

docs/graphbin_usage.md

@@ -1 +1,31 @@
-# Using GraphBin
+# Using GraphBin
+
+Run `gbintk graphbin --help` or `gbintk graphbin -h` to list the help message for GraphBin.
+
+```shell
+Usage: gbintk graphbin [OPTIONS]
+
+  GraphBin: Refined Binning of Metagenomic Contigs using Assembly Graphs
+
+Options:
+  --assembler [spades|megahit|flye]
+                                  name of the assembler used (SPAdes, MEGAHIT
+                                  or Flye)  [required]
+  --graph PATH                    path to the assembly graph file  [required]
+  --contigs PATH                  path to the contigs file  [required]
+  --paths PATH                    path to the contigs.paths (metaSPAdes) or
+                                  assembly.info (metaFlye) file
+  --binned PATH                   path to the .csv file with the initial
+                                  binning output from an existing tool
+                                  [required]
+  --output PATH                   path to the output folder  [required]
+  --prefix TEXT                   prefix for the output file
+  --max_iteration INTEGER         maximum number of iterations for label
+                                  propagation algorithm  [default: 100]
+  --diff_threshold FLOAT RANGE    difference threshold for label propagation
+                                  algorithm  [default: 0.1; 0<=x<=1]
+  --delimiter [,|;|$'\t'|" "]     delimiter for input/output results. Supports
+                                  a comma (,), a semicolon (;), a tab ($'\t'),
+                                  a space (" ") and a pipe (|)  [default: ,]
+  -h, --help                      Show this message and exit.
+```

docs/metacoag_usage.md

@@ -1 +1,50 @@
-# Using MetaCoAG
+# Using MetaCoAG
+
+Run `gbintk metacoag --help` or `gbintk metacoag -h` to list the help message for MetaCoAG.
+
+```shell
+Usage: gbintk metacoag [OPTIONS]
+
+  MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly
+  Graphs
+
+Options:
+  --assembler [spades|megahit|flye]
+                                  name of the assembler used (SPAdes, MEGAHIT
+                                  or Flye)  [required]
+  --graph PATH                    path to the assembly graph file  [required]
+  --contigs PATH                  path to the contigs file  [required]
+  --paths PATH                    path to the contigs.paths (metaSPAdes) or
+                                  assembly.info (metaFlye) file
+  --abundance PATH                path to the abundance file  [required]
+  --output PATH                   path to the output folder  [required]
+  --hmm TEXT                      path to marker.hmm file.  [default:
+                                  auxiliary/marker.hmm]
+  --prefix TEXT                   prefix for the output file
+  --min_length INTEGER            minimum length of contigs to consider for
+                                  binning.  [default: 1000]
+  --p_intra FLOAT RANGE           minimum probability of an edge matching to
+                                  assign to the same bin.  [default: 0.1;
+                                  0<=x<=1]
+  --p_inter FLOAT RANGE           maximum probability of an edge matching to
+                                  create a new bin.  [default: 0.01; 0<=x<=1]
+  --d_limit INTEGER               distance limit for contig matching.
+                                  [default: 20]
+  --depthlp INTEGER               depth to consider for label propagation.
+                                  [default: 10]
+  --n_mg INTEGER                  total number of marker genes.  [default:
+                                  108]
+  --no_cut_tc                     do not use --cut_tc for hmmsearch.
+  --mg_threshold FLOAT RANGE      length threshold to consider marker genes.
+                                  [default: 0.5; 0<=x<=1]
+  --bin_mg_threshold FLOAT RANGE  minimum fraction of marker genes that should
+                                  be present in a bin.  [default: 0.33333;
+                                  0<=x<=1]
+  --min_bin_size INTEGER          minimum size of a bin to output in base
+                                  pairs (bp).  [default: 200000]
+  --delimiter [,|;|$'\t'|" "]     delimiter for input/output results. Supports
+                                  a comma (,), a semicolon (;), a tab ($'\t'),
+                                  a space (" ") and a pipe (|)  [default: ,]
+  --nthreads INTEGER              number of threads to use.  [default: 8]
+  -h, --help                      Show this message and exit.
+```

docs/prepare.md

@@ -1 +1,22 @@
-# Formatting binning results for GraphBin/GraphBin2
+# Formatting binning results for GraphBin/GraphBin2
+
+Run `gbintk prepare --help` or `gbintk prepare -h` to list the help message for formatting.
+
+```shell
+Usage: gbintk prepare [OPTIONS]
+
+  Format the initial binning result from an existing binning tool
+
+Options:
+  --assembler [spades|megahit|flye]
+                                  name of the assembler used (SPAdes, MEGAHIT
+                                  or Flye)  [required]
+  --resfolder PATH                path to the folder containing FASTA files
+                                  for individual bins  [required]
+  --delimiter [,|;|     |" "]         delimiter for input/output results. Supports
+                                  a comma (,), a semicolon (;), a tab ($'\t'),
+                                  a space (" ") and a pipe (|)  [default: ,]
+  --prefix TEXT                   prefix for the output file
+  --output PATH                   path to the output folder  [required]
+  -h, --help                      Show this message and exit.
+```

docs/visualise.md

@@ -1 +1,36 @@
-# Visualising binning results
+# Visualising binning results
+
+Run `gbintk visualise --help` or `gbintk visualise -h` to list the help message for visualisation.
+
+```shell
+Usage: gbintk visualise [OPTIONS]
+
+  Visualise binning and refinement results
+
+Options:
+  --assembler [spades|megahit|flye]
+                                  name of the assembler used (SPAdes, MEGAHIT
+                                  or Flye)  [required]
+  --initial PATH                  path to the initial binning result
+                                  [required]
+  --final PATH                    path to the final binning result  [required]
+  --graph PATH                    path to the assembly graph file  [required]
+  --paths PATH                    path to the contigs.paths (metaSPAdes) or
+                                  assembly.info (metaFlye) file
+  --output PATH                   path to the output folder  [required]
+  --prefix TEXT                   prefix for the output file
+  --dpi INTEGER                   dpi value  [default: 300]
+  --width INTEGER                 width of the image in pixels  [default:
+                                  2000]
+  --height INTEGER                height of the image in pixels  [default:
+                                  2000]
+  --vsize INTEGER                 size of the vertices  [default: 50]
+  --lsize INTEGER                 size of the vertex labels  [default: 8]
+  --margin INTEGER                margin of the figure  [default: 50]
+  --type TEXT                     type of the image (jpg, png, eps, svg)
+                                  [default: png]
+  --delimiter [,|;|$'\t'|" "]     delimiter for input/output results. Supports
+                                  a comma (,), a semicolon (;), a tab ($'\t'),
+                                  a space (" ") and a pipe (|)  [default: ,]
+  -h, --help                      Show this message and exit.
+```