diff README.md @ 0:0b8ddf650752 draft

planemo upload for repository https://github.com/HegemanLab/VKMZ commit 7c299d22bdce251ce599cd34df76919d297a7007-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Wed May 02 18:31:06 2018 -0400
@@ -0,0 +1,87 @@
+# VKMZ version 1.0 
+
+VKMZ is a metabolomics vizualization tool which creates van Krevelen diagrams from mass spectrometry data. A van Krevelen diagram (VKD) plots a molecule on a scatterplot based on the molecule's oxygen to carbon ratio (O:C) against it's hydrogen to carbon ratio (H:C). Classes of metabolites cluster together on a VKD [0]. Plotting a complex mixture of metabolites on a VKD can be used to briefly convey untargeted metabolomics data.
+
+VKMZ can be used as a standalone tool or on the Galaxy Project web platform [1].
+## Using VKMZ
+
+VKMZ is designed to use XCMS [2] data as input. Tabular data can also be used as input. For each feature in the data VKMZ attempts to predict it's molecular formula by comparing the features mass to a database of known formula masses. Heristically generated databases for unlabeled and labeled data is included with VKMZ. Users can define their own database. A VKD is created from formulas with predictions and outputed as a webpage and tabular file.
+
+### Input modes
+
+VKMZ has three modes:
+  1. `tsv` mode reads a specially formatted tabular file
+  2. `xcms` mode reads features in [XCMS](https://bioconductor.org/packages/release/bioc/html/xcms.html) data
+  3. `plot` mode replots VKMZ tabular data
+
+Select a mode by declaring it as the first argument to `vkmz.py`.
+
+> **Example:**
+> ```
+> python vkmz.py xcms [options]
+> ```
+
+Different modes take different parameters.
+
+All modes require an output parameter:
+  * `--output [FILENAME]`
+    * A `.tsv` and/or `.html` will be generated by VKMZ with this paraameter as the file name.
+    * A `.tsv` and `.html` files generated by VKMZ are named by this option
+
+All modes allow these options:
+  * `--plot-type [scatter-2d]`
+  * `--size [INTEGER]`
+    * Set base size of marker dots of the VKD
+  * `--size-algorithm [{1,2}]`
+    * Choose algorithm to modify marker size
+      1. Uniform base size
+      2. Intensity relative size
+
+#### xcms and tsv modes
+
+Both xcms and tsv mode require the mass error, in parts-per-million, of the mass spectrometer which generated the data:
+  * `--error [PPM_ERROR_NUMBER]`
+
+There are several options for xcms and tsv modes:
+  * `--database [DATABASE_FILE]`
+    * default is BMRB's monoisotopic heuristically generated database [3]
+  * `--directory [TOOL_PATH]`
+    * define tool directory
+  * `--no-plot`
+    * disable html plot generation
+
+#### xcms mode
+
+xcms mode requires tabular files generated by XCMS:
+  * `--data-matrix [XCMS_DATA_MATRIX_FILE]`
+  * `--sample-metadata [XCMS_SAMPLE_METADATAFILE]`
+  * `--variable-metadata [XCMS_VARIABLE_METADATAFILE]`
+
+##### xcms mode example:
+```
+python vkmz.py xcms --data-matrix test-data/datamatrix.tabular --sample-metadata test-data/sampleMetadata.tabular --variable-metadata test-data/variableMetadata.tabular --output report --error 3
+```
+
+#### tsv mode
+
+tsv mode requires a tabular file of a specific format as input.
+  * `--input [TSV FILE]`
+
+The first five columns of the input tabular file must be:
+
+| sample ID | polarity | mz | retention time | intensity |
+|-----------|----------|----|----------------|-----------|
+
+#### plot mode
+
+plot mode reads previously generated VKMZ tabular files to create VKD html files. 
+
+Specifying the VKMZ tabular file is required:
+  * `--input [VKMZ_TSV_FILE]`
+
+## Citations
+
+0. Brockman et al. [doi:10.1007/s11306-018-1343-y](https://doi.org/10.1007/s11306-018-1343-y)
+1. Galaxy Project [Galaxy](https://github.com/galaxyproject/galaxy)
+2. Giacomoni et al. [doi:10.1093/bioinformatics/btu813](https://doi.org/10.1093/bioinformatics/btu813)
+3. Hegeman et al. [doi:10.1021/ac070346t](https://doi.org/10.1021/ac070346t)