diff docs/scripts/txt/ElementalAnalysisTextFiles.txt @ 0:4816e4a8ae95 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docs/scripts/txt/ElementalAnalysisTextFiles.txt	Wed Jan 20 09:23:18 2016 -0500
@@ -0,0 +1,158 @@
+NAME
+    ElementalAnalysisTextFiles.pl - Perform elemental analysis using formula
+    column in TextFile(s)
+
+SYNOPSIS
+    ElementalAnalysisTextFiles.pl TextFile(s)...
+
+    ElementalAnalysisTextFiles.pl [-c, --colmode colnum | collabel] [-d,
+    --detail infolevel] [-f, --fast] [-f, --formulacol colnum | collabel]
+    [-h, --help] [--indelim comma | semicolon] [-m, --mode All |
+    "ElementalAnysis, [MolecularWeight, ExactMass]"] [-o, --overwrite]
+    [--outdelim comma | tab | semicolon] [-p, --precision number] [-q,
+    --quote yes | no] [-r, --root rootname] [-s, --startcol colnum |
+    collabel] [--startcolmode before | after] -v --valuecollabels [Name,
+    Label, [Name, Label,...]] [-w, --workingdir dirname] TextFile(s)...
+
+DESCRIPTION
+    Perform elemental analysis using molecular formula column specified by a
+    column number or label in *TextFile(s)*.
+
+    In addition to straightforward molecular formulas - H2O, HCl, C3H7O2N -
+    other supported variations are: Ca3(PO4)2, [PCl4]+, [Fe(CN)6]4-,
+    C37H42N2O6+2, Na2CO3.10H2O, 8H2S.46H2O, and so on. Charges are simply
+    ignored. Isotope symbols in formulas specification, including D and T,
+    are not supported.
+
+    The valid file extensions are *.csv* and *.tsv* for comma/semicolon and
+    tab delimited text files respectively. All other file names are ignored.
+    All the text files in a current directory can be specified by **.csv*,
+    **.tsv*, or the current directory name. The --indelim option determines
+    the format of *TextFile(s)*. Any file which doesn't correspond to the
+    format indicated by --indelim option is ignored.
+
+OPTIONS
+    -c, --colmode *colnum | collabel*
+        Specify how columns are identified in *TextFile(s)*: using column
+        number or column label. Possible values: *colnum or collabel*.
+        Default value: *colnum*.
+
+    -d, --detail *infolevel*
+        Level of information to print about lines being ignored. Default:
+        *1*. Possible values: *1, 2 or 3*.
+
+    -h, --help
+        Print this help message.
+
+    --fast
+        In this mode, the formula column specified using -f, --formulacol
+        option is assumed to contain valid molecular formula data and
+        initial formula validation check is skipped.
+
+    -f, --formulacol *col number | col name*
+        This value is mode specific. It specifies molecular formula column
+        to use for performing elemental analysis on *TextFile(s)*. Possible
+        values: *col number or col label*. Default value: *first column
+        containing the word formula in its column label*.
+
+    -m, --mode *All | "ElementalAnalysis,[MolecularWeight,ExactMass]"*
+        Specify what values to calculate using molecular formula in
+        *TextFile(s)*: calculate all supported values or specify a comma
+        delimited list of values. Possible values: *All |
+        "ElementalAnalysis, [MolecularWeight, ExactMass]"*. Default: *All*
+
+    --indelim *comma | semicolon*
+        Input delimiter for CSV *TextFile(s)*. Possible values: *comma or
+        semicolon*. Default value: *comma*. For TSV files, this option is
+        ignored and *tab* is used as a delimiter.
+
+    -o, --overwrite
+        Overwrite existing files.
+
+    --outdelim *comma | tab | semicolon*
+        Output text file delimiter. Possible values: *comma, tab, or
+        semicolon* Default value: *comma*.
+
+    -p, --precision *number*
+        Precision of calculated values in the output file. Default: up to
+        *2* decimal places. Valid values: positive integers.
+
+    -q, --quote *yes | no*
+        Put quotes around column values in output text file. Possible
+        values: *yes or no*. Default value: *yes*.
+
+    -r, --root *rootname*
+        New text file name is generated using the root: <Root>.<Ext>.
+        Default new file name: <InitialTextFileName>ElementalAnalysis.<Ext>.
+        The csv, and tsv <Ext> values are used for comma/semicolon, and tab
+        delimited text files respectively. This option is ignored for
+        multiple input files.
+
+    -s, --startcol *colnum | collabel*
+        This value is mode specific. It specifies the column in text files
+        which is used for start adding calculated column values. For
+        *colnum* mode, specify column number and for *collabel* mode,
+        specify column label.
+
+        Default value: *last*. Start merge after the last column.
+
+    --startcolmode *before | after*
+        Start adding calculated column values after the -s, --startcol
+        value. Possible values: *before or after*. Default value: *after*.
+
+    -v --valuecollabels *Name,Label,[Name,Label,...]*
+        Specify column labels to use for calculated values. In general, it's
+        a comma delimited list of value name and column label pairs.
+        Supported value names: *ElementalAnalysis, MolecularWeight, and
+        ExactMass*. Default labels: *ElementalAnalysis, MolecularWeight, and
+        ExactMass*.
+
+    -w, --workingdir *dirname*
+        Location of working directory. Default: current directory.
+
+EXAMPLES
+    To perform elemental analysis, calculate molecular weight and exact mass
+    using formulas in a column with the word Formula in its column label and
+    generate a new CSV text file NewSample1.csv, type:
+
+        % ElementalAnalysisTextFiles.pl -o -r NewSample1 Sample1.csv
+
+    To perform elemental analysis using formulas in column number two, use
+    column label Analysis for calculated data, and generate a new CSV text
+    file NewSample1.csv, type:
+
+        % ElementalAnalysisTextFiles.pl --m ElementalAnalysis --formulacol 2
+          --valuecollabels "ElementalAnalysis,Analysis" -o -r NewSample1
+          Sample1.csv
+
+    To calculate molecular weight using formula in column label Formula with
+    four decimal precision and generate a new CSV text file NewSample1.csv,
+    type
+
+        % ElementalAnalysisTextFiles.pl --m MolecularWeight --colmode collabel
+          --formulacol Formula --precision 4 -o -r NewSample1 Sample1.csv
+
+    To calculate exact mass using formula in column label Formula with four
+    decimal precision, adding column for exact mass right after Formula
+    column, and generate a new CSV text file NewSample1.csv, type
+
+        % ElementalAnalysisTextFiles.pl --m ExactMass --colmode collabel
+          --formulacol Formula --precision 4 --startcolmode after
+          --startcol Formula -o -r NewSample1 Sample1.csv
+
+AUTHOR
+    Manish Sud <[e-mail]>
+
+SEE ALSO
+    AnalyzeTextFilesData.pl, InfoTextFiles.pl, ExtractFromTextFiles.pl
+
+COPYRIGHT
+    Copyright (C) 2015 Manish Sud. All rights reserved.
+
+    This file is part of MayaChemTools.
+
+    MayaChemTools is free software; you can redistribute it and/or modify it
+    under the terms of the GNU Lesser General Public License as published by
+    the Free Software Foundation; either version 3 of the License, or (at
+    your option) any later version.
+