Command Processing¶
To support data analysis without starting a GUI Application, Cascade provides three commands. By combining these, it is possible to automate analysis with Cascade. When specifying a file path to each command, you must specify the path including the extension.
rca Command¶
This command supports the analysis of raw data as input and
the generation of results.
For the types of raw data that can be input,
see Supported File Types
for the measurement data that can be input.
It is mandatory to specify the file path
to save the analysis results.
In addition, you can optionally customize the content
of the analysis by specifying the file path
of the analysis template that defines the analysis method.
C:\> rca
Reifycs Cascade(TM) 1.2.0.0000
(C) 2020 Reifycs Inc.
Usage: rca {inputFilePath|inputDirectoryPath}... <-o projectFilePath.cpj> [-t analysisTemplateFilePath.cct]
Extensions supported as input data: .d, .wiff, .lcd, .qgd, .raw, .abf, .hmd, .mzB
Option Description
--------- ---------------------------------------------------------
-h Display this help.
-v Display Cascade version.
-o Specify the file path to output Cascade result project.
This option must be specified.
-t Specify the file path of analysis template,
if not specified, default analysis template will be used.
Examples:
Example 1. Analyze two raw data
C:\> rca “d:/input/data1.raw” “d:/input/data2.d” -o “d:/output/result.cpj”
Example 2. Analyze all raw data in the specified directory
C:\> rca “d:/input” -o “d:/output/result.cpj”
Example 3. Analyze according to the specified analysis template
C:\> rca “d:/input” -o “d:/output/result.cpj” -t “d:/template.cct”
Example 4. Display detailed descriptions of each option
C:\> rca -h
rce Command¶
This command supports entering analysis results
created with other commands or GUI and reporting the results
in various formats such as Excel and PDF.
It is possible to output in Excel format (.xlsx),
CSV format (.csv), tab-separated text format (.txt),
and PDF format (.pdf).
You can switch the processing content by specifying a subcommand
(excel, csv, text, pdf) that corresponds to the output format
immediately after the command.
The output file path must be specified for all submommands.
For the csv, text, and pdf subcommands,
it is also possible to separate the results for each compound
into multiple files by specifying a directory path
instead of a file path as the output destination.
C:\> rce
Reifycs Cascade(TM) 1.2.0.0000
(C) 2020 Reifycs Inc.
Usage: rce <subcommand> <projectFilePath.cpj> {-o outputFilePath|outputDirectoryPath} [-t pdfTemplateFilePath.cpt] [options]
Subcommand Description
--------------------- ------------------------------------------------------------------
excel Export an Excel file (.xlsx) from analysis result (.cpj).
csv Exprot CSV files (.csv) from analysis result (.cpj).
text Export Text files (.txt) from analysis result (.cpj).
pdf Export PDF files (.pdf) from analysis result (.cpj).
Option Description
--------------------- ------------------------------------------------------------------
-h Display this help.
-v Display Cascade version.
-o Specify the file or directory path to output the exported results.
This option must be specified.
When specifying file path, include the appropriate extension
(.xlsx/.csv/.txt/.pdf) according to the subcommand.
The excel subcommand does not accept directory path.
-t Specify the path of pdf template,
if not specified, default pdf template will be used.
This option is valid only in the pdf subcommand.
--all-compounds Set all compounds as export targets,
if not specified, compounds except ISTDs will be exported.
--all-transitions Set all transitions as export targets,
if not specified, only selected transitions will be exported.
--single-worksheet Export all results in one worksheet,
if not specified, in multiple worksheets for each compound.
This option is valid only in the excel subcommand.
--no-blankline Skip insertion of blankline separating compounds,
if not specified, blankline will be used as the separator.
This option is valid when specifying the --single-worksheet option
with the excel subcommand.
This option is valid when exporting to a single file
with the csv/text subcommand.
Examples:
Example 1. Export an excel file with results of all transitions in separate worksheets for each compounds except ISTDs
C:\> rce excel “d:/output/result.cpj” -o “d:/output/result.xlsx” --all-transitions
Example 2. Export an excel file with results of selected transitons for all compounds in one worksheet
C:\> rce excel “d:/output/result.cpj” -o “d:/output/result2.xlsx” --all-compounds --single-worksheet
Example 3. Export an csv file without blankline for each compunds
C:\> rce csv “d:/output/result.cpj” -o “d:/output/result.csv” --no-blankline
Example 4. Export text files named by each compound name
C:\> rce text “d:/output/result.cpj” -o “d:/output”
Example 5. Export a pdf file according to the specified pdf template
C:\> rce pdf “d:/output/result.cpj” -o “d:/output/result.pdf” -t “d:/template.cpt”
Example 6. Display detailed descriptions of each option
C:\> rce -h
rcx Command¶
This command performs an analysis by entering an XML file
in a specific format that defines the procedures
from analysis to result output.
By defining in advance the raw data to be analyzed,
the template to be used, and where to save the results,
analysis can be performed with simple commands.
Reifycs Cascade(TM) 1.2.0.0000
(C) 2020 Reifycs Inc.
Usage: rcx <xmlFilePath.xml>
XML Schema: https://www.reifycs.com/products/cascade/schema/rcx1.1.xsd
Option Description
--------- ---------------------------------------------------------
-h Display this help.
-v Display Cascade version.
Example:
C:\> rcx “d:/procedure.xml”
Spported XML File Format¶
Any XML file that conforms to the definition published as
XML Schema (https://www.reifycs.com/products/cascade/schema/rcx1.1.xsd)
can be used as input.
You can use an online XML Validator
(e.g. https://www.freeformatter.com/xml-validator-xsd.html)
to check that the XML file created conforms to the XML Schema.
The following is an example of an XML file
that performs the same processing as executing Example 3
of the rca command and
Example 1 through Example 5 of the rce command.
<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE runCascade SYSTEM "https://www.reifycs.com/products/cascade/schema/rcx1.1.xsd">
<runCascade xmlns="https://www.reifycs.com/products/cascade/schema/rcx1.1.xsd">
<!-- rca Example 3. -->
<analysis>
<inputRawData>
<directoryPath>d:/input</directoryPath>
</inputRawData>
<cascadeProject>
<output>
<filePath>d:/output/result.cpj</filePath>
</output>
</cascadeProject >
<template>
<filePath>d:/template.cct</filePath>
</template>
</analysis>
<export>
<!-- rce Example 1. -->
<excel targetTransition="All">
<useSingleWorksheet>false</useSingleWorksheet>
<output>
<filePath>d:/output/result.xlsx</filePath>
</output>
</excel>
<!-- rce Example 2. -->
<excel compoundType="All">
<useSingleWorksheet>true</useSingleWorksheet>
<output>
<filePath>d:/output/result2.xlsx</filePath>
</output>
</excel>
<!-- rce Example 3. -->
<csv>
<output>
<filePath>d:/output/result.csv</filePath>
</output>
<singleFileOption compoundSeparator="None" />
</csv>
<!-- rce Example 4. -->
<text>
<output>
<directoryPath>d:/output</directoryPath>
</output>
</text>
<!-- rce Example 5. -->
<pdf>
<output>
<filePath>d:/output/result.pdf</filePath>
</output>
<template>
<filePath>d:/template.cpt</filePath>
</template>
</pdf>
</export>
</runCascade>