Commit 1fcd5a69 authored by Edlira Nano's avatar Edlira Nano
Browse files

doc/examples updated

git-svn-id: https://subversion.renater.fr/masschroq/trunk@2265 e4b6dbb4-9209-464b-83f7-6257456c460c
parent 85854cca
This file is part of the masschroq_examples.zip archive (or of the examples
directory of your MassChroQ Windows installation) which contain
ready to use examples to test masschroq v1.0.
directory of your MassChroQ Windows installation) which contains
ready to use examples to test masschroq v1.2.
In the masschroq_examples (resp. examples) directory you will find ready-to-use
examples to run masschroq. They are intended to illustrate how masschroq
......@@ -8,16 +8,19 @@ works and the results it can provide. They are also intended to provide
usage and parameter values support for your further analysis.
The input masschroqML example files are the ones named
example_blabla_masschroq.masschroqML.
example_blabla.masschroqML.
To run them go into the masschroq_examples directory and simply type:
masschroq example_blabla_masschroq.masschroqML
on the command line.
The mzXML files provided are the LC-MS/MS data files used in these examples.
on the command line. On Windows you can also run them automatically by
double-clicking on the masschroqML files.
The mzXML files provided are the LC-MS/MS run data files used in these examples.
MassChroQ will put all the result files in the results directory of the
masschroq_examples one.
The following examples are provided :
- example_labelling_dimethylation_masschroq.masschroqML (only in the website archive)
This example analysis the BSA_labeling_mix_light_intermediaire.mzXML
- example_labelling_dimethylation_masschroq.masschroqML (only on the website archive)
In this example we analyze the BSA_labeling_mix_light_intermediaire.mzXML
data file produced by a low resolution LTQ spectrometer
in a profile mode and where dimethyl labeling (with light and heavy
dimethyl groups) has been performed.
......@@ -37,8 +40,16 @@ The following examples are provided :
Also, in this example we ask masschroq to produce trace files for the
quantification procedure (xic extraction, filtering and peak detection
steps) concerning a given list of peptides (pep0 - pep4). After execution
you should notice a newly created directory named peplist_xics_traces
containing these traces for each detected peptide in each run.
you should notice a newly created directory in results named
peplist_xics_traces containing these traces for each detected peptide
in each run.
Also, in this example we ask masschroq to produce another type of output
result file: a masschroqML output file named Result_LTQ_masschroqml_output.xml.
Indeed, the masschroqML file format can be an input file to MassChroQ but also
an output file produced by MassChroQ and containing the initial input file,
the date and time MassChroQ was executed on it, plus the results of this
execution. This output file is mainly intended for development use.
- example_orbitrap_masschroq.masschroqML
In this example we analyze the BSA_Orbitrap.mzXML data file obtained
......@@ -55,12 +66,9 @@ The following examples are provided :
You can then run masschroq directly on this new file in order to
perform the analysis.
- masschroq_complete_input_example.xml (only with the Windows installation)
- masschroq_complete_input_example.xml
This is a complete input masschroqML example file that you can edit with
any text or xml editor. This file contains every possible masschroqML
instruction. It is intended to be used as a reference for users, run with
MassChroQ this file will not be validated because of its completeness.
instruction. It is intended to be used as a reference for users, and running
this file with MassChroQ will fail in validation because of its completeness.
- masschroqML_output_example.xml
This is an example of the masschroqML output file generated by the XML
output result type of MassChroQ.
......@@ -271,9 +271,10 @@
<quantification>
<quantification_results>
<quantification_result format="tsv" output_file="Result_LTQ"/>
<quantification_result format="masschroqml" output_file="results/Result_LTQ_masschroqml_output"/>
</quantification_results>
<quantification_traces>
<peptide_traces format="tsv" output_dir="peplist_xics_traces/" peptide_ids="pep0 pep1 pep2 pep3 pep4"/>
<peptide_traces format="tsv" output_dir="results/peplist_xics_traces/" peptide_ids="pep0 pep1 pep2 pep3 pep4"/>
</quantification_traces>
<quantify id="q1" quantification_method_id="quant1" withingroup="G1">
<peptides_in_peptide_list mode="real_or_mean"/>
......
......@@ -30,7 +30,7 @@
</quantification_methods>
<quantification>
<quantification_results>
<quantification_result format="tsv" output_file="Result_orbitrap"/>
<quantification_result format="tsv" output_file="results/Result_orbitrap"/>
</quantification_results>
<quantify id="q1" quantification_method_id="quant1" withingroup="G1">
<peptides_in_peptide_list mode="real_or_mean"/>
......
This diff is collapsed.
......@@ -62,7 +62,7 @@
<quantification_methods>
<quantification_method id="my_qzivy">
<xic_extraction xic_type="sum">
<mz_range max="1.5" min="0.5"/>
<mz_range max="0.3" min="0.3"/>
</xic_extraction>
<xic_filters>
<anti_spike half="5"/>
......@@ -81,7 +81,7 @@
</quantification_method>
<quantification_method id="my_qmoulon">
<xic_extraction xic_type="max">
<ppm_range max="1.5" min="0.5"/>
<ppm_range max="10" min="10"/>
</xic_extraction>
<xic_filters>
<background half_mediane="5" half_min_max="15"/>
......@@ -100,7 +100,7 @@
<quantification_result output_file="result1" format ="tsv"/>
<quantification_result output_file="result2" format="gnumeric"/>
<quantification_result output_file="result3" format ="xhtmltable"/>
<quantification_result output_file="result4" format ="xml" xic_traces="true"/>
<quantification_result output_file="result4" format ="masschroqml" xic_traces="true"/>
</quantification_results>
<quantification_traces>
<peptide_traces peptide_ids="pep0 pep1" output_dir="pep_traces" format="tsv"/>
......@@ -117,7 +117,7 @@
<peptides_in_peptide_list mode="real_or_mean"/>
</quantify>
<quantify id="q2" withingroup="G2" quantification_method_id="my_moulon">
<peptides_in_peptide_list mode="real_or_mean" isotope_label_refs="iso1 iso2"/>
<peptides_in_peptide_list mode="post_matching" isotope_label_refs="iso1 iso2"/>
<mz_list>732.317 449.754 552.234 464.251 381.577 569.771 575.256</mz_list>
<mzrt_list>
<mzrt mz="732.317" rt="230.712"/>
......
//#include "obiwarper.h"
#include "qtquanti/visualqms/visual_qms.h"
#include <QString>
#include <iostream>
using namespace std;
int main(int argc, char **argv) {
QString fileName;
if (argc > 1) {
fileName = argv[1];
} else {
cerr << "missing input filename for MassChroQ" << endl;
return 1;
}
VisualQms mass_chroq_engine;
try {
mass_chroq_engine.setXmlFilename(fileName);
mass_chroq_engine.runXmlFile();
} catch (mcqError error) {
cerr << "Oops! an error occurred in MassChroQ :" << endl;
cerr << error.what();
}
return 0;
}
/** LICENCE
This file is part of "quantimscpp".
quantimscpp is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
quantimscpp is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with quantimscpp. If not, see <http://www.gnu.org/licenses/>.
authors:
Olivier Langella <olivier.langella@moulon.inra.fr>
Benoit Valot <benoit.valot@moulon.inra.fr>
*/
/** \brief xicextractor
*
* uses a list of mass to analyze
* this detects and quantify peaks
* and produces a list of detected peaks
*
* \author Olivier Langella <olivier.langella@moulon.inra.fr>
*
* \param xml file (cf schema) containing parameters and list of mass
*/
/*
*
XML parameters file example :
doc/xicextractor_data_file.xml
*/
#include "lib/xic_extractor.h"
using namespace std;
int main (int argc, char **argv) {
QString fileName(argv[1]);
xicExtractor the_extractor;
the_extractor.setParam(fileName);
the_extractor.detectAndQuantify();
//the_extractor.printExtractorResults(cout);
the_extractor.printXmlResults();
return 0;
}
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