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xcms_plot_chromatogram.xml
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<tool id="xcms_plot_chromatogram" name="xcms plot chromatogram" version="@TOOL_VERSION@+galaxy0">
<description>Plots base peak intensity chromatogram (BPI) and total ion current chromatogram (TIC) from MSnbase or xcms experiment(s)</description>
<macros>
<import>macros.xml</import>
<import>macros_xcms.xml</import>
</macros>
<expand macro="requirements"/>
<expand macro="stdio"/>
<command><![CDATA[
@COMMAND_RSCRIPT@//xcms_plot_chromatogram.r
images 'c("${"\",\"".join(map(str, $images))}")'
#if str($sampleMetadata) != 'None':
sampleMetadata '$sampleMetadata'
#end if
@COMMAND_FILE_LOAD@
]]></command>
<inputs>
<param name="images" type="data" format="rdata.msnbase.raw,rdata.xcms.findchrompeaks,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks, groupChromPeaks or adjustRtime" multiple="true" />
<param name="sampleMetadata" label="Sample metadata file " format="tabular" type="data" optional="true" help="Must contain at least one column with the sample id and one column with the sample class"/>
<expand macro="input_file_load"/>
</inputs>
<outputs>
<data name="ticsPdf" format="pdf" label="TICs.pdf" from_work_dir="TICs.pdf"/>
<data name="bpisPdf" format="pdf" label="BPIs.pdf" from_work_dir="BPIs.pdf" />
</outputs>
<tests>
<test>
<param name="images" value="faahKO-single-class.xset.merged.group.retcor.RData" ftype="rdata"/>
<expand macro="test_file_load_single"/>
<param name="sampleMetadata" value="sampleMetadata.tab" ftype="tabular"/>
<output name="ticsPdf" value="TICs.pdf" ftype="pdf" compare="sim_size" delta="5000" />
<output name="bpisPdf" value="BPIs.pdf" ftype="pdf" compare="sim_size" delta="5000" />
</test>
<!-- DISABLE FOR TRAVIS
<test>
<param name="images" value="ko15-raw.RData,ko16-raw.RData,wt15-raw.RData,wt16-raw.RData" ftype="rdata"/>
<expand macro="test_file_load_single"/>
<output name="ticsPdf" value="TICs.pdf" ftype="pdf" compare="sim_size" delta="600" />
<output name="bpisPdf" value="BPIs.pdf" ftype="pdf" compare="sim_size" delta="600" />
</test>
-->
</tests>
<help><![CDATA[
@HELP_AUTHORS@
======================
xcms plot chromatogram
======================
-----------
Description
-----------
This tool will plot Base Peak Intensity chromatogram (BPI) and Total Ion Current chromatogram (TIC) from xcms experiments.
-----------------
Workflow position
-----------------
**Upstream tools**
=========================== ======================== ==============================
Name Output file Format
=========================== ======================== ==============================
MSnbase.readMSData ``*``.raw.RData rdata.msnbase.raw
--------------------------- ------------------------ ------------------------------
xcms.findChromPeaks ``*``.raw.xset.RData rdata.xcms.findchrompeaks
--------------------------- ------------------------ ------------------------------
xcms.findChromPeaks Merger xset.merged.RData rdata.xcms.retcor
--------------------------- ------------------------ ------------------------------
xcms.adjustRtime ``*``.adjustRtime.RData rdata.xcms.retcor
=========================== ======================== ==============================
.. image:: xcms_plot_chromatogram_workflow.png
---------------------------------------------------
------------
Output files
------------
**Total Ion Current (TIC) chromatogram**
| Sum of intensity (Y) of all ions detected at each retention time (X)
**Base Peak Intensity Chromatogram (BPI)**
| Sum of intensity (Y) of the most intense peaks at each retention time (X)
---------------------------------------------------
Changelog/News
--------------
@HELP_XCMS_NEWVERSION_31200@
**Galaxy Version 3.6.1+galaxy2 - 23/09/2020**
- BUGFIX: sample group colours did not match group labels.
@HELP_XCMS_NEWVERSION_3610@
@HELP_XCMS_NEWVERSION_3440@
**Version 3.0.0.0 - 07/03/2018**
- NEW: This new tool will plot base peak intensity chromatogram (BPI) and total ion chromatogram (TIC) from xcms experience. It will replace those created by xcmsSet and retcor tools.
]]></help>
<expand macro="citation" />
</tool>