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abims_xcms_summary.xml
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<tool id="abims_xcms_summary" name="xcms process history" version="@TOOL_VERSION@+galaxy0">
<description>Create a summary of XCMS analysis</description>
<macros>
<import>macros.xml</import>
<import>macros_xcms.xml</import>
</macros>
<requirements>
<requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement>
<requirement type="package" version="1.46.0">bioconductor-camera</requirement>
<requirement type="package" version="1.1_5">r-batch</requirement>
</requirements>
<expand macro="stdio"/>
<command><![CDATA[
@COMMAND_RSCRIPT@/xcms_summary.r
image '$image'
htmlOutput '$htmlOutput'
user_email $__user_email__
]]></command>
<inputs>
<param name="image" type="data" format="rdata.xcms.findchrompeaks,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, group, retcor, fillpeaks etc.)" />
</inputs>
<outputs>
<data name="htmlOutput" format="html" label="xcms summary html" />
</outputs>
<tests>
<!--<test>
<param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData" ftype="rdata"/>
<output name="htmlOutput" file="faahKO.xset.group.retcor.group.fillpeaks.summary.html" />
</test>-->
<test>
<param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData" ftype="rdata"/>
<output name="htmlOutput" file="faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html" />
</test>
</tests>
<help><![CDATA[
@HELP_AUTHORS@
====================
xcms process history
====================
-----------
Description
-----------
This tool provide a HTML summary which summarizes your analysis using the [W4M] XCMS and CAMERA tools
-----------------
Workflow position
-----------------
**Upstream tools**
========================= =========================== ================================
Name Output file Format
========================= =========================== ================================
xcms.findChromPeaks xset.RData rdata.xcms.findchrompeaks
------------------------- --------------------------- --------------------------------
xcms.groupChromPeaks ``*``.groupChromPeaks.RData rdata.xcms.group
------------------------- --------------------------- --------------------------------
xcms.adjustRtime ``*``.adjustRtime.RData rdata.xcms.retcor
------------------------- --------------------------- --------------------------------
xcms.fillChromPeaks ``*``.fillChromPeaks.RData rdata.xcms.fillpeaks
------------------------- --------------------------- --------------------------------
CAMERA.annotate ``*``.annotate.*.RData rdata.camera.``*``
========================= =========================== ================================
.. image:: xcms_summary_workflow.png
---------------------------------------------------
Changelog/News
--------------
@HELP_XCMS_NEWVERSION_31200@
**Version 3.6.1+galaxy2 - 23/09/2020**
- BUGFIX: "Error: object 'sampleNamesList' not found" in case of .RData input from CAMERA
**Version 3.6.1+galaxy1 - 05/04/2020**
- UPGRADE: upgrade the CAMERA version from 1.38.0 to 1.42.0
- BUGFIX: "Error in chromPeaks(from)[, "is_filled"] : subscript out of bounds"
@HELP_XCMS_NEWVERSION_3610@
@HELP_XCMS_NEWVERSION_3440@
**Version 3.0.0.0 - 14/02/2018**
- UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods
- IMPROVEMENT: the tool now shows all the parameters and not only those which were set.
**Version 1.0.4 - 13/02/2018**
- UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0
**Version 1.0.3 - 03/02/2017**
- IMPROVEMENT: xcms.summary can deal with merged individual data
**Version 1.0.2 - 06/07/2016**
- UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
**Version 1.0.1 - 04/04/2016**
- TEST: refactoring to pass planemo test using conda dependencies
**Version 1.0.0 - 10/02/2016**
- NEW: Create a summary of XCMS analysis
]]></help>
<expand macro="citation" />
</tool>