Mercurial > repos > lecorguille > xcms_summary
diff abims_xcms_summary.xml @ 15:97ca0321931b draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
author | lecorguille |
---|---|
date | Tue, 18 Sep 2018 16:14:05 -0400 |
parents | 4c757d1ba7b4 |
children | 46be2c523a7f |
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--- a/abims_xcms_summary.xml Tue Feb 13 04:51:37 2018 -0500 +++ b/abims_xcms_summary.xml Tue Sep 18 16:14:05 2018 -0400 @@ -1,20 +1,20 @@ -<tool id="abims_xcms_summary" name="xcms.summary" version="1.0.4"> +<tool id="abims_xcms_summary" name="xcms process history" version="@WRAPPER_VERSION@.0"> <description>Create a summary of XCMS analysis</description> <macros> <import>macros.xml</import> + <import>macros_xcms.xml</import> </macros> - <requirements> + <expand macro="requirements"> <requirement type="package" version="1.32.0">bioconductor-camera</requirement> - <requirement type="package" version="1.1_4">r-batch</requirement> - </requirements> + </expand> <expand macro="stdio"/> <command><![CDATA[ - $__tool_directory__/xcms_summary.r + @COMMAND_RSCRIPT@/xcms_summary.r image '$image' htmlOutput '$htmlOutput' @@ -24,7 +24,7 @@ <inputs> - <param name="image" type="data" format="rdata.xcms.raw,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.)" /> + <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> @@ -33,12 +33,12 @@ </outputs> <tests> - <test> - <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData" /> + <!--<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>--> <test> - <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData" /> + <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> @@ -47,9 +47,9 @@ @HELP_AUTHORS@ -============ -Xcms.summary -============ +==================== +xcms process history +==================== ----------- Description @@ -63,19 +63,19 @@ **Upstream tools** -========================= ================= ===================== ========== -Name output file format parameter -========================= ================= ===================== ========== -xcms.xcmsSet xset.RData rdata.xcms.raw RData file -------------------------- ----------------- --------------------- ---------- -xcms.group xset.RData rdata.xcms.group RData file -------------------------- ----------------- --------------------- ---------- -xcms.retcor xset.RData rdata.xcms.retcor RData file -------------------------- ----------------- --------------------- ---------- -xcms.fillpeaks xset.RData rdata.xcms.fillpeaks RData file -------------------------- ----------------- --------------------- ---------- -CAMERA.annotate xset.RData rdata.camera.* RData file -========================= ================= ===================== ========== +========================= =========================== ================================ +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 @@ -85,18 +85,28 @@ Changelog/News -------------- +**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