Mercurial > repos > lecorguille > xcms_summary
diff abims_xcms_summary.xml @ 32:de3b88417327 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
| author | lecorguille |
|---|---|
| date | Tue, 03 Apr 2018 11:40:57 -0400 |
| parents | 0b5521b78c92 |
| children | 79fe34cedc56 |
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--- a/abims_xcms_summary.xml Thu Mar 08 05:55:26 2018 -0500 +++ b/abims_xcms_summary.xml Tue Apr 03 11:40:57 2018 -0400 @@ -4,6 +4,7 @@ <macros> <import>macros.xml</import> + <import>macros_xcms.xml</import> </macros> <expand macro="requirements"> @@ -13,7 +14,7 @@ <expand macro="stdio"/> <command><![CDATA[ - $__tool_directory__/xcms_summary.r + @COMMAND_RSCRIPT@/xcms_summary.r image '$image' htmlOutput '$htmlOutput' @@ -23,7 +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> @@ -33,11 +34,11 @@ <tests> <!--<test> - <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData" /> + <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" /> + <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> @@ -62,19 +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 parameter +========================= ================= ================================ ========== +xcms.xcmsSet xset.RData rdata.xcms.findchrompeaks 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 +========================= ================= ================================ ========== .. image:: xcms_summary_workflow.png