Mercurial > repos > lecorguille > xcms_group
diff abims_xcms_group.xml @ 27:36b470f3ebcf draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
| author | lecorguille |
|---|---|
| date | Tue, 24 Oct 2017 11:47:07 -0400 |
| parents | e121f6d76dfb |
| children | a18fc7554c6d |
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--- a/abims_xcms_group.xml Fri May 19 09:35:20 2017 -0400 +++ b/abims_xcms_group.xml Tue Oct 24 11:47:07 2017 -0400 @@ -15,9 +15,8 @@ image '$image' xsetRdataOutput '$xsetRData' - rplotspdf '$rplotsPdf' - method $methods.method + method $methods.method #if $methods.method == "density": ## minsamp $methods.minsamp minfrac $methods.minfrac @@ -53,7 +52,7 @@ <option value="nearest" >nearest</option> </param> <when value="density"> - <param name="bw" type="integer" value="30" label="Bandwidth" help="[bw] bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram" /> + <param name="bw" type="float" value="30" label="Bandwidth" help="[bw] bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram" /> <param name="minfrac" type="float" value="0.5" label="Minimum fraction of samples necessary" help="[minfrac] in at least one of the sample groups for it to be a valid group" /> <param name="mzwid" type="float" value="0.25" label="Width of overlapping m/z slices" help="[mzwid] to use for creating peak density chromatograms and grouping peaks across samples " /> <!-- @@ -98,7 +97,7 @@ <outputs> <data name="xsetRData" format="rdata.xcms.group" label="${image.name[:-6]}.group.RData"/> - <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.group.Rplots.pdf"/> + <data name="rplotsPdf" format="pdf" from_work_dir="Rplots.pdf" label="${image.name[:-6]}.group.Rplots.pdf"/> <expand macro="output_peaklist" function="group"/> <data name="log" format="txt" label="xset.log.txt" hidden="true" /> </outputs> @@ -282,29 +281,26 @@ Xcms.Group ========== ------------ Description ----------- After peak identification with xcmsSet, this tool groups the peaks which represent the same analyte across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time. Allows rejection of features, which are only partially detected within the replicates of a sample class. - ------------------ Workflow position ----------------- **Upstream tools** -========================= ================= =================== ========== -Name output file format parameter -========================= ================= =================== ========== -xcms.xcmsSet xset.RData rdata.xcms.raw RData file -------------------------- ----------------- ------------------- ---------- -xcms.xcmsSet Merger xset.RData rdata.xcms.raw RData file -------------------------- ----------------- ------------------- ---------- -xcms.retcor xset.RData rdata.xcms.retcor RData file -========================= ================= =================== ========== ++------------------------+-----------------+--------------------+------------+ +| Name | output file | format | parameter | ++========================+=================+====================+============+ +| xcms.xcmsSet | xset.RData | rdata.xcms.raw | RData file | ++------------------------+-----------------+--------------------+------------+ +| xcms.xcmsSet Merger | xset.RData | rdata.xcms.raw | RData file | ++------------------------+-----------------+--------------------+------------+ +| xcms.retcor | xset.RData | rdata.xcms.retcor | RData file | ++------------------------+-----------------+--------------------+------------+ **Downstream tools** @@ -317,23 +313,23 @@ |xcms.fillPeaks | xset.RData | rdata.xcms.group | +---------------------------+--------------------------------------+ -The output file is an xcmsSet.RData file. You can continue your analysis using it in **xcms.retcor** tool as an next step and then **xcms.fillPeaks**. - **General schema of the metabolomic workflow** .. image:: xcms_group_workflow.png +--------------------------------------------------- + ----------- Input files ----------- +---------------------------+-----------------------+ -| Parameter : num + label | Format | +| Parameter | Format | +===========================+=======================+ -| Or : RData file | rdata.xcms.raw | +| OR : RData file | rdata.xcms.raw | +---------------------------+-----------------------+ -| Or : RData file | rdata.xcms.retcor | +| OR : RData file | rdata.xcms.retcor | +---------------------------+-----------------------+ @@ -357,22 +353,19 @@ | Groups peaks together across samples by creating a master peak list and assigning corresponding peaks from all samples. It is inspired by the alignment algorithm of mzMine. +@HELP_GET_PEAK_LIST@ + ------------ Output files ------------ -xset.group.Rplots.pdf - xset.group.RData: rdata.xcms.group format | Rdata file that will be necessary in the third and fourth step of the workflow (xcms.retcor and xcms.fillpeaks). - ------- +xset.group.Rplots.pdf -.. class:: infomark - -The output file is an xset.group.RData file. You can continue your analysis using it in **xcms.retcor** tool. +@HELP_GET_PEAK_LIST_OUTPUTS@ --------------------------------------------------- @@ -390,23 +383,12 @@ Parameters ---------- - | Method -> **density** - | bw -> **5** - | minfrac -> **0.3** - | mzwid -> **0.01** - | Advanced options: **show** - | max -> **50** - - -Output files ------------- - - | **1) xset.RData: RData file** - - | **2) Example of an xset.group.Rplots pdf file** - -.. image:: xcms_group.png - :width: 700 + | **Method**: density + | **bw**: 10 + | **minfrac**: 0.5 + | **mzwid**: 0.05 + | **Advanced options**: show + | **max**: 10 ---------------------------------------------------