Mercurial > repos > lecorguille > xcms_xcmsset
diff abims_xcms_xcmsSet.xml @ 37:9ada611dd63f draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3922356e5edae763800a4311146e2fdeb52c296e
| author | lecorguille |
|---|---|
| date | Fri, 31 Aug 2018 08:59:03 -0400 |
| parents | d39b9aff9cf7 |
| children | e66eeca443e4 |
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--- a/abims_xcms_xcmsSet.xml Thu Apr 05 18:05:45 2018 -0400 +++ b/abims_xcms_xcmsSet.xml Fri Aug 31 08:59:03 2018 -0400 @@ -46,14 +46,14 @@ #elif $methods.method == "MatchedFilter": fwhm $methods.fwhm binSize $methods.binSize - impute $methods.impute_cond.impute - #if $methods.impute_cond.impute == "linbase": - #if $methods.impute_cond.baseValue != "": - baseValue $methods.impute_cond.baseValue + ## Advanced + impute $methods.MatchedFilterAdv.impute_cond.impute + #if $methods.MatchedFilterAdv.impute_cond.impute == "linbase": + #if $methods.MatchedFilterAdv.impute_cond.baseValue != "": + baseValue $methods.MatchedFilterAdv.impute_cond.baseValue #end if - distance $methods.impute_cond.distance + distance $methods.MatchedFilterAdv.impute_cond.distance #end if - ## Advanced #if $methods.MatchedFilterAdv.sigma != "": sigma $methods.MatchedFilterAdv.sigma #end if @@ -113,22 +113,22 @@ <when value="MatchedFilter"> <param argument="fwhm" type="integer" value="30" label="Full width at half maximum of matched filtration gaussian model peak" help="Only used to calculate the actual sigma" /> <param argument="binSize" type="float" value="0.1" label="Step size to use for profile generation" help="The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size. (Previously step)" /> - <conditional name="impute_cond"> - <param argument="impute" type="select" label="Method to be used for missing value imputation" help="(previously profmethod)"> - <option value="none">none - no linear interpolation</option> - <option value="lin">lin - linear interpolation</option> - <option value="linbase">linbase - linear interpolation within a certain bin-neighborhood</option> - <option value="intlin">intlin - integral of the linearly interpolated data from plus to minus half the step size</option> - </param> - <when value="none" /> - <when value="lin" /> - <when value="linbase"> - <param argument="baseValue" type="float" value="" optional="true" label="The base value to which empty elements should be set" help="The default for the ‘baseValue’ is half of the smallest value in ‘x’ (‘NA’s being removed)." /> - <param argument="distance" type="integer" value="0" label="Number of non-empty neighboring element of an empty element that should be considered for linear interpolation." /> - </when> - <when value="intlin" /> - </conditional> <section name="MatchedFilterAdv" title="Advanced Options" expanded="False"> + <conditional name="impute_cond"> + <param argument="impute" type="select" label="Method to be used for missing value imputation" help="(previously profmethod)"> + <option value="none">none - no linear interpolation</option> + <option value="lin">lin - linear interpolation</option> + <option value="linbase">linbase - linear interpolation within a certain bin-neighborhood</option> + <option value="intlin">intlin - integral of the linearly interpolated data from plus to minus half the step size</option> + </param> + <when value="none" /> + <when value="lin" /> + <when value="linbase"> + <param argument="baseValue" type="float" value="" optional="true" label="The base value to which empty elements should be set" help="The default for the ‘baseValue’ is half of the smallest value in ‘x’ (‘NA’s being removed)." /> + <param argument="distance" type="integer" value="0" label="Number of non-empty neighboring element of an empty element that should be considered for linear interpolation." /> + </when> + <when value="intlin" /> + </conditional> <param argument="sigma" type="float" value="" optional="true" label="Standard deviation (width) of matched filtration model peak" help="Leave it to empty to calculate it using fwhm by default at fwhm/2.3548" /> <param argument="max" type="integer" value="5" label="Maximum number of peaks that are expected/will be identified per slice" /> <param argument="snthresh" type="integer" value="10" label="Signal to Noise ratio cutoff" help="defining the signal to noise cutoff to be used in the chromatographic peak detection step" /> @@ -218,7 +218,7 @@ </assert_stdout> </test>--> <test> - <param name="image" value="ko15-raw.Rdata" ftype="rdata" /> + <param name="image" value="ko15-raw.RData" ftype="rdata" /> <conditional name="methods"> <param name="method" value="CentWave" /> <param name="ppm" value="25" /> @@ -237,9 +237,9 @@ </assert_stdout> </test> <!-- DISABLE FOR TRAVIS - Useful to generate test-data for the further steps --> + Useful to generate test-data for the further steps <test> - <param name="image" value="ko16-raw.Rdata" ftype="rdata" /> + <param name="image" value="ko16-raw.RData" ftype="rdata" /> <conditional name="methods"> <param name="method" value="CentWave" /> <param name="ppm" value="25" /> @@ -255,7 +255,7 @@ </assert_stdout> </test> <test> - <param name="image" value="wt15-raw.Rdata" ftype="rdata" /> + <param name="image" value="wt15-raw.RData" ftype="rdata" /> <conditional name="methods"> <param name="method" value="CentWave" /> <param name="ppm" value="25" /> @@ -271,7 +271,7 @@ </assert_stdout> </test> <test> - <param name="image" value="wt16-raw.Rdata" ftype="rdata" /> + <param name="image" value="wt16-raw.RData" ftype="rdata" /> <conditional name="methods"> <param name="method" value="CentWave" /> <param name="ppm" value="25" /> @@ -286,19 +286,21 @@ <has_text text="Sample classes: ." /> </assert_stdout> </test> - + --> <!-- DISABLE FOR TRAVIS Test to test the different methods parameters <test> - <param name="image" value="ko15-raw.Rdata" ftype="rdata" /> + <param name="image" value="ko15-raw.RData" ftype="rdata" /> <conditional name="methods"> <param name="method" value="MatchedFilter" /> <param name="fwhm" value="35" /> - <conditional name="impute_cond"> - <param name="impute" value="linbase" /> - <param name="baseValue" value="0.1" /> - <param name="distance" value="1" /> - </conditional> + <section name="MatchedFilterAdv" + <conditional name="impute_cond"> + <param name="impute" value="linbase" /> + <param name="baseValue" value="0.1" /> + <param name="distance" value="1" /> + </conditional> + </section> </conditional> <assert_stdout> <has_text text="fwhm: 35" /> @@ -308,7 +310,7 @@ </assert_stdout> </test> <test> - <param name="image" value="ko15-raw.Rdata" ftype="rdata" /> + <param name="image" value="ko15-raw.RData" ftype="rdata" /> <conditional name="methods"> <param name="method" value="CentWavePredIso" /> <param name="ppm" value="56" /> @@ -323,7 +325,7 @@ </assert_stdout> </test> <test> - <param name="image" value="ko15-raw.Rdata" ftype="rdata" /> + <param name="image" value="ko15-raw.RData" ftype="rdata" /> <conditional name="methods"> <param name="method" value="MSW" /> <param name="snthresh" value="4" /> @@ -479,7 +481,7 @@ xset.RData: rdata.xcms.findchrompeaks format - | Rdata file that is necessary in the second step of the workflow "xcms.group". + | RData file that is necessary in the second step of the workflow "xcms.group". ---------------------------------------------------