Mercurial > repos > lecorguille > ipo
changeset 7:dd0a593dded1 draft
planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd
| author | lecorguille |
|---|---|
| date | Wed, 12 Apr 2017 08:53:04 -0400 |
| parents | 03fdfbd914ab |
| children | 80de755766a8 |
| files | ipo4retgroup.xml ipo4xcmsSet.xml macros.xml test-data/MM14_IPO_parameters4xcmsSet.tsv test-data/MM14_IPO_parameters4xcmsSet_peakwidth.tsv test-data/MM14_IPO_parameters4xcmsSet_ppm.tsv test-data/faahKO_IPO_parameters4retgroup_bw.tsv |
| diffstat | 7 files changed, 316 insertions(+), 249 deletions(-) [+] |
line wrap: on
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--- a/ipo4retgroup.xml Thu Mar 30 11:27:09 2017 -0400 +++ b/ipo4retgroup.xml Wed Apr 12 08:53:04 2017 -0400 @@ -4,6 +4,14 @@ <macros> <import>macros.xml</import> + + <macro name="group_density_bw_fixed"> + <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" /> + </macro> + + <macro name="group_density_mzwid_fixed"> + <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 " /> + </macro> </macros> <expand macro="requirements"/> @@ -24,43 +32,27 @@ sleep 0.001 #if $group.methods.method == "density": - bw "c($group.methods.bw)" - minfrac "c($group.methods.minfrac)" - mzwid "c($group.methods.mzwid)" - ## minsamp "c($group.methods.minsamp)" - #if $group.methods.density_options.option == "show": - max "c($group.methods.density_options.max)" - #end if + bw "c($group.methods.section_group_density_optiomizable.conditional_parameter.bw)" + mzwid "c($group.methods.section_group_density_optiomizable.conditional_parameter.mzwid)" + + minfrac $group.methods.section_group_density_non_optimizable.minfrac + max $group.methods.section_group_density_non_optimizable.max #end if - - ## retcor methods #if $retcor.methods.method == "obiwarp": retcorMethod obiwarp - profStep "c($methods.profStep)" - - ## $distFunc [1] "cor_opt" - ## $gapInit [1] 0.0 0.4 - ## $gapExtend [1] 2.1 2.7 - ## $$plottype [1] "none" - ## $response [1] 1 - ## $factorDiag [1] 2 - ## $factorGap [1] 1 - ## $localAlignment [1] 0 + profStep $methods.section_retcor_obiwarp_non_optimizable.profStep #elif $retcor.methods.method == "peakgroups": - ## smooth loess retcorMethod loess - smooth loess - extra "c($retcor.methods.extra)" - missing "c($retcor.methods.missing)" - #if $retcor.methods.options.option == "show": - span "c($retcor.methods.options.span)" - family "$retcor.methods.options.family" - plottype "$retcor.methods.options.plottype" - #end if + smooth $retcor.methods.section_retcor_peakgroups_non_optimizable.smooth + extra $retcor.methods.section_retcor_peakgroups_non_optimizable.extra + missing $retcor.methods.section_retcor_peakgroups_non_optimizable.missing + span $retcor.methods.section_retcor_peakgroups_non_optimizable.span + family $retcor.methods.section_retcor_peakgroups_non_optimizable.family + plottype $retcor.methods.section_retcor_peakgroups_non_optimizable.plottype #elif $retcor.methods.method == "none": retcorMethod none #end if @@ -76,92 +68,75 @@ <param name="samplebyclass" type="integer" value="2" label="Number of samples used per class to estimate the best parameters" help="Set to 0 to use the whole dataset. To save time, reduce this number" /> - <section name="group" title="Group Options" expanded="False"> - + <section name="group" title="Group Options" expanded="True"> <conditional name="methods"> - <param name="method" type="select" label="Method to use for grouping" help="[method] See the help section below"> + <param name="method" type="select" label="Method to use for grouping" help="[method] See the help section below. Only the density method is available so far"> <option value="density" selected="true">density</option> </param> <when value="density"> - <param name="bw" type="text" value="22,38" label="Range for Bandwidth" help="[bw] bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram (ex: 30 or 22,38)" /> - <param name="minfrac" type="text" value="0.3,0.7" label="Range for Minimum fraction of samples necessary" help="[minfrac] in at least one of the sample groups for it to be a valid group (ex: 0.5 or 0.3,0.7)" /> - <param name="mzwid" type="text" value="0.015,0.035" label="Range for Width of overlapping m/z slices" help="[mzwid] to use for creating peak density chromatograms and grouping peaks across samples (ex: 0.25 or 0.015,0.035)" /> - <!-- - <param name="minsamp" type="hidden" value="1" label="Range for Minimum number of samples necessary in at least one of the sample groups for it to be a valid group" help="[minsamp] (ex: 1 or 0,5" /> - --> - <conditional name="density_options"> - <param name="option" type="select" label="Advanced options"> - <option value="show">show</option> - <option value="hide" selected="true">hide</option> - </param> - <when value="show"> - <param name="max" type="text" value="50" label="Range for Maximum number of groups to identify in a single m/z slice" help="[max] (ex: 50 or 25,75)" /> - </when> - <when value="hide"> - </when> - </conditional> - + <section name="section_group_density_optiomizable" title="Optimizable parameters" expanded="True"> + <conditional name="conditional_parameter"> + <param name="select_parameter" type="select" label="Which parameter do you want to optimize?" help="Only one paramter can be optimized at once. The other will require fixed values"> + <option value="bw">Bandwidth [bw]</option> + <option value="mzwid">Width of overlapping m/z slices [mzwid]</option> + </param> + <when value="bw"> + <param name="bw" type="text" value="22,38" label="Range for Bandwidth" help="[bw] bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram (ex: 22,38)"> + <validator type="regex" message="Should be this format XX,YY">[0-9]+,[0-9]+</validator> + </param> + <expand macro="group_density_mzwid_fixed" /> + </when> + <when value="mzwid"> + <param name="mzwid" type="text" value="0.015,0.035" label="Range for Width of overlapping m/z slices" help="[mzwid] to use for creating peak density chromatograms and grouping peaks across samples (ex: 0.015,0.035)" > + <validator type="regex" message="Should be one combinaison of those format: XX,YY or -XX,YY or XX.XX,YY.YY">[\-]?[0-9]+[\.]?[0-9]*,[\-]?[0-9]+[\.]?[0-9]*</validator> + </param> + <expand macro="group_density_bw_fixed" /> + </when> + </conditional> + </section> + <section name="section_group_density_non_optimizable" title="Non optimizable parameters" expanded="True"> + <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="max" type="integer" value="50" label="Maximum number of groups to identify in a single m/z slice" help="[max]" /> + </section> </when> </conditional> - - </section> - <section name="retcor" title="Retcor Options" expanded="False"> + <section name="retcor" title="Retcor Options" expanded="True"> <conditional name="methods"> <param name="method" type="select" label="Method to use for retention time correction" help="[method] See the help section below" > <option value="obiwarp">obiwarp</option> <option value="peakgroups">peakgroups</option> </param> <when value="obiwarp"> - <param name="profStep" type="text" value="0.7,1.0" label="Range for Step size (in m/z)" help="[profStep] to use for profile generation from the raw data files (ex: 1 or 0.7 1.0)" /> - <!-- - ## $distFunc [1] "cor_opt" - ## $gapInit [1] 0.0 0.4 - ## $gapExtend [1] 2.1 2.7 - ## $$plottype [1] "none" - ## $response [1] 1 - ## $factorDiag [1] 2 - ## $factorGap [1] 1 - ## $localAlignment [1] 0 - --> + <section name="section_retcor_obiwarp_non_optimizable" title="Non optimizable parameters" expanded="True"> + <param name="profStep" type="text" value="0.7,1.0" label="Range for Step size (in m/z)" help="[profStep] to use for profile generation from the raw data files (ex: 1 or 0.7 1.0)" /> + </section> </when> <when value="peakgroups"> - <param name="smooth" type="select" label="Smooth method" help="[smooth] either 'loess’ for non-linear alignment or ‘linear’ for linear alignment" > - <option value="loess">loess</option> - </param> - <param name="extra" type="text" value="1" label="Range for Number of extra peaks to allow in retention time correction correction groups" help="[extra] (ex: 1 or 1,3)" /> - <param name="missing" type="text" value="1" label="Range for Number of missing samples to allow in retention time correction groups" help="[missing] (ex: 1or 1,3)" /> - - <conditional name="options"> - <param name="option" type="select" label="Advanced options"> - <option value="show">show</option> - <option value="hide" selected="true">hide</option> + <section name="section_retcor_peakgroups_non_optimizable" title="Non optimizable parameters" expanded="True"> + <param name="smooth" type="select" label="Smooth method" help="[smooth] only the 'loess’ for non-linear alignment is available so far" > + <option value="loess">loess</option> </param> - <when value="show"> - <param name="span" type="text" value="0.1,0.3" label="Range for Degree of smoothing for local polynomial regression fitting" help="[span] (ex: 0.2 or 0.1,0.3)"/> - <!-- @TODO multiple="true" --> - <param name="family" type="select" label="Family" help="[family] if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re descending M estimator is used with Tukey's biweight function, allowing outlier removal"> - <option value="gaussian" selected="true">gaussian</option> - <option value="symmetric">symmetric</option> - </param> - <!-- @TODO multiple="true" --> - <param name="plottype" type="select" help="[plottype] if deviation plot retention time deviation points and regression fit, and if mdevden also plot peak overall peak density and retention time correction peak density"> - <option value="none" selected="true">none</option> - <option value="deviation">deviation</option> - <option value="mdevden">mdevden</option> - </param> - - </when> - <when value="hide"> - </when> - </conditional> + <param name="extra" type="integer" value="1" label="Number of extra peaks to allow in retention time correction correction groups" help="[extra]" /> + <param name="missing" type="integer" value="1" label="Number of missing samples to allow in retention time correction groups" help="[missing]" /> + <param name="span" type="float" value="0.2" label="Degree of smoothing for local polynomial regression fitting" help="[span]"/> + <param name="family" type="select" label="Family" help="[family] if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re descending M estimator is used with Tukey's biweight function, allowing outlier removal"> + <option value="gaussian" selected="true">gaussian</option> + <option value="symmetric">symmetric</option> + </param> + <param name="plottype" type="select" help="[plottype] if deviation plot retention time deviation points and regression fit, and if mdevden also plot peak overall peak density and retention time correction peak density"> + <option value="none" selected="true">none</option> + <option value="deviation">deviation</option> + <option value="mdevden">mdevden</option> + </param> + </section> </when> </conditional> </section> - <expand macro="file_load"/> + <expand macro="input_file_load"/> </inputs> @@ -182,27 +157,41 @@ <param name="retcor|methods|smooth" value="loess"/> <param name="retcor|methods|extra" value="1"/> <param name="retcor|methods|missing" value="1"/> - <param name="file_load_conditional|file_load_select" value="yes" /> - <param name="file_load_conditional|inputs|zip_file" value="faahKO_reduce.zip" ftype="zip" /> + <expand macro="test_file_load_zip"/> <output name="parametersOutput" file="faahKO_IPO_parameters4retgroup.tsv" /> </test>--> <test> <param name="image" value="faahKO.xset.RData"/> - <param name="group|methods|method" value="density"/> - <param name="group|methods|bw" value="28,32"/> - <param name="group|methods|minfrac" value="1"/> - <param name="group|methods|mzwid" value="0.25"/> - <param name="retcor|methods|method" value="peakgroups"/> - <param name="retcor|methods|smooth" value="loess"/> - <param name="retcor|methods|extra" value="1"/> - <param name="retcor|methods|missing" value="1"/> - <param name="file_load_conditional|file_load_select" value="yes" /> - <param name="file_load_conditional|inputs|zip_file" value="faahKO_reduce.zip" ftype="zip" /> + <section name="group"> + <conditional name="methods"> + <param name="method" value="density"/> + <section name="section_group_density_optiomizable"> + <conditional name="conditional_parameter"> + <param name="bw" value="28,32"/> + <param name="mzwid" value="0.25"/> + </conditional> + </section> + <section name="section_group_density_non_optimizable"> + <param name="minfrac" value="1"/> + </section> + </conditional> + </section> + <section name="retcor"> + <conditional name="methods"> + <param name="method" value="peakgroups"/> + <section name="section_retcor_peakgroups_non_optimizable"> + <param name="smooth" value="loess"/> + <param name="rextra" value="1"/> + <param name="missing" value="1"/> + </section> + </conditional> + </section> + <expand macro="test_file_load_zip"/> <output name="parametersOutput" file="faahKO_IPO_parameters4retgroup_bw.tsv" /> </test> - <test> + <!--<test> <param name="image" value="faahKO.xset.RData"/> <param name="group|methods|method" value="density"/> <param name="group|methods|bw" value="30"/> @@ -212,10 +201,9 @@ <param name="retcor|methods|smooth" value="loess"/> <param name="retcor|methods|extra" value="1"/> <param name="retcor|methods|missing" value="1"/> - <param name="file_load_conditional|file_load_select" value="yes" /> - <param name="file_load_conditional|inputs|zip_file" value="faahKO_reduce.zip" ftype="zip" /> + <expand macro="test_file_load_zip"/> <output name="parametersOutput" file="faahKO_IPO_parameters4retgroup_mzmid.tsv" /> - </test> + </test>--> <!--<test> <param name="image" value="MM-xset-merge.RData"/> @@ -228,8 +216,7 @@ <param name="retcor|methods|extra" value="1"/> <param name="retcor|methods|missing" value="1"/> <param name="file_load_conditional|file_load_select" value="yes" /> - <param name="file_load_conditional|inputs|input" value="single_file" /> - <param name="file_load_conditional|inputs|single_file" value="MM8.mzML,MM14.mzML" ftype="mzxml" /> + <expand macro="test_file_load_single"/> <output name="parametersOutput" file="MM_IPO_parameters4retgroup.tsv" /> </test>--> </tests>
--- a/ipo4xcmsSet.xml Thu Mar 30 11:27:09 2017 -0400 +++ b/ipo4xcmsSet.xml Wed Apr 12 08:53:04 2017 -0400 @@ -1,21 +1,39 @@ <tool id="ipo4xcmsSet" name="IPO for xcmsSet" version="0.0.3"> - + <description>IPO optimization process for xcms.xcmsSet</description> - + <macros> <import>macros.xml</import> + + <macro name="centwave_ppm_fixed"> + <param name="ppm" type="integer" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="[ppm]" /> + </macro> + <macro name="centwave_peakwidth_fixed"> + <param name="min_peakwidth" type="float" value="20" label="Min peak width range in seconds" optional="true" help="[min_peakwidth]" /> + <param name="max_peakwidth" type="float" value="50" label="Max peak width range in seconds" optional="true" help="[max_peakwidth]" /> + </macro> + <macro name="centwave_mzdiff_fixed"> + <param name="mzdiff" type="float" value="-0.001" label="Minimum difference in m/z for peaks with overlapping Retention Times" help="[mzdiff] Can be negative to allow overlap" /> + </macro> + + <macro name="matchedfilter_fwhm_fixed"> + <param name="fwhm" type="integer" value="30" label="Full width at half maximum of matched filtration gaussian model peak" help="[fwhm] Only used to calculate the actual sigma" /> + </macro> + <macro name="matchedfilter_mzdiff_fixed"> + <param name="mzdiff" type="float" value="0.6" label="Minimum difference in m/z for peaks with overlapping Retention Times" help="[mzdiff] By default: 0.8-step*steps " /> + </macro> </macros> <expand macro="requirements"/> <expand macro="stdio"/> - + <command><![CDATA[ LANG=C Rscript $__tool_directory__/ipo4xcmsSet.r - #if $inputs.input == "zip_file": - zipfile $inputs.zip_file - #elif $inputs.input == "single_file": - singlefile_galaxyPath $inputs.single_file singlefile_sampleName $inputs.single_file.name + #if $input.is_of_type("mzxml") or $input.is_of_type("mzml") or $input.is_of_type("mzdata") or $input.is_of_type("netcdf"): + singlefile_galaxyPath '$input' singlefile_sampleName '$input.name' + #else + zipfile '$input' #end if parametersOutput $parametersOutput @@ -23,51 +41,37 @@ samplebyclass $samplebyclass - ## profmethod $profmethod + ## profmethod $profmethod @COMMAND_NSLAVES@ - method $methods.method + method $methods.method #if $methods.method == "centWave": - ppm "c($methods.ppm)" - min_peakwidth "c($methods.min_peakwidth)" - max_peakwidth "c($methods.max_peakwidth)" - #if $methods.options_c.option == "show": - mzdiff "c($methods.options_c.mzdiff)" - snthresh "c($methods.options_c.snthresh)" - integrate "$methods.options_c.integrate" - noise "c($methods.options_c.noise)" - prefilter "c($methods.options_c.prefilter)" - prefilter_value "c($methods.options_c.prefilter_value)" - #end if + ppm "c($methods.section_centwave_optiomizable.conditional_parameter.ppm)" + min_peakwidth "c($methods.section_centwave_optiomizable.conditional_parameter.min_peakwidth)" + max_peakwidth "c($methods.section_centwave_optiomizable.conditional_parameter.max_peakwidth)" + mzdiff "c($methods.section_centwave_optiomizable.conditional_parameter.mzdiff)" + + snthresh $methods.section_centwave_non_optiomizable.snthresh + integrate $methods.section_centwave_non_optiomizable.integrate + noise $methods.section_centwave_non_optiomizable.noise + prefilter "c($methods.section_centwave_non_optiomizable.prefilter)" + #elif $methods.method == "matchedFilter": - step "c($methods.step)" - fwhm "c($methods.fwhm)" - #if $methods.options_m.option == "show": - sigma "c($methods.options_m.sigma)" - max "c($methods.options_m.max)" - snthresh "c($methods.options_m.snthresh)" - mzdiff "c($methods.options_m.mzdiff)" - steps "c($methods.options_m.steps)" - #end if + fwhm "c($methods.section_matchedfilter_optiomizable.conditional_parameter.fwhm)" + mzdiff "c($methods.section_matchedfilter_optiomizable.conditional_parameter.mzdiff)" + + step $methods.section_matchedfilter_non_optimizable.step + steps $methods.section_matchedfilter_non_optimizable.steps + max $methods.section_matchedfilter_non_optimizable.max + snthresh $methods.section_matchedfilter_non_optimizable.snthresh #end if - @COMMAND_LOG_EXIT@ + @COMMAND_LOG_EXIT@ ]]></command> - + <inputs> - <conditional name="inputs"> - <param name="input" type="select" label="Choose your inputs method" > - <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option> - <option value="single_file">mzXML file from your history</option> - </param> - <when value="zip_file"> - <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" /> - </when> - <when value="single_file"> - <param name="single_file" type="data" format="mzxml" label="Single file" /> - </when> - </conditional> - + <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." /> + <param name="samplebyclass" type="integer" value="2" label="Number of samples used per class to estimate the best parameters" help="Set to 0 to use the whole dataset. To save time, reduce this number" /> <conditional name="methods"> @@ -78,70 +82,126 @@ <!-- centWave Filter options --> <when value="centWave"> - <param name="ppm" type="text" value="17,32" label="Range for Max tolerated ppm m/z deviation in consecutive scans in ppm" optional="false" help="[ppm] (ex: 25 or 17,32)" /> - <param name="min_peakwidth" type="text" value="12,18" label="Range for Min peak width range in seconds" optional="true" help="[min_peakwidth] (ex: 20 or 12,18)" /> - <param name="max_peakwidth" type="text" value="35,65" label="Range for Max peak width range in seconds" optional="true" help="[max_peakwidth] (ex: 50 or 35,65)" /> - <conditional name="options_c"> - <param name="option" type="select" label="Advanced options" > - <option value="show">show</option> - <option value="hide" selected="true">hide</option> + <section name="section_centwave_optiomizable" title="Optimizable parameters" expanded="True"> + <conditional name="conditional_parameter"> + <param name="select_parameter" type="select" label="Which parameter do you want to optimize?" help="Only one paramter can be optimized at once. The other will require fixed values"> + <option value="ppm">Max tolerated ppm m/z deviation in consecutive scans in ppm [ppm]</option> + <option value="peakwidth">Min,Max peak width in seconds [peakwidth]</option> + <option value="mzdiff">Minimum difference in m/z for peaks with overlapping Retention Times [mzdiff]</option> + </param> + <when value="ppm"> + <param name="ppm" type="text" value="17,32" label="Range for Max tolerated ppm m/z deviation in consecutive scans in ppm" optional="false" help="[ppm] (ex: 25 or 17,32)"> + <validator type="regex" message="Should be this format XX,YY">[0-9]+,[0-9]+</validator> + </param> + <expand macro="centwave_peakwidth_fixed" /> + <expand macro="centwave_mzdiff_fixed" /> + </when> + <when value="peakwidth"> + <param name="min_peakwidth" type="text" value="12,18" label="Range for Min peak width range in seconds" optional="true" help="[min_peakwidth] (ex: 12,18)"> + <validator type="regex" message="Should be one combinaison of those format: XX,YY or XX.XX,YY.YY">[0-9]+[\.]?[0-9]*,[0-9]+[\.]?[0-9]*</validator> + </param> + <param name="max_peakwidth" type="text" value="35,65" label="Range for Max peak width range in seconds" optional="true" help="[max_peakwidth] (ex: 35,65)"> + <validator type="regex" message="Should be one combinaison of those format: XX,YY or XX.XX,YY.YY">[0-9]+[\.]?[0-9]*,[0-9]+[\.]?[0-9]*</validator> + </param> + <expand macro="centwave_ppm_fixed" /> + <expand macro="centwave_mzdiff_fixed" /> + </when> + <when value="mzdiff"> + <param name="mzdiff" type="text" value="-0.001,0.010" label="Range for Minimum difference in m/z for peaks with overlapping retention times" help="[mzdiff] Can be negative to allow overlap (ex: -0.001,0.010)"> + <validator type="regex" message="Should be one combinaison of those format: XX,YY or -XX,YY or XX.XX,YY.YY">[\-]?[0-9]+[\.]?[0-9]*,[\-]?[0-9]+[\.]?[0-9]*</validator> + </param> + <expand macro="centwave_ppm_fixed" /> + <expand macro="centwave_peakwidth_fixed" /> + </when> + </conditional> + </section> + + <section name="section_centwave_non_optiomizable" title="Non optimizable parameters" expanded="True"> + <param name="snthresh" type="integer" value="10" label="Signal/Noise threshold" help="[snthresh] Signal to noise ratio cutoff" /> + <param name="integrate" type="select" label="Peak limits method" help="[integrate]" > + <option value="1">peak limits based on smoothed 2nd derivative (less precise)</option> + <option value="2">peak limits based on real data (more sensitive to noise)</option> </param> - <when value="show"> - <param name="snthresh" type="text" value="10" label="Range for Signal/Noise threshold" help="[snthresh] Signal to noise ratio cutoff (ex: 10 or 5,15)" /> - <param name="mzdiff" type="text" value="-0.001,0.010" label="Range for Min m/z difference" help="[mzdiff] Min m/z difference for peaks with overlapping RT (ex: -0.001 or -0.001,0.010)" /> - <!-- @TODO multiple="true" --> - <param name="integrate" type="select" label="Peak limits method" help="[integrate]" > - <option value="1">1 - peak limits based on smoothed 2nd derivative (less precise)</option> - <option value="2">2 - peak limits based on real data (more sensitive to noise)</option> - </param> - <param name="prefilter" type="text" value="3" label="Range for the k value for the Prefilter step for the first phase" help="[prefilter] Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’ (ex: 3 or 2,3)"/> - <param name="prefilter_value" type="text" value="100" label="Range for the I value for the Prefilter step for the first phase" help="[prefilter_value] Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’ (ex: 100 or 95,105)"/> - <param name="noise" type="text" value="0" label="Range for the Noise filter" help="[noise] optional argument which is useful for data that was centroided without any intensity threshold, centroids with intensity smaller than ‘noise’ are omitted from ROI detection (ex: 0 or 0,0.1)"/> - </when> - <when value="hide" /> - </conditional> + <param name="prefilter" type="text" value="3,100" label="Prefilter step for the first phase" help="[prefilter] Separate by coma k,I. Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’"/> + <param name="noise" type="integer" value="0" label="Noise filter" help="[noise] optional argument which is useful for data that was centroided without any intensity threshold, centroids with intensity smaller than ‘noise’ are omitted from ROI detection"/> + </section> </when> <!-- matched Filter options --> <when value="matchedFilter"> - <param name="step" type="text" value="0.05,0.15" label="Range for Step size to use for profile generation" optional="true" help="[step] The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size (ex: 0.1 or 0.05,0.15)" /> - <param name="fwhm" type="text" value="25,35" label="Range for Full width at half maximum of matched filtration gaussian model peak" optional="true" help="[fwhm] Only used to calculate the actual sigma (ex: 30 or 25,35)" /> - <conditional name="options_m"> - <param name="option" type="select" label="Advanced options" > - <option value="show">show</option> - <option value="hide" selected="true">hide</option> - </param> - <when value="show"> - <param name="sigma" type="text" value="0" label="sigma" help="Range for standard deviation (fwhm/2.3548) (ex: 0 or 0,1)" /> - <param name="max" type="text" value="5" label="Range for Maximum number of peaks per extracted ion chromatogram" help="[max] (ex: 5 or 4,6)" /> - <param name="snthresh" type="text" value="3,17" label="Range for Signal to noise ratio cutoff" help="[snthresh] (ex: 10 or 3,17)" /> - <param name="steps" type="text" value="1,3" label="Range for Number of steps to merge prior to filtration" help="[steps] The peak identification algorithm combines a given number of EIBPCs prior to filtration and peak detection, as defined by the steps argument (ex: 2 or 1,3)" /> - <param name="mzdiff" type="text" value="0" label="m/z difference" help="Range for min m/z difference for peaks with overlapping RT (0.8-step*steps) (ex: 2 or 1,3)" /> - </when> - <when value="hide" /> - </conditional> + <section name="section_matchedfilter_optiomizable" title="Optimizable parameters" expanded="True"> + <conditional name="conditional_parameter"> + <param name="select_parameter" type="select" label="Which parameter do you want to optimize?" help="Only one paramter can be optimized at once. The other will require fixed values"> + <option value="fwhm">Full width at half maximum of matched filtration gaussian model peak [fwhm]</option> + <option value="mzdiff">Minimum difference in m/z for peaks with overlapping Retention Times [mzdiff]</option> + </param> + <when value="fwhm"> + <param name="fwhm" type="text" value="25,35" label="Range for Full width at half maximum of matched filtration gaussian model peak" optional="true" help="[fwhm] Only used to calculate the actual sigma (ex: 25,35)"> + <validator type="regex" message="Should be this format: XX,YY">[0-9]+,[0-9]+</validator> + </param> + <expand macro="matchedfilter_mzdiff_fixed" /> + </when> + <when value="mzdiff"> + <param name="mzdiff" type="text" value="0.4,0.7" label="Range for Minimum difference in m/z for peaks with overlapping Retention Times" help="[mzdiff] By default: 0.8-step*steps (ex: 0.4,0.7)"> + <validator type="regex" message="Should be one combinaison of those format: XX,YY or -XX,YY or XX.XX,YY.YY">[\-]?[0-9]+[\.]?[0-9]*,[\-]?[0-9]+[\.]?[0-9]*</validator> + </param> + <expand macro="matchedfilter_fwhm_fixed" /> + </when> + </conditional> + </section> + + <section name="section_matchedfilter_non_optimizable" title="Non optimizable parameters" expanded="True"> + <param name="step" type="float" value="0.1" label="Step size to use for profile generation" help="[step] The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size" /> + <param name="steps" type="integer" value="2" label="Number of steps to merge prior to filtration" help="[steps] The peak identification algorithm combines a given number of EIBPCs prior to filtration and peak detection, as defined by the steps argument" /> + <param name="max" type="integer" value="5" label="Maximum number of peaks per extracted ion chromatogram" help="[max]" /> + <param name="snthresh" type="integer" value="10" label="Signal to noise ratio cutoff" help="[snthresh]" /> + </section> </when> - </conditional> + </conditional> </inputs> - + <outputs> <data name="xsetRData" format="rdata.xcms.raw" label="xset.RData" /> <data name="parametersOutput" format="tabular" label="IPO_parameters4xcmsSet.tsv" /> <data name="log" format="txt" label="ipo4xcmsSet.log.txt" /> </outputs> - + <tests> <test> - <param name="inputs|input" value="single_file" /> - <param name="inputs|single_file" value="MM14.mzML" ftype="mzxml" /> + <param name="input" value="MM14.mzML" ftype="mzxml" /> <param name="samplebyclass" value="0" /> - <param name="methods|method" value="centWave" /> - <param name="methods|ppm" value="56" /> - <param name="methods|min_peakwidth" value="3,9.5" /> - <param name="methods|max_peakwidth" value="10,20" /> - <output name="parametersOutput" file="MM14_IPO_parameters4xcmsSet.tsv" /> + <conditional name="methods"> + <param name="method" value="centWave" /> + <section name="section_centwave_optiomizable" > + <conditional name="conditional_parameter"> + <param name="select_parameter" value="peakwidth" /> + <param name="min_peakwidth" value="3,9.5" /> + <param name="max_peakwidth" value="10,20" /> + <param name="ppm" value="56" /> + <param name="mzdiff" value="-0.001" /> + </conditional> + </section> + </conditional> + <output name="parametersOutput" file="MM14_IPO_parameters4xcmsSet_peakwidth.tsv" /> + </test> + <test> + <param name="input" value="MM14.mzML" ftype="mzxml" /> + <param name="samplebyclass" value="0" /> + <conditional name="methods"> + <param name="method" value="centWave" /> + <section name="section_centwave_optiomizable" > + <conditional name="conditional_parameter"> + <param name="select_parameter" value="ppm" /> + <param name="ppm" value="50,60" /> + <param name="min_peakwidth" value="3.325" /> + <param name="max_peakwidth" value="11" /> + <param name="mzdiff" value="-0.001" /> + </conditional> + </section> + </conditional> + <output name="parametersOutput" file="MM14_IPO_parameters4xcmsSet_ppm.tsv" /> </test> <!-- Too long for Travis CI --> <!--<test> @@ -165,7 +225,7 @@ <output name="parametersOutput" file="sacuri_2files_matchedFilter_IPO_parameters4xcmsSet.tsv" /> </test>--> <!--Failed: - Error in resultIncreased(history) : + Error in resultIncreased(history) : No isotopes have been detected, peak picking not optimizable by IPO!--> <!--<test> <param name="inputs|input" value="zip_file" /> @@ -178,7 +238,7 @@ <output name="parametersOutput" file="faahKO_IPO_parameters4xcmsSet.tsv" /> </test>--> </tests> - + <help><![CDATA[ @HELP_AUTHORS@ @@ -203,7 +263,7 @@ ========================= ================= ======= ========= Name output file format parameter ========================= ================= ======= ========= -NA NA zip NA +NA NA zip NA ========================= ================= ======= ========= @@ -289,7 +349,7 @@ **Matched Filter** - | One parameter to consider is the Gaussian model peak width used for matched filtration,an integral part of the peak detection algorithm. + | One parameter to consider is the Gaussian model peak width used for matched filtration,an integral part of the peak detection algorithm. | For a discussion of how model peak width affects the signal to noise ratio, see Danielsson et al. (2002).
--- a/macros.xml Thu Mar 30 11:27:09 2017 -0400 +++ b/macros.xml Wed Apr 12 08:53:04 2017 -0400 @@ -33,41 +33,50 @@ <!-- zipfile load for planemo test --> <token name="@COMMAND_FILE_LOAD@"> - #if $file_load_conditional.file_load_select == "yes": - #if $file_load_conditional.inputs.input == "zip_file": - zipfile $file_load_conditional.inputs.zip_file + #if $file_load_section.file_load_conditional.file_load_select == "yes": + #if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"): + #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] ) + #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] ) + + singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName' #else - #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_conditional.inputs.single_file ] ) - #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_conditional.inputs.single_file ] ) - - singlefile_galaxyPath $singlefile_galaxyPath singlefile_sampleName $singlefile_sampleName + zipfile '$file_load_section.file_load_conditional.input' #end if #end if </token> - <xml name="file_load"> - <conditional name="file_load_conditional"> - <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server." > - <option value="no" >no need</option> - <option value="yes" >yes</option> - </param> - <when value="no"> - </when> - <when value="yes"> - <conditional name="inputs"> - <param name="input" type="select" label="Choose your inputs method" > - <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option> - <option value="single_file">A mzXML or netCDF file from your history</option> - </param> - <when value="zip_file"> - <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" /> - </when> - <when value="single_file"> - <param name="single_file" type="data" format="mzxml,netcdf" label="Single file" multiple="true"/> - </when> - </conditional> - </when> - </conditional> + <xml name="input_file_load"> + <section name="file_load_section" title="Resubmit your raw dataset or your zip file"> + <conditional name="file_load_conditional"> + <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server." > + <option value="no" >no need</option> + <option value="yes" >yes</option> + </param> + <when value="no"> + </when> + <when value="yes"> + <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." /> + </when> + </conditional> + </section> + </xml> + + <xml name="test_file_load_zip"> + <section name="file_load_section"> + <conditional name="file_load_conditional"> + <param name="file_load_select" value="yes" /> + <param name="input" value="faahKO_reduce.zip" ftype="zip" /> + </conditional> + </section> + </xml> + + <xml name="test_file_load_single"> + <section name="file_load_section"> + <conditional name="file_load_conditional"> + <param name="file_load_select" value="yes" /> + <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" /> + </conditional> + </section> </xml> <token name="@HELP_AUTHORS@">
--- a/test-data/MM14_IPO_parameters4xcmsSet.tsv Thu Mar 30 11:27:09 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,11 +0,0 @@ -min_peakwidth 5.275 -max_peakwidth 13.5 -mzdiff 0.01 -ppm 56 -snthresh 10 -noise 0 -prefilter 3 -value_of_prefilter 100 -mzCenterFun wMean -integrate 1 -fitgauss FALSE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MM14_IPO_parameters4xcmsSet_peakwidth.tsv Wed Apr 12 08:53:04 2017 -0400 @@ -0,0 +1,11 @@ +min_peakwidth 3.325 +max_peakwidth 11 +prefilter 3 +ppm 56 +mzdiff -0.001 +snthresh 10 +integrate 1 +noise 0 +value_of_prefilter 100 +mzCenterFun wMean +fitgauss FALSE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MM14_IPO_parameters4xcmsSet_ppm.tsv Wed Apr 12 08:53:04 2017 -0400 @@ -0,0 +1,11 @@ +ppm 60 +prefilter 3 +min_peakwidth 3.325 +max_peakwidth 11 +mzdiff -0.001 +snthresh 10 +integrate 1 +noise 0 +value_of_prefilter 100 +mzCenterFun wMean +fitgauss FALSE
--- a/test-data/faahKO_IPO_parameters4retgroup_bw.tsv Thu Mar 30 11:27:09 2017 -0400 +++ b/test-data/faahKO_IPO_parameters4retgroup_bw.tsv Wed Apr 12 08:53:04 2017 -0400 @@ -1,13 +1,13 @@ bw 4.168192 -span 0.22 +mzwid 0.25 minfrac 1 -mzwid 0.25 +max 50 retcorMethod loess smooth loess extra 1 missing 1 +span 0.2 family gaussian plottype none minsamp 1 -max 50 center 2