| Previous changeset 8:c043e1fd79d1 (2024-04-16) Next changeset 10:2d94da58904b (2024-05-22) |
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Commit message:
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e |
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modified:
macros.xml ramclustr.xml |
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added:
test-data/test6.fillpeaks test-data/test6_out.msp |
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| diff -r c043e1fd79d1 -r d70dd1d6ac4d macros.xml --- a/macros.xml Tue Apr 16 11:30:05 2024 +0000 +++ b/macros.xml Wed Apr 17 07:51:23 2024 +0000 |
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| @@ -184,9 +184,55 @@ help="NA, NaN, and Inf values are replaced with zero, and zero values are sometimes returned from peak peaking. When TRUE, zero values will be replaced with a small amount of noise, with noise level set based on the detected signal intensities for that feature."/> + <param label="Quality control" name="quality_control" type="boolean" truevalue="TRUE" falsevalue="FALSE" + checked="false" + help="Add graph to Rplots.pdf output which contains summarize quality control for clustering and for quality + control sample variation based on compound ($SpecAbund) and feature ($MSdata and $MSMSdata, if present)."/> <param label="Experimental design metadata" name="ExpDes" type="data" format="csv" optional="true" help="Definition of experimental design in CSV format." /> </section> + + <section name="filtering" title="Filtering"> + <conditional name="feature_filter_blanks"> + <param label="Filter blanks" name="filter_blanks" type="select" + help="Is used to remove features which are found at similar intensity in blank samples"> + <option value="FALSE" selected="true">FALSE</option> + <option value="TRUE">TRUE</option> + </param> + <when value="TRUE"> + <param label="qc tag" name="qc_tag" type="text" value="QC" + help="Character vector of length one or two. If length is two, enter search string and factor name in $phenoData slot + (i.e. c('QC', 'sample.type'). If length one (i.e. 'QC'), will search for this string in the 'sample.names' slot by default. + Default is 'QC'"/> + <param label="blank tag" name="blank_tag" type="text" value="blank" + help="See 'qc tag' , but for blanks to use as background. Default is 'blank'"/> + <param label="signal to noise (sn)" name="sn" type="integer" value="3" + help="Numeric defines the ratio for 'signal'. i.e. sn = 3 indicates that signal intensity must be 3 fold higher in sample than in blanks, + on average, to be retained. Default is '3'"/> + <param label="Remove blanks" name="remove_blanks" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" + help="TRUE by default. This removes any recognized blanks samples from the MSdata and MSMSdata sets after they are used to filter + contaminant features."/> + </when> + <when value="FALSE"></when> + </conditional> + + <conditional name="feature_filter_cv"> + <param label="Filter cv" name="filter_cv" type="select" + help="Extractor for xcms objects in preparation for clustering. This function offers normalization + by total extracted ion signal. It is recommended to first run 'Filter blanks' to remove non-sample derived signal"> + <option value="FALSE" selected="true">FALSE</option> + <option value="TRUE">TRUE</option> + </param> + <when value="TRUE"> + <param label="qc tag" name="qc_tag" type="text" value="QC" + help="Character vector of length one or two. If length is two, enter search string and factor name in $phenoData slot + (i.e. c('QC', 'sample.type'). If length one (i.e. 'QC'), will search for this string in the 'sample.names' slot by default. + Default is 'QC'"/> + <param label="Max cv" name="max_cv" type="float" value="0.5" help="Numeric maximum allowable cv for any feature. Default = 0.5."/> + </when> + <when value="FALSE"></when> + </conditional> + </section> </xml> <xml name="output_msp"> @@ -197,6 +243,9 @@ <data label="Mass spectra from ${tool.name} on ${on_string}" name="mass_spectra_merged" format="msp"> <filter>msp_output_details['merge_msp']</filter> </data> + <data format="pdf" name="pdf_plot" from_work_dir="Rplots.pdf" label="PDF plot."> + <filter>extras['quality_control'] or filtering['feature_filter_cv']['filter_cv'] == "TRUE"</filter> + </data> </xml> <xml name="citations"> |
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| diff -r c043e1fd79d1 -r d70dd1d6ac4d ramclustr.xml --- a/ramclustr.xml Tue Apr 16 11:30:05 2024 +0000 +++ b/ramclustr.xml Wed Apr 17 07:51:23 2024 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy4" profile="21.09"> +<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy5" profile="21.09"> <description>A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.</description> <macros> <import>macros.xml</import> @@ -72,6 +72,16 @@ ramclustObj = RAMClustR::rc.feature.replace.na(ramclustObj = ramclustObj) #end if + #if $filtering.feature_filter_blanks.filter_blanks == "TRUE": + ramclustObj = RAMClustR::rc.feature.filter.blanks( + ramclustObj = ramclustObj, + qc.tag = "${filtering.feature_filter_blanks.qc_tag}", + blank.tag = "${filtering.feature_filter_blanks.blank_tag}", + sn = $filtering.feature_filter_blanks.sn, + remove.blanks = $filtering.feature_filter_blanks.remove_blanks + ) + #end if + #if $normalisation.normalisation_method.normalize != "none": ramclustObj = apply_normalisation( ramclustr_obj = ramclustObj, @@ -89,6 +99,14 @@ ) #end if + #if $filtering.feature_filter_cv.filter_cv == "TRUE": + ramclustObj = RAMClustR::rc.feature.filter.cv( + ramclustObj = ramclustObj, + qc.tag = "${filtering.feature_filter_cv.qc_tag}", + max.cv = $filtering.feature_filter_cv.max_cv + ) + #end if + ramclustObj = RAMClustR::rc.ramclustr( ramclustObj = ramclustObj, st = $filetype.required.st, @@ -104,6 +122,10 @@ rt.only.low.n = $extras.rt_only_low_n, fftempdir = NULL, ) + + #if $extras.quality_control == "TRUE": + ramclustObj = RAMClustR::rc.qc(ramclustObj = ramclustObj) + #end if store_output( ramclustr_obj = ramclustObj, @@ -235,6 +257,40 @@ </section> <output name="mass_spectra_merged" file="test5_spectra.msp" ftype="msp" lines_diff="10"/> </test> + <test expect_num_outputs="3"><!-- TEST 6 --> + <section name="filetype"> + <param name="type_choice" value="xcms"/> + <section name="xcms"> + <param name="input_xcms" value="test6.fillpeaks" ftype="rdata.xcms.fillpeaks"/> + </section> + </section> + <section name="msp_output_details"> + <param name="mzdec" value="4"/> + </section> + <section name="extras"> + <param name="quality_control" value="TRUE"/> + </section> + <section name="filtering"> + <section name="feature_filter_blanks"> + <param name="filter_blanks" value="TRUE"/> + <param name="blank_tag" value="Blanc"/> + </section> + <section name="feature_filter_cv"> + <param name="filter_cv" value="TRUE"/> + </section> + </section> + <output name="mass_spectra_merged" file="test6_out.msp" ftype="msp"/> + <output name="spec_abundance"> + <assert_contents> + <has_size value="309" delta="10"/> + </assert_contents> + </output> + <output name="pdf_plot"> + <assert_contents> + <has_size value="6842" delta="100"/> + </assert_contents> + </output> + </test> </tests> <help> |
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| diff -r c043e1fd79d1 -r d70dd1d6ac4d test-data/test6.fillpeaks |
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| Binary file test-data/test6.fillpeaks has changed |
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| diff -r c043e1fd79d1 -r d70dd1d6ac4d test-data/test6_out.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test6_out.msp Wed Apr 17 07:51:23 2024 +0000 |
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| @@ -0,0 +1,53 @@ +NAME:C1 +IONMODE:Negative +SPECTRUMTYPE:Centroid +RETENTIONTIME:54.89 +Num Peaks:10 +135.0295 9979069 +179.056 5594441 +195.0506 2625643 +165.0401 1960745 +187.0372 1743661 +148.0279 995311 +146.0145 950514 +219.0448 540250 +189.0327 411265 +180.0589 227648 + +NAME:C2 +IONMODE:Negative +SPECTRUMTYPE:Centroid +RETENTIONTIME:63.74 +Num Peaks:8 +191.0193 28601409 +111.0086 2371386 +129.0192 2125989 +192.0223 1724583 +85.0294 991832 +87.0087 956947 +359.0473 811419 +101.0241 397166 + +NAME:C3 +IONMODE:Negative +SPECTRUMTYPE:Centroid +RETENTIONTIME:59.06 +Num Peaks:7 +149.0451 7763606 +151.0067 3434565 +166.0174 822559 +75.0087 771138 +177.0401 707232 +209.066 258300 +178.0633 166079 + +NAME:C4 +IONMODE:Negative +SPECTRUMTYPE:Centroid +RETENTIONTIME:50.66 +Num Peaks:4 +96.9692 6132644 +102.9565 1867855 +176.8926 120442 +184.8312 80882 + |