| Previous changeset 4:5c2beb4eb41c (2023-02-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit aa5f4a19e76ec636812865293b8ee9b196122121 |
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modified:
MaxQuantProcessingScript.R macros.xml mqppep_preproc.xml |
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| diff -r 5c2beb4eb41c -r b889e05ce77d MaxQuantProcessingScript.R --- a/MaxQuantProcessingScript.R Tue Feb 14 17:37:36 2023 +0000 +++ b/MaxQuantProcessingScript.R Fri Feb 17 22:38:40 2023 +0000 |
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| @@ -368,6 +368,8 @@ local_prob_cutoff <- args$localProbCutoff enriched <- args$enriched collapse_fn <- args$collapse_func +if (collapse_fn == "average") + collapse_fn <- "mean" ### EXTRACT PARAMETERS from arguments end ------------------------------------ |
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| diff -r 5c2beb4eb41c -r b889e05ce77d macros.xml --- a/macros.xml Tue Feb 14 17:37:36 2023 +0000 +++ b/macros.xml Fri Feb 17 22:38:40 2023 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">0.1.18</token> + <token name="@TOOL_VERSION@">0.1.19</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> @@ -22,6 +22,10 @@ <requirement type="package" version="1.7.3" >r-optparse</requirement> <requirement type="package" version="1.4.4" >r-reshape2</requirement> <requirement type="package" version="2.17" >r-rmarkdown</requirement> + <!-- + <requirement type="package" version="2.2.18" >r-rsqlite</requirement> + <requirement type="package" version="0.4.2" >r-sass</requirement> + --> <requirement type="package" version="1.2.2" >r-sessioninfo</requirement> <requirement type="package" version="0.4_11" >r-sqldf</requirement> <requirement type="package" version="1.4.1" >r-stringr</requirement> |
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| diff -r 5c2beb4eb41c -r b889e05ce77d mqppep_preproc.xml --- a/mqppep_preproc.xml Tue Feb 14 17:37:36 2023 +0000 +++ b/mqppep_preproc.xml Fri Feb 17 22:38:40 2023 +0000 |
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| @@ -35,7 +35,7 @@ --startCol '$startcol_script' --intervalCol $intervalCol --localProbCutoff $localProbCutoff - --collapse_func $collapse_func + --collapse_func $merge_function -o '$phosphoPepIntensities' --locProbCutoffGraph $locProbCutoffGraph --enrichGraph $enrichGraph @@ -121,22 +121,17 @@ <option value="st" selected="true">pST</option> <option value="y">pY</option> </param> - <param name="collapse_func" type="select" + <param name="merge_function" type="select" label="Intensity merge function" help="When a peptide is multiply phosphorylated, how should intensities be merged? [default: sum]" > <option value="sum" selected="true">sum</option> - <option value="mean">average</option> + <option value="average">average</option> </param> <param name="localProbCutoff" type="float" value="0.75" min="0" max="1.0" label="Localization Probability Cutoff" help="See help below for an explanation." /> - <param name="merge_function" type="select" label="intensity merge-function" - help="Specifies how intensities for identical phosphosites should be merged"> - <option value="sum" selected="true">sum</option> - <option value="average">average</option> - </param> <param name="protein_fasta" type="data" format="fasta" label="UniProtKB/SwissProt FASTA database" help="Sequence database; supply the same FASTA file as you supplied to by MaxQuant" /> @@ -187,7 +182,6 @@ <param name="phosphoCol" value="^Number of Phospho [(][STY][STY]*[)]$"/> <param name="startCol" value="^Intensity[^_]"/> <param name="intervalCol" value="1"/> - <param name="collapse_func" value="sum"/> <param name="localProbCutoff" value="0.75"/> <param name="species" value="human"/> @@ -252,7 +246,6 @@ <param name="phosphoCol" value="^Number of Phospho [(][STY][STY]*[)]$"/> <param name="startCol" value="^Intensity[^_]"/> <param name="intervalCol" value="1"/> - <param name="collapse_func" value="sum"/> <param name="localProbCutoff" value="0.75"/> <param name="species" value="human"/> @@ -355,7 +348,7 @@ Minimum localization probability; see above. Intensity merge-function - Specifies how intensities for identical phosphosites should be merged; see above. + Specifies how intensities for identical phosphosites should be merged. Choosing "sum" means that relative intensities reflect number of phospho-*residues*; choosing "average" means that relative intensities reflect number of phospho-*peptides*. Output datasets =============== |