| Previous changeset 1:cc96abdef027 (2017-06-01) Next changeset 3:83f8b5ceff43 (2019-12-03) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231 |
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modified:
masigpro.R masigpro.xml test-data/masigpro_out.tab |
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added:
test-data/masigpro_out_no_cluster.tab |
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| diff -r cc96abdef027 -r db04ba860dab masigpro.R --- a/masigpro.R Thu Jun 01 11:10:22 2017 -0400 +++ b/masigpro.R Thu Jul 13 18:23:17 2017 -0400 |
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| @@ -92,6 +92,7 @@ make_option("--significant_intercept", type="character", default="dummy"), make_option("--cluster_data", type="integer", default=1), make_option(c("-k", "--k"), type="integer", default=9), + make_option("--print_cluster", type="logical", default=FALSE), make_option("--cluster_method", type="character", default="hclust"), make_option("--distance", type="character", default="cor"), make_option("--agglo_method", type="character", default="ward.D"), @@ -143,6 +144,17 @@ show.lines = opt$show_lines, cexlab = opt$cexlab, legend = opt$legend) +if (opt$print_cluster) { + for (i in 1:length(results$sig.genes)) { + + colname <- paste(names(results$sig.genes)[i], "cluster", sep = "_") + + results$summary[colname] <- "" + results$summary[[colname]][1:length(results$sig.genes[[i]]$sig.profiles$`cluster$cut`)] <- + results$sig.genes[[i]]$sig.profiles$`cluster$cut` + } +} + filename <- opt$outfile write.table((results$summary), file=filename, sep="\t", quote=FALSE, |
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| diff -r cc96abdef027 -r db04ba860dab masigpro.xml --- a/masigpro.xml Thu Jun 01 11:10:22 2017 -0400 +++ b/masigpro.xml Thu Jul 13 18:23:17 2017 -0400 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="masigpro" name="maSigPro" version="1.49.3.0"> +<tool id="masigpro" name="maSigPro" version="1.49.3.1"> <description>Significant Gene Expression Profile Differences in Time Course Gene Expression Data</description> <requirements> <requirement type="package" version="1.49.3">bioconductor-masigpro</requirement> @@ -70,6 +70,7 @@ #if $pdf.pdf_selector: --cluster_data $pdf.seeGenes.clusterData -k $pdf.seeGenes.k + --print_cluster $pdf.seeGenes.print_cluster --cluster_method $pdf.seeGenes.clustering.clusterMethod #if str($pdf.seeGenes.clustering.clusterMethod) == "hclust": --distance $pdf.seeGenes.clustering.distance @@ -277,6 +278,9 @@ ‘c(sig.profiles,coefficients,t.score)’ of their list position (1,2 or 3)." /> <param name="k" type="integer" label="Number of clusters for data partioning" value="9" /> + <param name="print_cluster" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" + label="Add cluster information to summary file?" + help="Adds columns with the cluster assignment for each gene." /> <conditional name="clustering"> <param name="clusterMethod" label="Cluster Method" type="select" help="clustering method for data partioning. Currently @@ -313,6 +317,8 @@ <param name="iterMax" type="integer" label="Maximum number of iterations" value="500" help="Maximum number of iterations when ‘cluster.method’ is ‘kmeans’" /> </when> + <when value="Mclust"> + </when> </conditional> <param name="colorMode" label="Color Mode" type="select" help="Color scale for plotting profiles. Can be either ‘rainbow’ or ‘gray’"> <option selected="True" value="rainbow">Rainbow</option> @@ -328,10 +334,18 @@ help="Indicating whether legend must be added when plotting profiles" /> </section> </when> + <when value="0"> + </when> </conditional> </inputs> <outputs> - <data format="tabular" name="masigpro_out" label="maSigPro result file on ${on_string}"> + <data format="txt" name="data_out" label="maSigPro data file on ${on_string}"> + <filter> + (( + source['source_selector'] == 'advanced' and + source['enable_output'] == True + )) + </filter> </data> <data format="txt" name="edesign_out" label="maSigPro edesign file on ${on_string}"> <filter> @@ -341,14 +355,6 @@ )) </filter> </data> - <data format="txt" name="data_out" label="maSigPro data file on ${on_string}"> - <filter> - (( - source['source_selector'] == 'advanced' and - source['enable_output'] == True - )) - </filter> - </data> <data format="pdf" name="pdf_out" from_work_dir="Results.pdf" label="maSigPro Plot file on ${on_string}"> <filter> (( @@ -356,6 +362,8 @@ )) </filter> </data> + <data format="tabular" name="masigpro_out" label="maSigPro result file on ${on_string}"> + </data> </outputs> <tests> <test> @@ -397,6 +405,14 @@ <output name="masigpro_out" file="masigpro_out.tab" /> <output name="pdf_out" file="Results.pdf" /> </test> + <test> + <param name="source_selector" value="defaults" /> + <param name="edesign" value="edesign_out.txt" /> + <param name="data" value="data_out.txt" /> + <param name="print_cluster" value="FALSE" /> + <output name="masigpro_out" file="masigpro_out_no_cluster.tab" /> + <output name="pdf_out" file="Results.pdf" /> + </test> </tests> <help> <![CDATA[ |
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| diff -r cc96abdef027 -r db04ba860dab test-data/masigpro_out.tab --- a/test-data/masigpro_out.tab Thu Jun 01 11:10:22 2017 -0400 +++ b/test-data/masigpro_out.tab Thu Jul 13 18:23:17 2017 -0400 |
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| @@ -1,35 +1,35 @@ -Control TreatmentvsControl -FBgn0003358 FBgn0001112 -FBgn0004188 FBgn0003358 -FBgn0029723 FBgn0004188 -FBgn0030449 FBgn0013276 -FBgn0030769 FBgn0020299 -FBgn0032180 FBgn0020639 -FBgn0032860 FBgn0029723 -FBgn0033834 FBgn0029817 -FBgn0036494 FBgn0030449 -FBgn0041336 FBgn0030769 -FBgn0041337 FBgn0030952 -FBgn0050239 FBgn0031082 -FBgn0263626 FBgn0031945 -FBgn0264482 FBgn0032180 - FBgn0032860 - FBgn0032913 - FBgn0033640 - FBgn0033834 - FBgn0034197 - FBgn0034459 - FBgn0036494 - FBgn0038163 - FBgn0038468 - FBgn0039373 - FBgn0041336 - FBgn0041337 - FBgn0045479 - FBgn0047338 - FBgn0050239 - FBgn0261613 - FBgn0262146 - FBgn0263084 - FBgn0263626 - FBgn0264482 +Control TreatmentvsControl Control_cluster TreatmentvsControl_cluster +FBgn0003358 FBgn0001112 1 1 +FBgn0004188 FBgn0003358 1 2 +FBgn0029723 FBgn0004188 1 2 +FBgn0030449 FBgn0013276 2 3 +FBgn0030769 FBgn0020299 1 4 +FBgn0032180 FBgn0020639 1 1 +FBgn0032860 FBgn0029723 3 2 +FBgn0033834 FBgn0029817 4 1 +FBgn0036494 FBgn0030449 1 5 +FBgn0041336 FBgn0030769 5 2 +FBgn0041337 FBgn0030952 6 1 +FBgn0050239 FBgn0031082 7 1 +FBgn0263626 FBgn0031945 8 6 +FBgn0264482 FBgn0032180 9 2 + FBgn0032860 5 + FBgn0032913 1 + FBgn0033640 1 + FBgn0033834 7 + FBgn0034197 1 + FBgn0034459 1 + FBgn0036494 2 + FBgn0038163 1 + FBgn0038468 1 + FBgn0039373 8 + FBgn0041336 9 + FBgn0041337 2 + FBgn0045479 1 + FBgn0047338 1 + FBgn0050239 2 + FBgn0261613 1 + FBgn0262146 1 + FBgn0263084 1 + FBgn0263626 2 + FBgn0264482 2 |
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| diff -r cc96abdef027 -r db04ba860dab test-data/masigpro_out_no_cluster.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/masigpro_out_no_cluster.tab Thu Jul 13 18:23:17 2017 -0400 |
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| @@ -0,0 +1,35 @@ +Control TreatmentvsControl +FBgn0003358 FBgn0001112 +FBgn0004188 FBgn0003358 +FBgn0029723 FBgn0004188 +FBgn0030449 FBgn0013276 +FBgn0030769 FBgn0020299 +FBgn0032180 FBgn0020639 +FBgn0032860 FBgn0029723 +FBgn0033834 FBgn0029817 +FBgn0036494 FBgn0030449 +FBgn0041336 FBgn0030769 +FBgn0041337 FBgn0030952 +FBgn0050239 FBgn0031082 +FBgn0263626 FBgn0031945 +FBgn0264482 FBgn0032180 + FBgn0032860 + FBgn0032913 + FBgn0033640 + FBgn0033834 + FBgn0034197 + FBgn0034459 + FBgn0036494 + FBgn0038163 + FBgn0038468 + FBgn0039373 + FBgn0041336 + FBgn0041337 + FBgn0045479 + FBgn0047338 + FBgn0050239 + FBgn0261613 + FBgn0262146 + FBgn0263084 + FBgn0263626 + FBgn0264482 |