Mercurial > repos > iuc > sleuth
changeset 2:d6b5fc94062c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 10e44e324ee754d81a1b9d990ee0932b37e7a9bc
| author | iuc |
|---|---|
| date | Thu, 08 Jun 2023 19:57:53 +0000 |
| parents | d3e447dd52c8 |
| children | |
| files | macros.xml sleuth.R sleuth.xml test-data/design.tab test-data/design_three_factors.tab test-data/design_two_factors.tab test-data/test01_density.pdf test-data/test01_pca.pdf test-data/test02_density.pdf test-data/test02_pca.pdf test-data/test03_density.pdf test-data/test03_pca.pdf |
| diffstat | 12 files changed, 78 insertions(+), 47 deletions(-) [+] |
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--- a/macros.xml Wed Jun 07 11:47:30 2023 +0000 +++ b/macros.xml Thu Jun 08 19:57:53 2023 +0000 @@ -8,7 +8,7 @@ </requirements> </xml> <token name="@TOOL_VERSION@">0.30.1</token> - <token name="@SUFFIX_VERSION@">1</token> + <token name="@SUFFIX_VERSION@">2</token> <token name="@PROFILE@">20.01</token> <xml name="citations"> <citations>
--- a/sleuth.R Wed Jun 07 11:47:30 2023 +0000 +++ b/sleuth.R Thu Jun 08 19:57:53 2023 +0000 @@ -51,15 +51,11 @@ read.table(file = args$metadata_file, header = TRUE, sep = "\t") - paths <- c() - for (x in s2c$data_filename) { - paths <- c(paths, paste("./kallisto_outputs/", x, sep = "")) + + s2c$path <- file.path("./kallisto_outputs/", paste(s2c$path, ".h5", sep = "")) + for (f in args$factorLevel_counts) { + file.rename(f, paste(f, ".h5", sep = "")) } - for (f in paths) { - file.rename(f, gsub(".fastq.*", "", f)) - file.rename(f, paste(gsub(".fastq.*", "", f), ".h5", sep = "")) - } - s2c$path <- paste(gsub(".fastq.*", ".h5", paths), ".h5", sep = "") so <- sleuth_prep(s2c, full_model = ~ condition, num_cores = 1) so <- sleuth_fit(so)
--- a/sleuth.xml Wed Jun 07 11:47:30 2023 +0000 +++ b/sleuth.xml Thu Jun 08 19:57:53 2023 +0000 @@ -67,7 +67,7 @@ <conditional name="experiment_design"> <param name="selector" type="select" label="Experiment design" help="If you have multiple experimental conditions, you should use propably the complex design mode. In the help section you can find more information."> <option value="single">Simple design mode (one experimental factor)</option> - <option value="complex">Complex design mode (two experimental factors)</option> + <option value="complex">Complex design mode (two or more experimental factors)</option> </param> <when value="single"> <repeat name="rep_factorLevel" title="Factor level" min="2" default="2"> @@ -82,7 +82,7 @@ </when> <when value="complex"> <param name="countsFile" type="data_collection" format="h5" multiple="true" label="Counts file(s)"/> - <param argument="--metadata_file" type="data" format="txt" label="Input metadata file" help="You can find more details about it in the help section" /> + <param argument="--metadata_file" type="data" format="txt" label="Input metadata file" help="You can find more details about the format of the design table in the help section." /> </when> </conditional> <section name="advanced_options" title="Advanced options" expanded="true"> @@ -133,35 +133,64 @@ <output name="pca_plot" file="test01_pca.pdf" ftype="pdf" compare="sim_size"/> <output name="density_plot" file="test01_density.pdf" ftype="pdf" compare="sim_size"/> </test> - <test expect_num_outputs="3"> - <conditional name="experiment_design"> - <param name="selector" value="complex"/> - <param name="countsFile"> - <collection type="list"> - <element name="kallisto_output_01.h5" ftype="h5" value="kallisto_output_01.h5"/> - <element name="kallisto_output_02.h5" ftype="h5" value="kallisto_output_02.h5"/> - <element name="kallisto_output_03.h5" ftype="h5" value="kallisto_output_03.h5"/> - <element name="kallisto_output_04.h5" ftype="h5" value="kallisto_output_04.h5"/> - </collection> - </param> - <param name="metadata_file" value="design.tab"/> - </conditional> - <section name="advanced_options"> - <param name="normalization" value="true"/> - <param name="nbins" value="100"/> - <param name="lwr" value="0.25"/> - <param name="upr" value="0.75"/> - </section> - <output name="sleuth_table" ftype="tabular"> - <assert_contents> - <has_size value="756310" delta="100"/> - <has_text text="ENST00000394894.8"/> - <has_text text="ENST00000524187.1"/> - </assert_contents> - </output> - <output name="pca_plot" file="test02_pca.pdf" ftype="pdf" compare="sim_size"/> - <output name="density_plot" file="test02_density.pdf" ftype="pdf" compare="sim_size"/> - </test> + <test expect_num_outputs="3"> + <conditional name="experiment_design"> + <param name="selector" value="complex"/> + <param name="countsFile"> + <collection type="list"> + <element name="kallisto_output_01.h5" ftype="h5" value="kallisto_output_01.h5"/> + <element name="kallisto_output_02.h5" ftype="h5" value="kallisto_output_02.h5"/> + <element name="kallisto_output_03.h5" ftype="h5" value="kallisto_output_03.h5"/> + <element name="kallisto_output_04.h5" ftype="h5" value="kallisto_output_04.h5"/> + </collection> + </param> + <param name="metadata_file" value="design_two_factors.tab"/> + </conditional> + <section name="advanced_options"> + <param name="normalization" value="true"/> + <param name="nbins" value="100"/> + <param name="lwr" value="0.25"/> + <param name="upr" value="0.75"/> + </section> + <output name="sleuth_table" ftype="tabular"> + <assert_contents> + <has_size value="756310" delta="100"/> + <has_text text="ENST00000394894.8"/> + <has_text text="ENST00000524187.1"/> + </assert_contents> + </output> + <output name="pca_plot" file="test02_pca.pdf" ftype="pdf" compare="sim_size"/> + <output name="density_plot" file="test02_density.pdf" ftype="pdf" compare="sim_size"/> + </test> + <test expect_num_outputs="3"> + <conditional name="experiment_design"> + <param name="selector" value="complex"/> + <param name="countsFile"> + <collection type="list"> + <element name="kallisto_output_01.h5" ftype="h5" value="kallisto_output_01.h5"/> + <element name="kallisto_output_02.h5" ftype="h5" value="kallisto_output_02.h5"/> + <element name="kallisto_output_03.h5" ftype="h5" value="kallisto_output_03.h5"/> + <element name="kallisto_output_04.h5" ftype="h5" value="kallisto_output_04.h5"/> + </collection> + </param> + <param name="metadata_file" value="design_three_factors.tab"/> + </conditional> + <section name="advanced_options"> + <param name="normalization" value="true"/> + <param name="nbins" value="100"/> + <param name="lwr" value="0.25"/> + <param name="upr" value="0.75"/> + </section> + <output name="sleuth_table" ftype="tabular"> + <assert_contents> + <has_size value="756310" delta="100"/> + <has_text text="ENST00000394894.8"/> + <has_text text="ENST00000524187.1"/> + </assert_contents> + </output> + <output name="pca_plot" file="test03_pca.pdf" ftype="pdf" compare="sim_size"/> + <output name="density_plot" file="test03_density.pdf" ftype="pdf" compare="sim_size"/> + </test> </tests> <help><![CDATA[ @@ -196,8 +225,9 @@ filename_04.fastq.gz condition2 replicate2 -The tabular file **requires to have the same column names** as the example (data_file, condition, sample). The data file column correspond to original FASTQ filenames uploaded to Galaxy. -Condition includes the information about the first factor, and sample includes information about the second factor. **Only alphanumeric characters, undescores and dots are allowed**. +The tabular file **requires to have at least three columns with the same names as the previous example** (path, condition, sample). The path column correspond to original FASTQ filenames uploaded to Galaxy. +Condition includes the information about the first factor, and sample includes information about the second factor. **Only alphanumeric characters, undescores and dots are allowed**. +Additional factors can be included in the design table. ]]></help> <expand macro="citations" />
--- a/test-data/design.tab Wed Jun 07 11:47:30 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -sample condition data_filename -CAM_01 CAM kallisto_output_01.h5 -CAM_02 CAM kallisto_output_02.h5 -reC3_01 reC3 kallisto_output_03.h5 -reC3_02 reC3 kallisto_output_04.h5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/design_three_factors.tab Thu Jun 08 19:57:53 2023 +0000 @@ -0,0 +1,5 @@ +sample condition path colour +CAM_01 CAM kallisto_output_01.h5 blue +CAM_02 CAM kallisto_output_02.h5 green +reC3_01 reC3 kallisto_output_03.h5 yellow +reC3_02 reC3 kallisto_output_04.h5 blue