Mercurial > repos > iuc > brew3r_r
changeset 3:d3b0390f325f draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit d287d5688e57f4154d5875789e0cd4d5c87f11ce
| author | iuc |
|---|---|
| date | Thu, 03 Oct 2024 22:35:49 +0000 |
| parents | 05f8e9d1e8b8 |
| children | |
| files | brew3r.r_script.R brew3r_r.xml test-data/generate_test.R test-data/input_noexonid.gtf |
| diffstat | 4 files changed, 56 insertions(+), 1 deletions(-) [+] |
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--- a/brew3r.r_script.R Thu Jun 27 07:31:23 2024 +0000 +++ b/brew3r.r_script.R Thu Oct 03 22:35:49 2024 +0000 @@ -97,6 +97,18 @@ } } +if (is.null(input_gr_to_extend$exon_id)) { + is.exon <- which(input_gr_to_extend$type == "exon") + input_gr_to_extend$exon_id <- NA + input_gr_to_extend$exon_id[is.exon] <- paste0( + "EXON", + sprintf( + "%010d", + 1:length(is.exon) + ) + ) +} + # Run BREW3R.r main function if (length(input_gr_template) > 0) { new_gr_exons <- extend_granges(
--- a/brew3r_r.xml Thu Jun 27 07:31:23 2024 +0000 +++ b/brew3r_r.xml Thu Oct 03 22:35:49 2024 +0000 @@ -2,7 +2,7 @@ <description>Extend GTF</description> <macros> <token name="@TOOL_VERSION@">1.0.2</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> </macros> <xrefs> <xref type="bio.tools">brew3r.r</xref> @@ -67,6 +67,16 @@ <output name="output" value="output.gtf" compare="diff" lines_diff="2"/> </test> <test expect_num_outputs="1"> + <param name="gtf_to_extend" value="input_noexonid.gtf"/> + <param name="gtf_to_overlap" value="second_input.gtf"/> + <output name="output"> + <assert_contents> + <has_n_lines n="36"/> + <has_text text="BREW3R"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> <param name="gtf_to_extend" value="input.gtf"/> <param name="gtf_to_overlap" value="second_input.gtf"/> <param name="no_add" value="true"/>
--- a/test-data/generate_test.R Thu Jun 27 07:31:23 2024 +0000 +++ b/test-data/generate_test.R Thu Oct 03 22:35:49 2024 +0000 @@ -258,5 +258,7 @@ new.gr <- extend_granges(input_gr, big_gr) library("rtracklayer") export.gff(input_gr, "input.gtf") +input_gr$exon_id <- NULL +export.gff(input_gr, "input_noexonid.gtf") export.gff(big_gr, "second_input.gtf") export.gff(sort(new.gr, ignore.strand = TRUE), "output.gtf")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_noexonid.gtf Thu Oct 03 22:35:49 2024 +0000 @@ -0,0 +1,31 @@ +##gff-version 2 +##source-version rtracklayer 1.64.0 +##date 2024-10-02 +chr1 rtracklayer exon 5 10 . + . gene_id "gene11"; transcript_id "transcript11"; gene_name "gene11" +chr1 rtracklayer exon 20 30 . + . gene_id "gene12"; transcript_id "transcript12"; gene_name "gene12" +chr1 rtracklayer exon 105 110 . + . gene_id "gene21"; transcript_id "transcript21"; gene_name "gene21" +chr1 rtracklayer exon 120 125 . + . gene_id "gene22"; transcript_id "transcript22"; gene_name "gene22" +chr1 rtracklayer exon 205 210 . + . gene_id "gene31"; transcript_id "transcript31"; gene_name "gene31" +chr1 rtracklayer exon 220 222 . + . gene_id "gene32"; transcript_id "transcript32"; gene_name "gene32" +chr1 rtracklayer exon 305 310 . + . gene_id "gene41"; transcript_id "transcript41"; gene_name "gene41" +chr1 rtracklayer exon 305 322 . + . gene_id "gene42"; transcript_id "transcript42"; gene_name "gene42" +chr1 rtracklayer exon 405 410 . + . gene_id "gene51"; transcript_id "transcript51"; gene_name "gene51" +chr1 rtracklayer exon 405 425 . + . gene_id "gene52"; transcript_id "transcript52"; gene_name "gene52" +chr1 rtracklayer exon 505 510 . + . gene_id "gene61"; transcript_id "transcript61"; gene_name "gene61" +chr1 rtracklayer exon 520 522 . + . gene_id "gene62"; transcript_id "transcript62"; gene_name "gene62" +chr1 rtracklayer exon 601 610 . + . gene_id "gene71"; transcript_id "transcript71"; gene_name "gene71" +chr1 rtracklayer exon 601 610 . + . gene_id "gene71"; transcript_id "transcript72"; gene_name "gene71" +chr1 rtracklayer exon 630 640 . + . gene_id "gene71"; transcript_id "transcript72"; gene_name "gene71" +chr1 rtracklayer exon 701 710 . + . gene_id "gene81"; transcript_id "transcript81"; gene_name "gene81" +chr1 rtracklayer exon 701 710 . + . gene_id "gene82"; transcript_id "transcript82"; gene_name "gene82" +chr1 rtracklayer exon 730 740 . + . gene_id "gene82"; transcript_id "transcript82"; gene_name "gene82" +chr1 rtracklayer exon 801 808 . + . gene_id "gene1"; transcript_id "transcript91"; gene_name "gene1" +chr1 rtracklayer exon 801 810 . + . gene_id "gene1"; transcript_id "transcript92"; gene_name "gene1" +chr1 rtracklayer exon 830 840 . + . gene_id "gene1"; transcript_id "transcript92"; gene_name "gene1" +chr1 rtracklayer exon 901 908 . + . gene_id "gene101"; transcript_id "transcript101"; gene_name "gene101" +chr1 rtracklayer exon 901 910 . + . gene_id "gene102"; transcript_id "transcript102"; gene_name "gene102" +chr1 rtracklayer exon 930 940 . + . gene_id "gene102"; transcript_id "transcript102"; gene_name "gene102" +chr1 rtracklayer exon 1005 1010 . + . gene_id "gene111"; transcript_id "transcript111"; gene_name "Gm001" +chr1 rtracklayer exon 1055 1070 . + . gene_id "gene112"; transcript_id "transcript112"; gene_name "gene112" +chr1 rtracklayer exon 1100 1105 . + . gene_id "gene121"; transcript_id "transcript121"; gene_name "gene121" +chr1 rtracklayer exon 1110 1120 . - . gene_id "gene122"; transcript_id "transcript122"; gene_name "gene122"