| Previous changeset 32:de21b616f03a (2025-05-31) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar commit df3c3300ea4cb1aa93fee2934ac3b1fce19c5c5d |
|
modified:
macros.xml rg_rnaStar.xml |
| b |
| diff -r de21b616f03a -r 55c9ac3aa8f4 macros.xml --- a/macros.xml Sat May 31 19:52:54 2025 +0000 +++ b/macros.xml Mon Apr 13 15:15:49 2026 +0000 |
| b |
| @@ -5,7 +5,7 @@ the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ --> <!-- STAR version to be used --> <token name="@TOOL_VERSION@">2.7.11b</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">21.01</token> <!-- STAR index version compatible with this version of STAR This is the STAR version that introduced the index structure expected @@ -126,6 +126,8 @@ --runThreadN \${GALAXY_SLOTS:-4} ## in bytes --limitGenomeGenerateRAM \$((\${GALAXY_MEMORY_MB:-31000} * 1000000)) + ## Limits - useful to generate indices from large genomes with a lot of annotations + @LIMITS@ && #end if ]]></token> |
| b |
| diff -r de21b616f03a -r 55c9ac3aa8f4 rg_rnaStar.xml --- a/rg_rnaStar.xml Sat May 31 19:52:54 2025 +0000 +++ b/rg_rnaStar.xml Mon Apr 13 15:15:49 2026 +0000 |
| [ |
| @@ -1037,6 +1037,32 @@ <output name="splice_junctions" file="rnastar_test_splicejunctions_diploid.bed"/> <output name="mapped_reads" file="rnastar_test_mapped_reads_diploid.bam" compare="sim_size" delta="634" /> </test> + <!-- test limits during the index generation --> + <test expect_num_outputs="3"> + <conditional name="singlePaired"> + <param name="sPaired" value="paired" /> + <param name="input1" value="pbmc_1k_v2_L001.R1.10k.fastq.gz" ftype="fastqsanger.gz" /> + <param name="input2" value="pbmc_1k_v2_L001.R2.10k.fastq.gz" ftype="fastqsanger.gz" /> + </conditional> + <conditional name="refGenomeSource"> + <param name="geneSource" value="history" /> + <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" /> + <param name="genomeSAindexNbases" value="5" /> + </conditional> + <section name="algo"> + <conditional name="params"> + <param name="settingsType" value="full" /> + <section name="junction_limits"> + <param name="limitOutSJoneRead" value="100" /> + <param name="limitOutSJcollapsed" value="5000" /> + <param name="limitSjdbInsertNsj" value="5000" /> + </section> + </conditional> + </section> + <assert_stdout> + <has_line_matching expression=".*genomeGenerate.*--limitOutSJoneRead\s+100\s+--limitOutSJcollapsed\s+5000\s+--limitSjdbInsertNsj\s+5000" /> + </assert_stdout> + </test> </tests> <help><![CDATA[ **What it does** |