Mercurial > repos > iuc > rgrnastar
changeset 20:91e0f03268ca draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
| author | iuc |
|---|---|
| date | Wed, 08 Sep 2021 14:35:09 +0000 |
| parents | 44959aa06aeb |
| children | 4074fc1940e2 |
| files | rg_rnaStar.xml |
| diffstat | 1 files changed, 45 insertions(+), 5 deletions(-) [+] |
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--- a/rg_rnaStar.xml Fri Jul 02 20:18:29 2021 +0000 +++ b/rg_rnaStar.xml Wed Sep 08 14:35:09 2021 +0000 @@ -52,11 +52,15 @@ #end for #if str($twopass.twopassMode) != 'None': #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf': - #if not $refGenomeSource.GTFconditional.sjdbGTFfile: - ## case of cached index without built-in gene model, - ## when user does not supply the optional gtf, but - ## specifies the splice junction overhang - --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang + ## need to check first if its a cached index or from history + ## if it's cached then the sjdbGTFfile and sjdbOverhang params are not provided + #if str($refGenomeSource.geneSource) == 'history': + #if not $refGenomeSource.GTFconditional.sjdbGTFfile: + ## case of cached index without built-in gene model, + ## when user does not supply the optional gtf, but + ## specifies the splice junction overhang + --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang + #end if #end if #end if #end if @@ -834,6 +838,42 @@ <output name="splice_junctions" file="rnastar_test_splicejunctions_twopass.bed"/> <output name="mapped_reads" file="rnastar_test_mapped_reads_twopass.bam" compare="sim_size" delta="634" /> </test> + <!-- test Basic twopass with a built-in gtf index option --> + <test expect_num_outputs="3"> + <conditional name="singlePaired"> + <param name="sPaired" value="single" /> + <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> + </conditional> + <conditional name="refGenomeSource"> + <param name="geneSource" value="indexed" /> + <conditional name="GTFconditional"> + <param name="GTFselect" value="with-gtf" /> + <param name="genomeDir" value="001" /> + </conditional> + </conditional> + <conditional name="twopass"> + <param name="twopassMode" value="Basic" /> + </conditional> + <section name="oformat"> + <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> + <param name="outSAMmapqUnique" value="255" /> + </section> + <section name="filter"> + <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonical" /> + <conditional name="output_params2"> + <param name="output_select2" value="yes" /> + </conditional> + </section> + <section name="algo"> + <conditional name="params"> + <param name="settingsType" value="full" /> + </conditional> + </section> + + <output name="output_log" file="rnastar_test_twopass.log" compare="re_match_multiline" /> + <output name="splice_junctions" file="rnastar_test_splicejunctions_twopass.bed"/> + <output name="mapped_reads" file="rnastar_test_mapped_reads_twopass.bam" compare="sim_size" delta="634" /> + </test> <!-- test "multisample" twopass --> <test expect_num_outputs="3"> <conditional name="singlePaired">