| Previous changeset 11:41929aa1e7f3 (2019-08-17) Next changeset 13:850f3679b9b4 (2019-08-30) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba" |
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modified:
macros.xml |
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added:
test-data/41737_R1_sub240k.fastq.gz test-data/41737_R2_sub240k.fastq.gz |
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removed:
test-data/41737_R1.fastq.sub240k.gz test-data/41737_R2.fastq.sub240k.gz |
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| diff -r 41929aa1e7f3 -r 39bde80cd248 macros.xml --- a/macros.xml Sat Aug 17 09:38:21 2019 -0400 +++ b/macros.xml Tue Aug 27 05:58:33 2019 -0400 |
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| @@ -88,7 +88,7 @@ && #end if ]]></token> - <token name="@REFGENOMEHANDLING" ><![CDATA[ + <token name="@REFGENOMEHANDLING@" ><![CDATA[ --runThreadN \${GALAXY_SLOTS:-4} --genomeLoad NoSharedMemory --genomeDir @@ -97,7 +97,7 @@ #else: '${refGenomeSource.GTFconditional.genomeDir.fields.path}' ## Handle difference between indices with/without annotations - #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf': + #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf': #if $refGenomeSource.GTFconditional.sjdbGTFfile: --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}' @@ -114,6 +114,7 @@ <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/> <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/> <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/> + <yield /> </stdio> </xml> <xml name="refgenomehandling" > @@ -132,10 +133,10 @@ </param> <when value="with-gtf"> <expand macro="index_selection" with_gene_model="1" /> - <expand macro="@SJDBOPTIONS@" /> </when> <when value="without-gtf"> <expand macro="index_selection" with_gene_model="0" /> + <expand macro="@SJDBOPTIONS@" /> </when> </conditional> </when> |
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