Mercurial > repos > iuc > rgrnastar
changeset 11:41929aa1e7f3 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2911002ccd79fe062f6346ee5699ea262f92f04f"
| author | iuc |
|---|---|
| date | Sat, 17 Aug 2019 09:38:21 -0400 |
| parents | d82339e37e8e |
| children | 39bde80cd248 |
| files | macros.xml rg_rnaStar.xml test-data/rnastar_index2_versioned.loc |
| diffstat | 3 files changed, 8 insertions(+), 8 deletions(-) [+] |
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--- a/macros.xml Thu Aug 15 01:54:13 2019 -0400 +++ b/macros.xml Sat Aug 17 09:38:21 2019 -0400 @@ -21,7 +21,7 @@ </requirements> </xml> - <xml name="index_selection" token_with_gene_model="1"> + <xml name="index_selection" token_with_gene_model="0"> <param argument="--genomeDir" name="genomeDir" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> @@ -127,15 +127,15 @@ <param name="GTFselect" type="select" label="Reference genome with or without an annotation" help="Select the '... with builtin gene-model' option to select from the list of available indexes that were built with splice junction information. Select the '... without builtin gene-model' option to select from the list of available indexes without annotated splice junctions."> - <option value="without-gtf">use genome reference with builtin gene-model</option> - <option value="with-gtf">use genome reference without builtin gene-model</option> + <option value="without-gtf" selected='true'>use genome reference without builtin gene-model</option> + <option value="with-gtf">use genome reference with builtin gene-model</option> </param> <when value="with-gtf"> - <expand macro="index_selection" with_gene_model="0" /> + <expand macro="index_selection" with_gene_model="1" /> <expand macro="@SJDBOPTIONS@" /> </when> <when value="without-gtf"> - <expand macro="index_selection" with_gene_model="1" /> + <expand macro="index_selection" with_gene_model="0" /> </when> </conditional> </when>
--- a/rg_rnaStar.xml Thu Aug 15 01:54:13 2019 -0400 +++ b/rg_rnaStar.xml Sat Aug 17 09:38:21 2019 -0400 @@ -525,7 +525,7 @@ <param name="geneSource" value="indexed" /> <conditional name="GTFconditional"> <param name="GTFselect" value="with-gtf" /> - <param name="genomeDir" value="000" /> + <param name="genomeDir" value="001" /> </conditional> </conditional> <section name="oformat"> @@ -765,7 +765,7 @@ <param name="geneSource" value="indexed" /> <conditional name="GTFconditional"> <param name="GTFselect" value="without-gtf" /> - <param name="genomeDir" value="001" /> + <param name="genomeDir" value="000" /> </conditional> </conditional> <conditional name="twopass">
--- a/test-data/rnastar_index2_versioned.loc Thu Aug 15 01:54:13 2019 -0400 +++ b/test-data/rnastar_index2_versioned.loc Sat Aug 17 09:38:21 2019 -0400 @@ -1,4 +1,4 @@ ##STAR versioned indexes #build_id dbkey display_name path with_gene_model version 000 ? test_index ${__HERE__}/test-cache/tophat-test 0 2.7.1a -001 ? test_index2 ${__HERE__}/test-cache/tophat-test 1 2.7.1a +001 ? test_index_with_gene_model ${__HERE__}/test-cache/tophat-test 1 2.7.1a