Mercurial > repos > jackcurragh > ribogalaxy_bowtie_transcriptome
changeset 2:cd79614871c2 draft
index table name has changed
absolute path to indexes are added
author | triasteran |
---|---|
date | Sun, 27 Mar 2022 16:22:48 +0000 |
parents | 14fb4b4872e3 |
children | 14deb381fa27 |
files | bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml bowtie_transcriptome_wrapper/tool-data/bowtie_indices.loc.sample bowtie_transcriptome_wrapper/tool_data_table_conf.xml.sample |
diffstat | 3 files changed, 7 insertions(+), 39 deletions(-) [+] |
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--- a/bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml Tue Mar 22 12:34:36 2022 +0000 +++ b/bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml Sun Mar 27 16:22:48 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="bowtie_transcriptomic_wrapper" name="Align to transcriptome using Bowtie" version="1.2.0"> +<tool id="bowtie_transcriptomic_wrapper" name="Align to transcriptome using Bowtie" version="1.3.0ind"> <description></description> <requirements> <requirement type="package" version="1.2.0">bowtie</requirement> @@ -160,7 +160,7 @@ </param> <when value="indexed"> <param name="index" type="select" label="Select a reference" help="if your reference of interest is not listed - contact RiboGalaxy team"> - <options from_data_table="bowtie_indexes"> + <options from_data_table="bowtie_indexes_transcriptome"> <filter type="sort_by" column="2" /> <validator type="no_options" message="No indexes are available" /> </options>
--- a/bowtie_transcriptome_wrapper/tool-data/bowtie_indices.loc.sample Tue Mar 22 12:34:36 2022 +0000 +++ b/bowtie_transcriptome_wrapper/tool-data/bowtie_indices.loc.sample Sun Mar 27 16:22:48 2022 +0000 @@ -1,37 +1,5 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of Bowtie indexed sequences data files. You will -#need to create these data files and then create a bowtie_indices.loc -#file similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The bowtie_indices.loc -#file has this format (longer white space characters are TAB characters): -# #<unique_build_id> <dbkey> <display_name> <file_base_path> -# -#So, for example, if you had hg18 indexed stored in -#/depot/data2/galaxy/bowtie/hg18/, -#then the bowtie_indices.loc entry would look like this: -# -#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18 -# -#and your /depot/data2/galaxy/bowtie/hg18/ directory -#would contain hg18.*.ebwt files: -# -#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt -#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt -#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt -#...etc... -# -#Your bowtie_indices.loc file should include an entry per line for each -#index set you have stored. The "file" in the path does not actually -#exist, but it is the prefix for the actual index files. For example: -# -#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon -#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full -#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 -#...etc... -# -#Note that for backwards compatibility with workflows, the unique ID of -#an entry must be the path that was in the original loc file, because that -#is the value stored in the workflow for that parameter. That is why the -#hg19 entry above looks odd. New genomes can be better-looking. -# +hg38_gencode25_transcriptome hg38_gencode25_transcriptome hg38_gencode25_transcriptome /data/transcriptome/homo_sapiens_gencode25/gencode_v25_human +mus_musculus_transcriptome mus_musculus_transcriptome mus_musculus_transcriptome /data/transcriptome/Mus_musculus/mus_musculus +ecoli_transcriptome ecoli_transcriptome ecoli_transcriptome /data/transcriptome/e_coli/ecoli +sacCer3_transcriptome sacCer3_transcriptome sacCer3_transcriptome /data/transcriptome/saccharomyces_cerevisiae/yeast_index
--- a/bowtie_transcriptome_wrapper/tool_data_table_conf.xml.sample Tue Mar 22 12:34:36 2022 +0000 +++ b/bowtie_transcriptome_wrapper/tool_data_table_conf.xml.sample Sun Mar 27 16:22:48 2022 +0000 @@ -1,7 +1,7 @@ <!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> <tables> <!-- Locations of indexes in the Bowtie mapper format --> - <table name="bowtie_indexes" comment_char="#"> + <table name="bowtie_indexes_transcriptome" comment_char="#"> <columns>value, dbkey, name, path</columns> <file path="tool-data/bowtie_indices.loc" /> </table>