Mercurial > repos > lparsons > htseq_count
changeset 3:c6d73933f601
Fixed issues with tool shed parsing
| author | Lance Parsons <lparsons@princeton.edu> |
|---|---|
| date | Fri, 31 Aug 2012 16:50:42 -0400 |
| parents | 8f0f896ec527 |
| children | 359d40333595 |
| files | htseq-count.xml sam_fa_indices.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 3 files changed, 37 insertions(+), 1 deletions(-) [+] |
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--- a/htseq-count.xml Fri Aug 31 15:23:53 2012 -0400 +++ b/htseq-count.xml Fri Aug 31 16:50:42 2012 -0400 @@ -79,7 +79,7 @@ <when value="cached"> <param name="ref_file" type="select" label="Using reference genome"> <options from_data_table="sam_fa_indexes"> - <filter type="data_meta" key="dbkey" ref="samfile" column="value"/> + <filter type="data_meta" key="dbkey" ref="samfile" column="3"/> </options> <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> </param>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sam_fa_indices.loc.sample Fri Aug 31 16:50:42 2012 -0400 @@ -0,0 +1,28 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a sam_fa_indices.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The sam_fa_indices.loc +#file has this format (white space characters are TAB characters): +# +#index <seq> <location> +# +#So, for example, if you had hg18 indexed stored in +#/depot/data2/galaxy/sam/, +#then the sam_fa_indices.loc entry would look like this: +# +#index hg18 /depot/data2/galaxy/sam/hg18.fa +# +#and your /depot/data2/galaxy/sam/ directory +#would contain hg18.fa and hg18.fa.fai files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.fa +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.fa.fai +# +#Your sam_fa_indices.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#index hg18 /depot/data2/galaxy/sam/hg18.fa +#index hg19 /depot/data2/galaxy/sam/hg19.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Aug 31 16:50:42 2012 -0400 @@ -0,0 +1,8 @@ +<!-- 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> + <!-- Location of SAMTools indexes and other files --> + <table name="sam_fa_indexes" comment_char="#"> + <columns>line_type, value, path</columns> + <file path="tool-data/sam_fa_indices.loc" /> + </table> +</tables>