| Previous changeset 0:0dabb2ed6eb1 (2013-10-01) Next changeset 2:2d6a90609943 (2013-10-22) |
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Commit message:
Fix bias correction. |
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modified:
cuffdiff_wrapper.xml |
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added:
tool-data/sam_fa_indices.loc.sample |
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| diff -r 0dabb2ed6eb1 -r 60a52f8460a1 cuffdiff_wrapper.xml --- a/cuffdiff_wrapper.xml Tue Oct 01 12:54:00 2013 -0400 +++ b/cuffdiff_wrapper.xml Wed Oct 09 12:49:03 2013 -0400 |
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| @@ -26,14 +26,14 @@ ## Bias correction? #if $bias_correction.do_bias_correction == "Yes": - -b + -b #if $bias_correction.seq_source.index_source == "history": - --ref_file=$bias_correction.seq_source.ref_file + ## Custom genome from history. + $bias_correction.seq_source.ref_file #else: - --ref_file="None" + ## Built-in genome. + ${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')} #end if - --dbkey=${gtf_input.metadata.dbkey} - --index_dir=${GALAXY_DATA_INDEX_DIR} #end if #set labels = ','.join( [ str( $condition.name ) for $condition in $conditions ] ) @@ -116,6 +116,7 @@ </inputs> <stdio> + <regex match="Error" source="both" level="fatal" description="Error"/> <regex match=".*" source="both" level="log" description="tool progress"/> </stdio> |
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| diff -r 0dabb2ed6eb1 -r 60a52f8460a1 tool-data/sam_fa_indices.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/sam_fa_indices.loc.sample Wed Oct 09 12:49:03 2013 -0400 |
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| @@ -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 |