| Previous changeset 2:2d6a90609943 (2013-10-22) Next changeset 4:05d4e123f9f7 (2013-12-04) |
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Commit message:
Update to the new data table specification. |
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modified:
cuffdiff_wrapper.xml |
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added:
tool-data/fasta_indexes.loc.sample tool_data_table_conf.xml.sample |
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removed:
tool-data/sam_fa_indices.loc.sample |
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| diff -r 2d6a90609943 -r beab768feb92 cuffdiff_wrapper.xml --- a/cuffdiff_wrapper.xml Tue Oct 22 11:03:02 2013 -0400 +++ b/cuffdiff_wrapper.xml Wed Dec 04 13:24:38 2013 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="cuffdiff" name="Cuffdiff" version="0.0.6"> +<tool id="cuffdiff" name="Cuffdiff" version="0.0.7"> <!-- Wrapper supports Cuffdiff versions 2.1.0-2.1.1 --> <description>find significant changes in transcript expression, splicing, and promoter use</description> <requirements> @@ -33,7 +33,7 @@ $bias_correction.seq_source.ref_file #else: ## Built-in genome. - ${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')} + ${__get_data_table_entry__('fasta_indexes', 'value', $gtf_input.dbkey, 'path')} #end if #end if @@ -89,7 +89,14 @@ <option value="cached">Locally cached</option> <option value="history">History</option> </param> - <when value="cached"></when> + <when value="cached"> + <param name="index" type="select" label="Using reference genome"> + <options from_data_table="fasta_indexes"> + <filter type="data_meta" ref="gtf_input" key="dbkey" column="1" /> + <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> + </options> + </param> + </when> <when value="history"> <param name="ref_file" type="data" format="fasta" label="Using reference file" /> </when> |
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| diff -r 2d6a90609943 -r beab768feb92 tool-data/fasta_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Wed Dec 04 13:24:38 2013 -0500 |
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| @@ -0,0 +1,29 @@ +#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_new_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_new_indices.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the sam_fa_new_indices.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your sam_fa_new_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: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa |
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| diff -r 2d6a90609943 -r beab768feb92 tool-data/sam_fa_indices.loc.sample --- a/tool-data/sam_fa_indices.loc.sample Tue Oct 22 11:03:02 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,28 +0,0 @@ -#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 |
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| diff -r 2d6a90609943 -r beab768feb92 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Dec 04 13:24:38 2013 -0500 |
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| @@ -0,0 +1,4 @@ + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> |