| Previous changeset 16:07e71cf6c8ef (2018-04-03) |
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Commit message:
"planemo upload for repository https://github.com/BlankenbergLab/galaxy-tools-blankenberg/tree/master/tools/naive_variant_caller commit 3e2fca43a0b119b34befa5d7642a07682d1d77af" |
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modified:
naive_variant_caller.xml tool_data_table_conf.xml.sample |
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added:
tool-data/fasta_indexes.loc.sample |
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| diff -r 07e71cf6c8ef -r 6be51647d31a naive_variant_caller.xml --- a/naive_variant_caller.xml Tue Apr 03 10:52:11 2018 -0400 +++ b/naive_variant_caller.xml Thu Dec 05 12:23:12 2019 -0500 |
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| @@ -59,10 +59,25 @@ <inputs> <conditional name="reference_source"> <param name="reference_source_selector" type="select" label="Choose the source for the reference list"> - <option value="cached">Locally cached</option> + <option value="cached_fasta_indexes" selected="True">Locally cached</option> <option value="history">History</option> + <option value="cached">Locally cached (deprecated source)</option> </param> - <when value="cached"> + <when value="cached_fasta_indexes"> + <repeat name="input_bams" title="BAM file" min="1" > + <param name="input_bam" type="data" format="bam" label="BAM file"> + <validator type="unspecified_build" /> + <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select --> + </param> + </repeat> + <param name="ref_file" type="select" label="Using reference genome" > + <options from_data_table="fasta_indexes"> + <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--> + </options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="cached"> <!-- deprecated, uses older samtools data table --> <repeat name="input_bams" title="BAM file" min="1" > <param name="input_bam" type="data" format="bam" label="BAM file"> <validator type="unspecified_build" /> |
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| diff -r 07e71cf6c8ef -r 6be51647d31a tool-data/fasta_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Thu Dec 05 12:23:12 2019 -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 fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.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 fasta_indexes.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 fasta_indexes.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 07e71cf6c8ef -r 6be51647d31a tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Tue Apr 03 10:52:11 2018 -0400 +++ b/tool_data_table_conf.xml.sample Thu Dec 05 12:23:12 2019 -0500 |
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| @@ -1,5 +1,10 @@ <tables> <!-- Location of SAMTools indexes and other files --> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> + <!-- Deprecated 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" /> |