Mercurial > repos > elixir-it > somaticsniper
changeset 2:f7d69881bdec draft default tip
Uploaded
| author | elixir-it |
|---|---|
| date | Sat, 21 Sep 2019 13:22:28 -0400 |
| parents | 2ff18e84c946 |
| children | |
| files | somatic_sniper.xml tool-data/all_fasta.loc.sample tool-data/sniper_index.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 4 files changed, 42 insertions(+), 23 deletions(-) [+] |
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--- a/somatic_sniper.xml Mon Jul 02 11:37:26 2018 -0400 +++ b/somatic_sniper.xml Sat Sep 21 13:22:28 2019 -0400 @@ -19,7 +19,7 @@ ## BUILD SOMATICSNIPER COMMAND LINE - \$CONDA_DEFAULT_ENV/bin/bam-somaticsniper + bam-somaticsniper -F vcf -q $advancedsettings.q -Q $advancedsettings.Q @@ -83,7 +83,7 @@ </param> <when value="cached"> <param name="index" type="select" label="Reference Genome File" > - <options from_data_table="all_fasta" /> + <options from_data_table="sniper_index" /> </param> </when> <when value="history"> @@ -118,5 +118,8 @@ </tests> <help> http://gmt.genome.wustl.edu/packages/somatic-sniper/ + +this wrapper was developed from https://github.com/morinlab/tools-morinlab/tree/master/tools/somatic_sniper only the requirement and part of the command line have been changed in order to make it suitable for CONDA + </help> </tool>
--- a/tool-data/all_fasta.loc.sample Mon Jul 02 11:37:26 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ -#This file lists the locations and dbkeys of all the fasta files -#under the "genome" directory (a directory that contains a directory -#for each build). The script extract_fasta.py will generate the file -#all_fasta.loc. This file has the format (white space characters are -#TAB characters): -# -#<unique_build_id> <dbkey> <display_name> <file_path> -# -#So, all_fasta.loc could look something like this: -# -#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa -#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa -#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa -# -#Your all_fasta.loc file should contain an entry for each individual -#fasta file. So there will be multiple fasta files for each build, -#such as with hg19 above. -#
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/sniper_index.loc.sample Sat Sep 21 13:22:28 2019 -0400 @@ -0,0 +1,34 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of somatic-sniper indexed sequences data files. You will need +#to create these data files and then create a sniper_index.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The sniper_index.loc +#file has this format (longer white space characters are TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, for example, if you had phiX indexed stored in +#/depot/data2/galaxy/phiX/base/, +#then the bwa_index.loc entry would look like this: +# +#phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa +# +#and your /depot/data2/galaxy/phiX/base/ directory +#would contain phiX.dict, phiX.fa.fai files. +# +# +#Your sniper_index.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: +# +#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa +#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa +#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa +#...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. +#
--- a/tool_data_table_conf.xml.sample Mon Jul 02 11:37:26 2018 -0400 +++ b/tool_data_table_conf.xml.sample Sat Sep 21 13:22:28 2019 -0400 @@ -1,7 +1,7 @@ <tables> - <!-- Locations of all fasta files under genome directory --> - <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <!-- Locations of sniper index under genome directory --> + <table name="sniper_index" comment_char="#" allow_duplicate_entries="False"> <columns>value, dbkey, name, path</columns> - <file path="tool-data/all_fasta.loc" /> + <file path="tool-data/sniper_index.loc" /> </table> </tables>