Mercurial > repos > bgruening > deeptools
changeset 76:d54881c558b8 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 3bc1d1c6f4e28ac7ff8df79fe4e3f00a195938e6-dirty
| author | iuc |
|---|---|
| date | Fri, 02 Oct 2015 17:54:07 -0400 |
| parents | aa76a7fa6f82 |
| children | 002545a03ef1 |
| files | deepTools_macros.xml repository_dependencies.xml tool-data/deepTools_seqs.loc.sample tool-data/lastz_seqs.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
| diffstat | 6 files changed, 39 insertions(+), 32 deletions(-) [+] |
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--- a/deepTools_macros.xml Tue Sep 22 13:18:01 2015 -0400 +++ b/deepTools_macros.xml Fri Oct 02 17:54:07 2015 -0400 @@ -242,7 +242,7 @@ </param> <when value="cached"> <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> - <options from_data_table="deepTools_seqs"> + <options from_data_table="lastz_seqs"> <filter type="sort_by" column="1" /> <validator type="no_options" message="No indexes are available." /> </options>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Fri Oct 02 17:54:07 2015 -0400 @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories> + <repository changeset_revision="26e3ae5f74ed" name="data_manager_twobit_builder" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> +</repositories>
--- a/tool-data/deepTools_seqs.loc.sample Tue Sep 22 13:18:01 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of 2bit genome files for use with deepTools. You will -#need to supply these files and then create a deepTools_seqs.loc file -#similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The deepTools_seqs.loc -#file has this format: -# -#<unique_build_id> <display_name> <file_path> -# -#So, for example, if your deepTools_seqs.loc began like this: -# -#hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit -#hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit -#mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit -# -#then your /depot/data2/galaxy/twobit/ directory -#would need to contain the following 2bit files: -# -#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.2bit -#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg19.2bit -#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 mm9.2bit -# -#Your deepTools_seqs.loc file should include an entry per line for -#each file you have stored that you want to be available. Note that -#your files should all have the extension '2bit'. -# -#Please note that the <unique_build_id> is also used as "Species name abbreviation".
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/lastz_seqs.loc.sample Fri Oct 02 17:54:07 2015 -0400 @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of 2bit genome files for use with deepTools. +#This file is named lastz_seqs.loc file to make use of an already existing loc +#file from the lastz tool that is created by the twobit data-manager. +#You will need to supply these files and then create a lastz_seqs.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The lastz_seqs.loc +#file has this format: +# +#<unique_build_id> <display_name> <file_path> +# +#So, for example, if your lastz_seqs.loc began like this: +# +#hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit +#hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit +#mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit +# +#then your /depot/data2/galaxy/twobit/ directory +#would need to contain the following 2bit files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.2bit +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg19.2bit +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 mm9.2bit +# +#Your lastz_seqs.loc file should include an entry per line for +#each file you have stored that you want to be available. Note that +#your files should all have the extension '2bit'. +# +#Please note that the <unique_build_id> is also used as "Species name abbreviation".
--- a/tool_data_table_conf.xml.sample Tue Sep 22 13:18:01 2015 -0400 +++ b/tool_data_table_conf.xml.sample Fri Oct 02 17:54:07 2015 -0400 @@ -1,7 +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> - <!-- Locations of 2bit sequence files for use in deepTools --> - <table name="deepTools_seqs" comment_char="#"> + <!-- Locations of 2bit sequence files for use in Lastz --> + <table name="lastz_seqs" comment_char="#"> <columns>value, name, path</columns> - <file path="tool-data/deepTools_seqs.loc" /> + <file path="tool-data/lastz_seqs.loc" /> </table> </tables>
--- a/tool_dependencies.xml Tue Sep 22 13:18:01 2015 -0400 +++ b/tool_dependencies.xml Fri Oct 02 17:54:07 2015 -0400 @@ -4,6 +4,6 @@ <repository changeset_revision="94e61bd56e40" name="package_python_2_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="deepTools" version="1.5.11"> - <repository changeset_revision="0eaccc10220c" name="package_python_2_7_deeptools_1_5_11" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="6fe93c81bcd0" name="package_python_2_7_deeptools_1_5_11" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>