# HG changeset patch # User Eduardo # Date 1438597186 -3600 # Node ID 8a98bfab4d5616a2a0b7d30f8326f67b563ec2fe # Parent 48006f05c208071acfd7eb6e7a7663b584ec8eaf Cleanup diff -r 48006f05c208 -r 8a98bfab4d56 tool-data/bowtie2_indices.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/bowtie2_indices.loc.sample Mon Aug 03 11:19:46 2015 +0100 @@ -0,0 +1,37 @@ +# bowtie2_indices.loc.sample +# This is a *.loc.sample file distributed with Galaxy that enables tools +# to use a directory of indexed data files. This one is for Bowtie2 and Tophat2. +# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup +# First create these data files and save them in your own data directory structure. +# Then, create a bowtie_indices.loc file to use those indexes with tools. +# Copy this file, save it with the same name (minus the .sample), +# follow the format examples, and store the result in this directory. +# The file should include an one line entry for each index set. +# The path points to the "basename" for the set, not a specific file. +# It has four text columns seperated by TABS. +# +# +# +# So, for example, if you had hg18 indexes stored in: +# +# /depot/data2/galaxy/hg19/bowtie2/ +# +# containing hg19 genome and hg19.*.bt2 files, such as: +# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa +# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2 +# -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2 +# -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2 +# -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2 +# -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2 +# -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2 +# +# then the bowtie2_indices.loc entry could look like this: +# +#hg19 hg19 Human (hg19) /depot/data2/galaxy/hg19/bowtie2/hg19canon +# +#More examples: +# +#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/mm10/bowtie2/mm10 +#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/mm10/bowtie2/dm3 +# +# diff -r 48006f05c208 -r 8a98bfab4d56 url2bowtie/tool-data/bowtie2_indices.loc.sample --- a/url2bowtie/tool-data/bowtie2_indices.loc.sample Mon Aug 03 05:44:04 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ -# bowtie2_indices.loc.sample -# This is a *.loc.sample file distributed with Galaxy that enables tools -# to use a directory of indexed data files. This one is for Bowtie2 and Tophat2. -# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup -# First create these data files and save them in your own data directory structure. -# Then, create a bowtie_indices.loc file to use those indexes with tools. -# Copy this file, save it with the same name (minus the .sample), -# follow the format examples, and store the result in this directory. -# The file should include an one line entry for each index set. -# The path points to the "basename" for the set, not a specific file. -# It has four text columns seperated by TABS. -# -# -# -# So, for example, if you had hg18 indexes stored in: -# -# /depot/data2/galaxy/hg19/bowtie2/ -# -# containing hg19 genome and hg19.*.bt2 files, such as: -# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa -# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2 -# -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2 -# -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2 -# -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2 -# -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2 -# -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2 -# -# then the bowtie2_indices.loc entry could look like this: -# -#hg19 hg19 Human (hg19) /depot/data2/galaxy/hg19/bowtie2/hg19canon -# -#More examples: -# -#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/mm10/bowtie2/mm10 -#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/mm10/bowtie2/dm3 -# -# diff -r 48006f05c208 -r 8a98bfab4d56 url2bowtie/tool-data/test-data2 --- a/url2bowtie/tool-data/test-data2 Mon Aug 03 05:44:04 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,969 +0,0 @@ - - - - - - - - - - - - - tools-devteam/tools/bowtie2/test-data at master · galaxyproject/tools-devteam - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Skip to content -
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- Unify and collectionify read group handling. - … -

- 
The reusable macro file has:
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- - Defines widgets for common read group parameters.
- - Widgets can be used at top-level (e.g. ``picard_AddOrReplaceReadGroups`` where handling is required) of inputs or within a conditional (e.g. in the mappers).
- - The conditional (used by mappers) has fours modes:
-    - Set according the specification (only ID required - has all parameters). Current BWA approach.
-    - Set Picard-style (presumably useful for broad pipelines?) (``ID``, ``SM``, ``LB``, ``PU``, ``PL`` are all required and there are no params for ``KS``, ``PG``, or ``FO``). In terms of what is shown and what is required - this mirrors ``picard_AddOrReplaceReadGroups``.
-    - Just assign the ``ID`` and do so automatically (based either on collection or standalone dataset information). No extra form elements are shown to the user. (Should this be the new default?)
-    - Do not set read groups.
- - Utilities for conditionally including parameters and formatting them (eliminates many explicit conditionals in the mappers for instance).
- - An example "mapper" test tool which demonstrates optionally including read groups.
- - An example read group assign test tool which demonstrates unconditionally specifying macros.
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-In addition to unifying everything, the macro file defines enhanced ``ID``, ``SM``, and ``LB`` parameter inputs that are wrapped in a conditional. That conditional allows manual input but also allows the user to just say Galaxy should use collection information or dataset name (if input is not in a collection) to assign these parameters. This should simplify things and make simple workflows more robust, but is absolutely essential for collection-based workflows and newer tool form options that allow running a tool in parallel over many inputs.
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-This may look at first glance like it is really complicated - but if you focus just on the mappers for instance and treat the macro file like a library - the client interface is actually a good deal easier than doing this stuff by hand for each tool.
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-Updates from original version:
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- - Tests pass for ``picard_AddOrReplaceReadGroups`` as well as the BWA and Bowtie tools.
- - Remove the changes from tophat - it will require more work (it is less free form and won't accept certain valid read groups arguments).
- - Deleted empty lines I had previously introduced and idented the Cheetah code (hadn't realized I could do that).
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-Smaller Notes:
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-The new approach for BWA tools excludes empty read groups instead of adding them as empty - hopefully this is fine:
-
-```
--@RG    ID:rg1  SM:     PL:CAPILLARY
--@PG    ID:bwa  PN:bwa  VN:0.7.12-r1039 CL:bwa sampe -r @RG     ID:rg1  SM:     PL:CAPILLARY localref.fa first.sai second.sai /tmp/tmpn_I5mQ/files/000/dataset_9.dat /tmp/tmpn_I5mQ/files/000/dataset_10.dat
-+@RG    ID:rg1  PL:CAPILLARY
-+@PG    ID:bwa  PN:bwa  VN:0.7.12-r1039 CL:bwa sampe -r @RG     ID:rg1  PL:CAPILLARY localref.fa first.sai second.sai /tmp/tmpmN3j1j/files/000/dataset_9.dat /tmp/tmpmN3j1j/files/000/dataset_10.dat
-```
-
- - latest commit d0e3412c58 - -
- @jmchilton - jmchilton - authored - -
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- - - - bowtie2-fq1.fq - - - added test and test files - - - -
- - - - bowtie2-fq2.fq - - - added test and test files - - - -
- - - - bowtie2-ref.fasta - - - added test and test files - - - -
- - - - bowtie2-test1.bam - - - added test and test files - - - -
- - - - bowtie2-test2.bam - - - Unify and collectionify read group handling. - - - -
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