Galaxy wrappers corepipeline #171
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macros.xml filename should be more descriptive by Galaxy tutorial convention
Default color selectors changed to match four-color plot defaults. Macro XML affected and renamed more specifically
The '1' is stripped from the input and output ids to reduce confusion and better mimic 'resize coordinate' tool that this ScriptManager tool is replacing in the core pipeline
- adjust conditionals such that max/min insert cannot be set without requiring PE
- change format to 'scidx' for core pipeline support (sub-type of tabular)
- rename inputs and outputs ('BAM'--> 'input' and 'output1' --> 'output') for consistency with other SM wrappers
Add PEARC citation to macro file
- remove "level_options" for hiding "advanced" options - conditionally output two or one CDT heatmap matrix based on input "separate" vs "combined" input options - fix whitespace of XML tags on input options - add documentation link to help message - use pearc citation
To change the JAR filename more easily across XML tools, the macro file has a JAR_FILENAME token that each tool XML can reference in java call.
The heatmap wrapper should only contain the CDT to PNG behavior. This commit removes the TagPileup and merge heatmap calls and reduces the two-color heatmap calls to a single generalized format. also added links to documentation in the help section
- add pearc_citation macro to all XML wrappers - make help tag indentation and formatting consistent - reformat whitespace (auto by atom)
- standardize requirements with a macros expansion of openjdk and samtools requirements for convenient version incrementing - also fix scriptmanager_bam-correlation tool to use consistent tool id naming
- strip out python version information (allow galaxy to handle with defaults) b/c no python used by ScriptManager - set version for wrappers to the same (increment to 1.0 when published to toolshed) - set profile version (galaxy release)
- add standard handling for BAM file - add standard handling for multi-output files - remove unused "summary" flag - add optional outputs w filters for duplication statistics conditional on param - fix CDATA indentation
update macro to use `scriptmanager-v0.14-dev.jar` b/c features added to Galaxy XML files on this branch are not all part of the official ScriptManager-v0.14.jar release
- the input data params need to be specifically named to support display in PEGR for current paired_004 iteration - also update the max/min insert size filter to display conditional on required paired-end selection
include gzip toggle param for Expand GFF and BAM to ScIdx for the Galaxy XML wrappers
Galaxy XML wrapper option display should read "preset colors" for more precise description
update other bam-format converters to match bam-to-scidx with a gzip option and for min/max filter selection to be dependent on the user selecting required paired-end
update Galaxy XML wrapper to include toggle for gzipping output (also clean-up of whitespace)
the XML list of tools for `local_tool_conf.xml` is updated in this README
bed-to-gff and gff-to-bed GXML are updated here to include support for user to select gzip for output. gff-to-bed adjusted for consistent formatting and indentation with bed-to-gff and other tools
New wrapper from Scriptmanager dev
Adjust wrappers to use the tool macros for the scriptmanager jar filename and requirements/dependencies
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merge latest olivia updates to galaxy wrappers to master