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Merged in jmchilton/galaxy-central-multi-input-tool-fixes-2 (pull request #129)
Implement Macro Engine to Reduce Tool Config XML Duplication
This commit is contained in:
Jeremy Goecks
@@ -17,6 +17,7 @@ from galaxy.util.bunch import Bunch
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from galaxy.util.template import fill_template
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from galaxy import util, jobs, model
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from galaxy.jobs import ParallelismInfo
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from copy import deepcopy
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from elementtree import ElementTree
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from parameters import *
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from parameters.grouping import *
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@@ -520,7 +521,7 @@ class ToolBox( object ):
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def load_tool( self, config_file, guid=None, **kwds ):
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"""Load a single tool from the file named by `config_file` and return an instance of `Tool`."""
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# Parse XML configuration file and get the root element
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tree = util.parse_xml( config_file )
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tree = self._load_and_preprocess_tool_xml( config_file )
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root = tree.getroot()
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# Allow specifying a different tool subclass to instantiate
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if root.find( "type" ) is not None:
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@@ -704,7 +705,104 @@ class ToolBox( object ):
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rval = tools
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return rval
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def _load_and_preprocess_tool_xml(self, config_file):
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tree = util.parse_xml(config_file)
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root = tree.getroot()
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macros_el = root.find('macros')
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if not macros_el:
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return tree
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tool_dir = os.path.dirname(config_file)
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macros = self._load_macros(macros_el, tool_dir)
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self._expand_macros([root], macros)
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return tree
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def _expand_macros(self, elements, macros):
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for element in elements:
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# HACK for elementtree, newer implementations (etree/lxml) won't
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# require this parent_map data structure but elementtree does not
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# track parents or recongnize .find('..').
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parent_map = dict((c, p) for p in element.getiterator() for c in p)
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for expand_el in element.findall('.//expand'):
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macro_name = expand_el.get('macro')
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macro_def = deepcopy(macros[macro_name]) # deepcopy needed?
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yield_els = [yield_el for macro_def_el in macro_def for yield_el in macro_def_el.findall('.//yield')]
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expand_el_children = expand_el.getchildren()
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macro_def_parent_map = \
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dict((c, p) for macro_def_el in macro_def for p in macro_def_el.getiterator() for c in p)
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for yield_el in yield_els:
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self._xml_replace(yield_el, expand_el_children, macro_def_parent_map)
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# Recursively expand contained macros.
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self._expand_macros(macro_def, macros)
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self._xml_replace(expand_el, macro_def, parent_map)
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def _load_macros(self, macros_el, tool_dir):
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macros = {}
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# Import macros from external files.
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macros.update(self._load_imported_macros(macros_el, tool_dir))
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# Load all directly defined macros.
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macros.update(self._load_embedded_macros(macros_el, tool_dir))
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return macros
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def _load_embedded_macros(self, macros_el, tool_dir):
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macros = {}
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macro_els = []
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if macros_el:
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macro_els = macros_el.findall("macro")
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for macro in macro_els:
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macro_name = macro.get("name")
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macros[macro_name] = self._load_macro_def(macro)
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return macros
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def _load_imported_macros(self, macros_el, tool_dir):
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macros = {}
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macro_import_els = []
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if macros_el:
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macro_import_els = macros_el.findall("import")
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for macro_import_el in macro_import_els:
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raw_import_path = macro_import_el.text
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tool_relative_import_path = \
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os.path.basename(raw_import_path) # Sanitize this
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import_path = \
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os.path.join(tool_dir, tool_relative_import_path)
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file_macros = self._load_macro_file(import_path, tool_dir)
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macros.update(file_macros)
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return macros
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def _load_macro_file(self, path, tool_dir):
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tree = util.parse_xml(path)
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root = tree.getroot()
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return self._load_macros(root, tool_dir)
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def _load_macro_def(self, macro):
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return list(macro.getchildren())
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def _xml_replace(self, query, targets, parent_map):
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#parent_el = query.find('..') ## Something like this would be better with newer xml library
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parent_el = parent_map[query]
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matching_index = -1
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#for index, el in enumerate(parent_el.iter('.')): ## Something like this for newer implementation
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for index, el in enumerate(parent_el.getchildren()):
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if el == query:
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matching_index = index
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break
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assert matching_index >= 0
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current_index = matching_index
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for target in targets:
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current_index += 1
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parent_el.insert(current_index, deepcopy(target))
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parent_el.remove(query)
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class ToolSection( object ):
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"""
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A group of tools with similar type/purpose that will be displayed as a
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@@ -143,23 +143,12 @@
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</param>
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</when>
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</conditional>
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<conditional name="refGenomeSource">
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<param name="genomeSource" type="select" label="Use a built in reference genome or own from your history" help="Built-in genomes were created using default options">
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<option value="indexed" selected="True">Use a built-in genome</option>
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<option value="history">Use a genome from history</option>
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</param>
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<when value="indexed">
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<param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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<options from_data_table="tophat2_indexes">
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<filter type="sort_by" column="2"/>
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<validator type="no_options" message="No genomes are available for the selected input dataset"/>
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</options>
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</param>
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</when>
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<when value="history">
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<param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
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</when> <!-- history -->
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</conditional> <!-- refGenomeSource -->
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<expand macro="refGenomeSourceConditional">
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<options from_data_table="tophat2_indexes">
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<filter type="sort_by" column="2"/>
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<validator type="no_options" message="No genomes are available for the selected input dataset"/>
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</options>
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</expand>
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<conditional name="params">
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<param name="settingsType" type="select" label="TopHat settings to use" help="You can use the default settings or set custom values for any of Tophat's parameters.">
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<option value="preSet">Use Defaults</option>
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@@ -182,17 +171,7 @@
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<param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" />
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<param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." />
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<param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." />
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<conditional name="indel_search">
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<param name="allow_indel_search" type="select" label="Allow indel search">
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<option value="Yes">Yes</option>
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<option value="No">No</option>
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</param>
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<when value="No"/>
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<when value="Yes">
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<param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." />
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<param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." />
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</when>
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</conditional>
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<expand macro="indel_searchConditional" />
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alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" />
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<param name="max_multihits" type="integer" value="20" label="Maximum number of alignments to be allowed" />
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<param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" />
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@@ -201,40 +180,7 @@
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<param name="seg_length" type="integer" value="25" label="Minimum length of read segments" />
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<!-- Options for supplying own junctions. -->
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<conditional name="own_junctions">
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<param name="use_junctions" type="select" label="Use Own Junctions">
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<option value="No">No</option>
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<option value="Yes">Yes</option>
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</param>
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<when value="Yes">
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<conditional name="gene_model_ann">
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<param name="use_annotations" type="select" label="Use Gene Annotation Model">
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<option value="No">No</option>
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<option value="Yes">Yes</option>
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</param>
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<when value="No" />
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<when value="Yes">
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<param format="gtf,gff3" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/>
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</when>
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</conditional>
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<conditional name="raw_juncs">
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<param name="use_juncs" type="select" label="Use Raw Junctions">
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<option value="No">No</option>
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<option value="Yes">Yes</option>
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</param>
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<when value="No" />
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<when value="Yes">
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<param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/>
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</when>
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</conditional>
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<param name="no_novel_juncs" type="select" label="Only look for supplied junctions">
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<option value="No">No</option>
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<option value="Yes">Yes</option>
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</param>
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</when>
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<when value="No" />
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</conditional> <!-- /own_junctions -->
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<expand macro="own_junctionsConditional" />
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<!-- Coverage search. -->
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<conditional name="coverage_search">
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<param name="use_search" type="select" label="Use Coverage Search" help="Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity.">
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@@ -319,83 +265,40 @@
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<filter>(params['settingsType'] == 'full' and params['fusion_search']['do_search'] == 'Yes')</filter>
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</data>
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<data format="bed" name="insertions" label="${tool.name} on ${on_string}: insertions" from_work_dir="tophat_out/insertions.bed">
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<actions>
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<conditional name="refGenomeSource.genomeSource">
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<when value="indexed">
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<action type="metadata" name="dbkey">
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<option type="from_data_table" name="tophat2_indexes" column="1" offset="0">
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<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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<filter type="param_value" ref="refGenomeSource.index" column="0"/>
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</option>
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</action>
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</when>
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<when value="history">
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<action type="metadata" name="dbkey">
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<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
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</action>
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</when>
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</conditional>
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</actions>
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<expand macro="dbKeyActions" />
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</data>
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<data format="bed" name="deletions" label="${tool.name} on ${on_string}: deletions" from_work_dir="tophat_out/deletions.bed">
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<actions>
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<conditional name="refGenomeSource.genomeSource">
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<when value="indexed">
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<action type="metadata" name="dbkey">
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<option type="from_data_table" name="tophat2_indexes" column="1" offset="0">
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<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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<filter type="param_value" ref="refGenomeSource.index" column="0"/>
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</option>
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</action>
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</when>
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<when value="history">
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<action type="metadata" name="dbkey">
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<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
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</action>
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</when>
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</conditional>
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</actions>
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<expand macro="dbKeyActions" />
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</data>
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<data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions" from_work_dir="tophat_out/junctions.bed">
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<actions>
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<conditional name="refGenomeSource.genomeSource">
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<when value="indexed">
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<action type="metadata" name="dbkey">
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<option type="from_data_table" name="tophat2_indexes" column="1" offset="0">
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<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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<filter type="param_value" ref="refGenomeSource.index" column="0"/>
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</option>
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</action>
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</when>
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<when value="history">
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<action type="metadata" name="dbkey">
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<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
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</action>
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</when>
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</conditional>
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</actions>
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<expand macro="dbKeyActions" />
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</data>
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<data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits" from_work_dir="tophat_out/accepted_hits.bam">
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<actions>
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<conditional name="refGenomeSource.genomeSource">
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<when value="indexed">
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<action type="metadata" name="dbkey">
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<option type="from_data_table" name="tophat2_indexes" column="1" offset="0">
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<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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<filter type="param_value" ref="refGenomeSource.index" column="0"/>
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</option>
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</action>
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</when>
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<when value="history">
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<action type="metadata" name="dbkey">
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<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
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</action>
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</when>
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</conditional>
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</actions>
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<expand macro="dbKeyActions" />
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</data>
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</outputs>
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<macros>
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<import>tophat_macros.xml</import>
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<macro name="dbKeyActions">
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<actions>
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<conditional name="refGenomeSource.genomeSource">
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<when value="indexed">
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<action type="metadata" name="dbkey">
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<option type="from_data_table" name="tophat2_indexes" column="1" offset="0">
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<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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<filter type="param_value" ref="refGenomeSource.index" column="0"/>
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</option>
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</action>
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</when>
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<when value="history">
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<action type="metadata" name="dbkey">
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<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
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</action>
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</when>
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</conditional>
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</actions>
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</macro>
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</macros>
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<tests>
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<!-- Test base-space single-end reads with pre-built index and preset parameters -->
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<test>
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@@ -154,23 +154,12 @@
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</command>
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<inputs>
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<param format="fastqcssanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Color-space: Must have Sanger-scaled quality values with ASCII offset 33" />
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<conditional name="refGenomeSource">
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<param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
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<option value="indexed">Use a built-in index</option>
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<option value="history">Use one from the history</option>
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</param>
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<when value="indexed">
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<param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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<options from_data_table="tophat_indexes_color">
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<filter type="sort_by" column="2"/>
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<validator type="no_options" message="No indexes are available for the selected input dataset"/>
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</options>
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</param>
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</when>
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<when value="history">
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<param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
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</when> <!-- history -->
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</conditional> <!-- refGenomeSource -->
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<expand macro="refGenomeSourceConditional">
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<options from_data_table="tophat_indexes_color">
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<filter type="sort_by" column="2"/>
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<validator type="no_options" message="No indexes are available for the selected input dataset"/>
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</options>
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</expand>
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<conditional name="singlePaired">
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<param name="sPaired" type="select" label="Is this library mate-paired?">
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<option value="single">Single-end</option>
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@@ -194,17 +183,7 @@
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<param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" />
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<param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." />
|
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<param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." />
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<conditional name="indel_search">
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<param name="allow_indel_search" type="select" label="Allow indel search">
|
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<option value="Yes">Yes</option>
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<option value="No">No</option>
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</param>
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<when value="No"/>
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<when value="Yes">
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<param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." />
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<param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." />
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</when>
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</conditional>
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<expand macro="indel_searchConditional" />
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<param name="junction_filter" type="float" value="0.15" label="Minimum isoform fraction: filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" />
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<param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" />
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||||
<param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" />
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@@ -230,20 +209,8 @@
|
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<param format="gtf" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/>
|
||||
</when>
|
||||
</conditional>
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||||
<conditional name="raw_juncs">
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||||
<param name="use_juncs" type="select" label="Use Raw Junctions">
|
||||
<option value="No">No</option>
|
||||
<option value="Yes">Yes</option>
|
||||
</param>
|
||||
<when value="No" />
|
||||
<when value="Yes">
|
||||
<param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/>
|
||||
</when>
|
||||
</conditional>
|
||||
<param name="no_novel_juncs" type="select" label="Only look for supplied junctions">
|
||||
<option value="No">No</option>
|
||||
<option value="Yes">Yes</option>
|
||||
</param>
|
||||
<expand macro="raw_juncsConditional" />
|
||||
<expand macro="no_novel_juncsParam" />
|
||||
</when>
|
||||
<when value="No" />
|
||||
</conditional> <!-- /own_junctions -->
|
||||
@@ -301,17 +268,7 @@
|
||||
<param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" />
|
||||
<param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." />
|
||||
<param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." />
|
||||
<conditional name="indel_search">
|
||||
<param name="allow_indel_search" type="select" label="Allow indel search">
|
||||
<option value="Yes">Yes</option>
|
||||
<option value="No">No</option>
|
||||
</param>
|
||||
<when value="No"/>
|
||||
<when value="Yes">
|
||||
<param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." />
|
||||
<param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." />
|
||||
</when>
|
||||
</conditional>
|
||||
<expand macro="indel_searchConditional" />
|
||||
<param name="junction_filter" type="float" value="0.15" label="Minimum isoform fraction: filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" />
|
||||
<param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" />
|
||||
<param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" />
|
||||
@@ -399,90 +356,50 @@
|
||||
( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) )
|
||||
)
|
||||
</filter>
|
||||
<actions>
|
||||
<conditional name="refGenomeSource.genomeSource">
|
||||
<when value="indexed">
|
||||
<action type="metadata" name="dbkey">
|
||||
<option type="from_data_table" name="tophat_indexes_color" column="1" offset="0">
|
||||
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
|
||||
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
|
||||
</option>
|
||||
</action>
|
||||
</when>
|
||||
<when value="history">
|
||||
<action type="metadata" name="dbkey">
|
||||
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
|
||||
</action>
|
||||
</when>
|
||||
</conditional>
|
||||
</actions>
|
||||
<expand macro="dbKeyActions" />
|
||||
</data>
|
||||
<data format="bed" name="deletions" label="${tool.name} on ${on_string}: deletions" from_work_dir="tophat_out/deletions.bed">
|
||||
<filter>
|
||||
<expand macro="dbKeyActions" />
|
||||
</data>
|
||||
<data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions">
|
||||
<expand macro="dbKeyActions" />
|
||||
</data>
|
||||
<data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits">
|
||||
<expand macro="dbKeyActions" />
|
||||
</data>
|
||||
</outputs>
|
||||
<macros>
|
||||
<import>tophat_macros.xml</import>
|
||||
<macro name="bedFilter">
|
||||
<filter>
|
||||
(
|
||||
( ( 'sParams' in singlePaired ) and ( 'indel_search' in singlePaired['sParams'] ) and
|
||||
( singlePaired['sParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) or
|
||||
( ( 'pParams' in singlePaired ) and ( 'indel_search' in singlePaired['pParams'] ) and
|
||||
( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) )
|
||||
)
|
||||
</filter>
|
||||
<actions>
|
||||
<conditional name="refGenomeSource.genomeSource">
|
||||
<when value="indexed">
|
||||
<action type="metadata" name="dbkey">
|
||||
<option type="from_data_table" name="tophat_indexes_color" column="1" offset="0">
|
||||
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
|
||||
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
|
||||
</option>
|
||||
</action>
|
||||
</when>
|
||||
<when value="history">
|
||||
<action type="metadata" name="dbkey">
|
||||
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
|
||||
</action>
|
||||
</when>
|
||||
</conditional>
|
||||
</actions>
|
||||
</data>
|
||||
<data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions">
|
||||
<actions>
|
||||
<conditional name="refGenomeSource.genomeSource">
|
||||
<when value="indexed">
|
||||
<action type="metadata" name="dbkey">
|
||||
<option type="from_data_table" name="tophat_indexes_color" column="1" offset="0">
|
||||
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
|
||||
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
|
||||
</option>
|
||||
</action>
|
||||
</when>
|
||||
<when value="history">
|
||||
<action type="metadata" name="dbkey">
|
||||
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
|
||||
</action>
|
||||
</when>
|
||||
</conditional>
|
||||
</actions>
|
||||
</data>
|
||||
<data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits">
|
||||
<actions>
|
||||
<conditional name="refGenomeSource.genomeSource">
|
||||
<when value="indexed">
|
||||
<action type="metadata" name="dbkey">
|
||||
<option type="from_data_table" name="tophat_indexes_color" column="1" offset="0">
|
||||
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
|
||||
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
|
||||
</option>
|
||||
</action>
|
||||
</when>
|
||||
<when value="history">
|
||||
<action type="metadata" name="dbkey">
|
||||
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
|
||||
</action>
|
||||
</when>
|
||||
</conditional>
|
||||
</actions>
|
||||
</data>
|
||||
</outputs>
|
||||
</filter>
|
||||
</macro>
|
||||
<macro name="dbKeyActions">
|
||||
<actions>
|
||||
<conditional name="refGenomeSource.genomeSource">
|
||||
<when value="indexed">
|
||||
<action type="metadata" name="dbkey">
|
||||
<option type="from_data_table" name="tophat_indexes_color" column="1" offset="0">
|
||||
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
|
||||
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
|
||||
</option>
|
||||
</action>
|
||||
</when>
|
||||
<when value="history">
|
||||
<action type="metadata" name="dbkey">
|
||||
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
|
||||
</action>
|
||||
</when>
|
||||
</conditional>
|
||||
</actions>
|
||||
</macro>
|
||||
</macros>
|
||||
<tests>
|
||||
<!-- Test color-space single-end reads with user-supplied reference fasta and preset parameters -->
|
||||
<test>
|
||||
|
||||
@@ -0,0 +1,72 @@
|
||||
<macros>
|
||||
<macro name="refGenomeSourceConditional">
|
||||
<conditional name="refGenomeSource">
|
||||
<param name="genomeSource" type="select" label="Use a built in reference genome or own from your history" help="Built-ins genomes were created using default options">
|
||||
<option value="indexed" selected="True">Use a built-in genome</option>
|
||||
<option value="history">Use a genome from history</option>
|
||||
</param>
|
||||
<when value="indexed">
|
||||
<param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
|
||||
<yield />
|
||||
</param>
|
||||
</when>
|
||||
<when value="history">
|
||||
<param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
|
||||
</when> <!-- history -->
|
||||
</conditional> <!-- refGenomeSource -->
|
||||
</macro>
|
||||
<macro name="indel_searchConditional">
|
||||
<conditional name="indel_search">
|
||||
<param name="allow_indel_search" type="select" label="Allow indel search">
|
||||
<option value="Yes">Yes</option>
|
||||
<option value="No">No</option>
|
||||
</param>
|
||||
<when value="No"/>
|
||||
<when value="Yes">
|
||||
<param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." />
|
||||
<param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." />
|
||||
</when>
|
||||
</conditional>
|
||||
</macro>
|
||||
<macro name="own_junctionsConditional">
|
||||
<conditional name="own_junctions">
|
||||
<param name="use_junctions" type="select" label="Use Own Junctions">
|
||||
<option value="No">No</option>
|
||||
<option value="Yes">Yes</option>
|
||||
</param>
|
||||
<when value="Yes">
|
||||
<conditional name="gene_model_ann">
|
||||
<param name="use_annotations" type="select" label="Use Gene Annotation Model">
|
||||
<option value="No">No</option>
|
||||
<option value="Yes">Yes</option>
|
||||
</param>
|
||||
<when value="No" />
|
||||
<when value="Yes">
|
||||
<param format="gtf,gff3" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/>
|
||||
</when>
|
||||
</conditional>
|
||||
<expand macro="raw_juncsConditional" />
|
||||
<expand macro="no_novel_juncsParam" />
|
||||
</when>
|
||||
<when value="No" />
|
||||
</conditional> <!-- /own_junctions -->
|
||||
</macro>
|
||||
<macro name="raw_juncsConditional">
|
||||
<conditional name="raw_juncs">
|
||||
<param name="use_juncs" type="select" label="Use Raw Junctions">
|
||||
<option value="No">No</option>
|
||||
<option value="Yes">Yes</option>
|
||||
</param>
|
||||
<when value="No" />
|
||||
<when value="Yes">
|
||||
<param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/>
|
||||
</when>
|
||||
</conditional>
|
||||
</macro>
|
||||
<macro name="no_novel_juncsParam">
|
||||
<param name="no_novel_juncs" type="select" label="Only look for supplied junctions">
|
||||
<option value="No">No</option>
|
||||
<option value="Yes">Yes</option>
|
||||
</param>
|
||||
</macro>
|
||||
</macros>
|
||||
@@ -151,23 +151,12 @@
|
||||
</command>
|
||||
<inputs>
|
||||
<param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
|
||||
<conditional name="refGenomeSource">
|
||||
<param name="genomeSource" type="select" label="Use a built in reference genome or own from your history" help="Built-ins genomes were created using default options">
|
||||
<option value="indexed" selected="True">Use a built-in genome</option>
|
||||
<option value="history">Use a genome from history</option>
|
||||
</param>
|
||||
<when value="indexed">
|
||||
<param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
|
||||
<options from_data_table="tophat_indexes">
|
||||
<filter type="sort_by" column="2"/>
|
||||
<validator type="no_options" message="No genomes are available for the selected input dataset"/>
|
||||
</options>
|
||||
</param>
|
||||
</when>
|
||||
<when value="history">
|
||||
<param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
|
||||
</when> <!-- history -->
|
||||
</conditional> <!-- refGenomeSource -->
|
||||
<expand macro="refGenomeSourceConditional">
|
||||
<options from_data_table="tophat_indexes">
|
||||
<filter type="sort_by" column="2"/>
|
||||
<validator type="no_options" message="No genomes are available for the selected input dataset"/>
|
||||
</options>
|
||||
</expand>
|
||||
<conditional name="singlePaired">
|
||||
<param name="sPaired" type="select" label="Is this library mate-paired?">
|
||||
<option value="single">Single-end</option>
|
||||
@@ -298,17 +287,7 @@ alignments (number of reads divided by average depth of coverage)" help="0.0 to
|
||||
<param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" />
|
||||
<param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." />
|
||||
<param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." />
|
||||
<conditional name="indel_search">
|
||||
<param name="allow_indel_search" type="select" label="Allow indel search">
|
||||
<option value="Yes">Yes</option>
|
||||
<option value="No">No</option>
|
||||
</param>
|
||||
<when value="No"/>
|
||||
<when value="Yes">
|
||||
<param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." />
|
||||
<param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." />
|
||||
</when>
|
||||
</conditional>
|
||||
<expand macro="indel_searchConditional" />
|
||||
<param name="max_multihits" type="integer" value="20" label="Maximum number of alignments to be allowed" />
|
||||
<param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" />
|
||||
<param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" />
|
||||
@@ -316,40 +295,7 @@ alignments (number of reads divided by average depth of coverage)" help="0.0 to
|
||||
<param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" />
|
||||
<param name="seg_length" type="integer" value="25" label="Minimum length of read segments" />
|
||||
<!-- Options for supplying own junctions. -->
|
||||
<conditional name="own_junctions">
|
||||
<param name="use_junctions" type="select" label="Use Own Junctions">
|
||||
<option value="No">No</option>
|
||||
<option value="Yes">Yes</option>
|
||||
</param>
|
||||
<when value="Yes">
|
||||
<conditional name="gene_model_ann">
|
||||
<param name="use_annotations" type="select" label="Use Gene Annotation Model">
|
||||
<option value="No">No</option>
|
||||
<option value="Yes">Yes</option>
|
||||
</param>
|
||||
<when value="No" />
|
||||
<when value="Yes">
|
||||
<param format="gtf" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/>
|
||||
</when>
|
||||
</conditional>
|
||||
<conditional name="raw_juncs">
|
||||
<param name="use_juncs" type="select" label="Use Raw Junctions">
|
||||
<option value="No">No</option>
|
||||
<option value="Yes">Yes</option>
|
||||
</param>
|
||||
<when value="No" />
|
||||
<when value="Yes">
|
||||
<param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/>
|
||||
</when>
|
||||
</conditional>
|
||||
<param name="no_novel_juncs" type="select" label="Only look for supplied junctions">
|
||||
<option value="No">No</option>
|
||||
<option value="Yes">Yes</option>
|
||||
</param>
|
||||
</when>
|
||||
<when value="No" />
|
||||
</conditional> <!-- /own_junctions -->
|
||||
|
||||
<expand macro="own_junctionsConditional" />
|
||||
<!-- Closure search. -->
|
||||
<conditional name="closure_search">
|
||||
<param name="use_search" type="select" label="Use Closure Search">
|
||||
@@ -387,83 +333,40 @@ alignments (number of reads divided by average depth of coverage)" help="0.0 to
|
||||
|
||||
<outputs>
|
||||
<data format="bed" name="insertions" label="${tool.name} on ${on_string}: insertions" from_work_dir="tophat_out/insertions.bed">
|
||||
<actions>
|
||||
<conditional name="refGenomeSource.genomeSource">
|
||||
<when value="indexed">
|
||||
<action type="metadata" name="dbkey">
|
||||
<option type="from_data_table" name="tophat_indexes" column="1" offset="0">
|
||||
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
|
||||
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
|
||||
</option>
|
||||
</action>
|
||||
</when>
|
||||
<when value="history">
|
||||
<action type="metadata" name="dbkey">
|
||||
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
|
||||
</action>
|
||||
</when>
|
||||
</conditional>
|
||||
</actions>
|
||||
<expand macro="dbKeyActions" />
|
||||
</data>
|
||||
<data format="bed" name="deletions" label="${tool.name} on ${on_string}: deletions" from_work_dir="tophat_out/deletions.bed">
|
||||
<actions>
|
||||
<conditional name="refGenomeSource.genomeSource">
|
||||
<when value="indexed">
|
||||
<action type="metadata" name="dbkey">
|
||||
<option type="from_data_table" name="tophat_indexes" column="1" offset="0">
|
||||
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
|
||||
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
|
||||
</option>
|
||||
</action>
|
||||
</when>
|
||||
<when value="history">
|
||||
<action type="metadata" name="dbkey">
|
||||
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
|
||||
</action>
|
||||
</when>
|
||||
</conditional>
|
||||
</actions>
|
||||
<expand macro="dbKeyActions" />
|
||||
</data>
|
||||
<data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions" from_work_dir="tophat_out/junctions.bed">
|
||||
<actions>
|
||||
<conditional name="refGenomeSource.genomeSource">
|
||||
<when value="indexed">
|
||||
<action type="metadata" name="dbkey">
|
||||
<option type="from_data_table" name="tophat_indexes" column="1" offset="0">
|
||||
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
|
||||
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
|
||||
</option>
|
||||
</action>
|
||||
</when>
|
||||
<when value="history">
|
||||
<action type="metadata" name="dbkey">
|
||||
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
|
||||
</action>
|
||||
</when>
|
||||
</conditional>
|
||||
</actions>
|
||||
<expand macro="dbKeyActions" />
|
||||
</data>
|
||||
<data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits" from_work_dir="tophat_out/accepted_hits.bam">
|
||||
<actions>
|
||||
<conditional name="refGenomeSource.genomeSource">
|
||||
<when value="indexed">
|
||||
<action type="metadata" name="dbkey">
|
||||
<option type="from_data_table" name="tophat_indexes" column="1" offset="0">
|
||||
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
|
||||
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
|
||||
</option>
|
||||
</action>
|
||||
</when>
|
||||
<when value="history">
|
||||
<action type="metadata" name="dbkey">
|
||||
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
|
||||
</action>
|
||||
</when>
|
||||
</conditional>
|
||||
</actions>
|
||||
<expand macro="dbKeyActions" />
|
||||
</data>
|
||||
</outputs>
|
||||
|
||||
<macros>
|
||||
<import>tophat_macros.xml</import>
|
||||
<macro name="dbKeyActions">
|
||||
<actions>
|
||||
<conditional name="refGenomeSource.genomeSource">
|
||||
<when value="indexed">
|
||||
<action type="metadata" name="dbkey">
|
||||
<option type="from_data_table" name="tophat_indexes" column="1" offset="0">
|
||||
<filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
|
||||
<filter type="param_value" ref="refGenomeSource.index" column="0"/>
|
||||
</option>
|
||||
</action>
|
||||
</when>
|
||||
<when value="history">
|
||||
<action type="metadata" name="dbkey">
|
||||
<option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
|
||||
</action>
|
||||
</when>
|
||||
</conditional>
|
||||
</actions>
|
||||
</macro>
|
||||
</macros>
|
||||
<tests>
|
||||
<!-- Test base-space single-end reads with pre-built index and preset parameters -->
|
||||
<test>
|
||||
|
||||
Reference in New Issue
Block a user