Mercurial > repos > holtgrewe > ngs_roi
changeset 7:19597b57ada8 draft
Uploaded
| author | holtgrewe |
|---|---|
| date | Mon, 12 Aug 2013 09:58:57 -0400 |
| parents | 71241c4dc4d0 |
| children | 681bfc781c26 |
| files | bam2roi.ctd bam2roi.xml bed_sort.sh ctd2galaxy.py gff_sort.sh ngs_roi/app.py roi_feature_projection.ctd roi_feature_projection.xml roi_filter.sh roi_plot_9.sh roi_plot_thumbnails.ctd roi_plot_thumbnails.py roi_plot_thumbnails.xml |
| diffstat | 11 files changed, 409 insertions(+), 212 deletions(-) [+] |
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--- a/bam2roi.ctd Fri Jun 28 14:01:42 2013 -0400 +++ b/bam2roi.ctd Mon Aug 12 09:58:57 2013 -0400 @@ -1,26 +1,31 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool> - <name>Bam2roi</name> +<tool name="Bam2roi" version="0.1" docurl="http://www.seqan.de" category="" > <executableName>bam2roi</executableName> - <version>0.1</version> <description>Create ROI from BAM file.</description> <manual>Calculated consecutive regions of coverage from alignment file IN.bam and write regions of interst to file OUT.roi. Counting is performed over the entire region (including intron and N-regions) based on the CIGAR string of the alignment record. </manual> - <docurl>http://www.seqan.de</docurl> - <category></category> <cli> + <clielement optionIdentifier="--write-ctd-file-ext" isList="false"> + <mapping referenceName="bam2roi.write-ctd-file-ext" /> + </clielement> <clielement optionIdentifier="--verbose" isList="false"> <mapping referenceName="bam2roi.verbose" /> </clielement> - <clielement optionIdentifier="--vverbose" isList="false"> - <mapping referenceName="bam2roi.vverbose" /> + <clielement optionIdentifier="--very-verbose" isList="false"> + <mapping referenceName="bam2roi.very-verbose" /> </clielement> <clielement optionIdentifier="--input-file" isList="false"> <mapping referenceName="bam2roi.input-file" /> </clielement> + <clielement optionIdentifier="--input-file-file-ext" isList="false"> + <mapping referenceName="bam2roi.input-file-file-ext" /> + </clielement> <clielement optionIdentifier="--output-file" isList="false"> <mapping referenceName="bam2roi.output-file" /> </clielement> + <clielement optionIdentifier="--output-file-file-ext" isList="false"> + <mapping referenceName="bam2roi.output-file-file-ext" /> + </clielement> <clielement optionIdentifier="--strand-specific" isList="false"> <mapping referenceName="bam2roi.strand-specific" /> </clielement> @@ -31,15 +36,18 @@ <mapping referenceName="bam2roi.link-over-skipped" /> </clielement> </cli> - <PARAMETERS version="1.4" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_4.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> + <PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> <NODE name="bam2roi" description="Create ROI from BAM file."> - <ITEM name="verbose" value="false" type="string" description="Verbose mode." restrictions="true,false" /> - <ITEM name="vverbose" value="false" type="string" description="Very verbose mode." restrictions="true,false" /> - <ITEM name="input-file" value="" type="string" description="SAM/BAM formatted file. Must be sorted by coordinate." tags="input file,required" supported_formats="*sam,*bam" /> - <ITEM name="output-file" value="" type="string" description="Output file with regions of interest." tags="output file,required" supported_formats="*roi" /> - <ITEM name="strand-specific" value="false" type="string" description="Calculate strand-specific ROIs (see section Strand Specificness below." restrictions="true,false" /> - <ITEM name="ignore-pairing" value="false" type="string" description="Ignore paired information. Also see Section ROI Creation Details." restrictions="true,false" /> - <ITEM name="link-over-skipped" value="false" type="string" description="Link over skipped bases in the read alignment." restrictions="true,false" /> + <ITEM name="write-ctd-file-ext" value="" type="string" description="Override file extension for --write-ctd" required="false" advanced="true" /> + <ITEM name="verbose" value="false" type="string" description="Verbose mode." restrictions="true,false" required="false" advanced="false" /> + <ITEM name="very-verbose" value="false" type="string" description="Very verbose mode." restrictions="true,false" required="false" advanced="false" /> + <ITEM name="input-file" value="" type="input-file" description="SAM/BAM formatted file. Must be sorted by coordinate." supported_formats="*.sam,*.bam" required="true" advanced="false" /> + <ITEM name="input-file-file-ext" value="" type="string" description="Override file extension for --input-file" restrictions="sam,bam" required="false" advanced="true" /> + <ITEM name="output-file" value="" type="output-file" description="Output file with regions of interest." supported_formats="*.roi" required="true" advanced="false" /> + <ITEM name="output-file-file-ext" value="" type="string" description="Override file extension for --output-file" restrictions="roi" required="false" advanced="true" /> + <ITEM name="strand-specific" value="false" type="string" description="Calculate strand-specific ROIs (see section Strand Specificness below." restrictions="true,false" required="false" advanced="false" /> + <ITEM name="ignore-pairing" value="false" type="string" description="Ignore paired information. Also see Section ROI Creation Details." restrictions="true,false" required="false" advanced="false" /> + <ITEM name="link-over-skipped" value="false" type="string" description="Link over skipped bases in the read alignment." restrictions="true,false" required="false" advanced="false" /> </NODE> </PARAMETERS> </tool>
--- a/bam2roi.xml Fri Jun 28 14:01:42 2013 -0400 +++ b/bam2roi.xml Mon Aug 12 09:58:57 2013 -0400 @@ -1,77 +1,33 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="bam2roi" name="BAM to ROI"> - <command> - <!-- First, create link for the input file --> - ln -s ${bam2roi_input_file} ${bam2roi_input_file}.${bam2roi_input_file.ext}; - touch ${bam2roi_output_file}; - ln -s ${bam2roi_output_file} ${bam2roi_output_file}.${bam2roi_output_file.ext}; - - <!-- Call bam2roi --> - bam2roi - $bam2roi_verbosity +<tool id="bam2roi" name="Bam2roi"> + <command>bam2roi + $bam2roi_verbose + $bam2roi_very_verbose + --input-file "$bam2roi_input_file" + --output-file "$bam2roi_output_file" $bam2roi_strand_specific $bam2roi_ignore_pairing $bam2roi_link_over_skipped - --input-file $bam2roi_input_file.${bam2roi_input_file.ext} - --output-file $bam2roi_output_file.${bam2roi_output_file.ext}; - - <!-- Get rid of links again --> - rm -f ${bam2roi_input_file}.${bam2roi_input_file.ext}; - rm -f ${bam2roi_output_file}.${bam2roi_output_file.ext}; - </command> - + #if $bam2roi_input_file + --input-file-file-ext ${bam2roi_input_file.ext} + #end if + #if $bam2roi_output_file + --output-file-file-ext ${bam2roi_output_file.ext} + #end if</command> <description>Create ROI from BAM file.</description> - - <!-- - Input Files and Parameters - --> <inputs> - <param name="bam2roi_input_file" type="data" format="sam,bam" - label="Input File" - help="SAM/BAM formatted file. Must be sorted by coordinate." /> - - <param name="bam2roi_ignore_pairing" type="boolean" falsevalue="" truevalue="--ignore-pairing" - label="Ignore paired information" - help="By default, a whole fragment/template extends a ROI for paired-end data. When selected, reads are treated as in the single-end case." /> - <param name="bam2roi_link_over_skipped" type="boolean" falsevalue="" truevalue="--link-over-skipped" - label="Link over skipped bases" - help="When selected, a ROI continues over skipped bases." /> - <param name="bam2roi_strand_specific" type="boolean" falsevalue="" truevalue="--strand-specific" - label="Compute strand-specific ROIs" - help="When selected, the strands of the reads alignments are considered, e.g. there can be two or more ROIs on different strands that would overlap on the same strand." /> - - <param name="bam2roi_verbosity" type="select" label="Verbosity" force_select="true"> - <option value="" selected="true">normal</option> - <option value="--verbose">verbose</option> - <option value="--very-verbose">very verbose</option> - </param> + <param falsevalue="" truevalue="--verbose" type="boolean" name="bam2roi_verbose" label="Verbose mode." /> + <param falsevalue="" truevalue="--very-verbose" type="boolean" name="bam2roi_very_verbose" label="Very verbose mode." /> + <param falsevalue="" truevalue="--link-over-skipped" type="boolean" name="bam2roi_link_over_skipped" label="Link over skipped bases in the read alignment." /> + <param falsevalue="" truevalue="--ignore-pairing" type="boolean" name="bam2roi_ignore_pairing" label="Ignore paired information. Also see Section ROI Creation Details." /> + <param label="SAM/BAM formatted file. Must be sorted by coordinate." type="data" name="bam2roi_input_file" format="sam,bam" /> + <param falsevalue="" truevalue="--strand-specific" type="boolean" name="bam2roi_strand_specific" label="Calculate strand-specific ROIs (see section Strand Specificness below." /> </inputs> - - <!-- - Output Files - --> <outputs> - <data label="${bam2roi_input_file.name}.roi" name="bam2roi_output_file" format="roi" /> + <data label="Output file with regions of interest." name="bam2roi_output_file" format="roi" /> </outputs> - - <!-- - Recognize errors by return code and not output to stderr. - --> <stdio> <exit_code range="1:" level="fatal" /> <exit_code range=":-1" level="fatal" /> </stdio> - - <!-- - Tool Help - --> - <help>No help yet.</help> - - <!-- - Dependencies - --> - <requirements> - <requirement type="binary">bam2roi</requirement> - <requirement type="python-module">Cheetah</requirement> - </requirements> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bed_sort.sh Mon Aug 12 09:58:57 2013 -0400 @@ -0,0 +1,64 @@ +#!/bin/bash + +# Sorting of BED files. +# +# USAGE: sort_bed.sh [OPTIONS] -i IN.roi -o OUT.roi +# +# Options: +# -r reverse orientation +# -p sort by position (ref, start, end) -- default + +# The parameters that we will pass to sort. +SORT_POS_ARGS="-k 1,1 -k 2,2n -k 3,3n" +SORT_POS_ARGS_REV="-k 1,1r -k 2,2nr -k 3,3nr" + +# The arguments will go here. +SORT_BY=beginPos +REVERSE= + +# Parse option values. +while getopts "pc:i:o:n:r" opt; do + case $opt in + i) + IN_FILE=$OPTARG + ;; + o) + OUT_FILE=$OPTARG + ;; + r) + REVERSE=r + ;; + \?) + echo "Invalid option: -$OPTARG" >&2 + exit 1 + ;; + esac +done + +# Check that -i or -o are given. +if [[ "$IN_FILE" == "" || "$OUT_FILE" == "" ]]; then + echo "Missing option -i or -o" >&2 + exit 1 +fi + +# Setup sort args. +case $SORT_BY in + beginPos) + if [[ "$REVERSE" == "r" ]]; then + SORT_ARGS=${SORT_POS_ARGS_REV} + else + SORT_ARGS=${SORT_POS_ARGS} + fi + ;; +esac + +# Execute sorting. +#echo "OUT_FILE=${OUT_FILE}" 2>&2 +#echo "SORT_ARGS=${SORT_ARGS}" 1>&2 +( + export LC_ALL=C + #echo "sort ${SORT_ARGS} <(grep -v '^#' ${IN_FILE});" 1>&2 + sort ${SORT_ARGS} <(grep -v '^#' ${IN_FILE}); +) > ${OUT_FILE} + +exit $?
--- a/ctd2galaxy.py Fri Jun 28 14:01:42 2013 -0400 +++ b/ctd2galaxy.py Mon Aug 12 09:58:57 2013 -0400 @@ -5,6 +5,10 @@ only used here at the moment. """ +# TODO(holtgrew): Option lists do not work at the moment. + +__author__ = 'Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>' + try: import argparse except ImportError: @@ -14,6 +18,12 @@ import xml.sax import xml.sax.saxutils + +# The suffix to identify file extension options (for '--arg-${NO}${SUFFIX}' +# and '--${PARAM_NAME}${SUFFIX}'). +FILE_EXT_SUFFIX = '-file-ext' + + class CTDFormatException(Exception): """Raised when there is a format error in CTD.""" @@ -59,10 +69,12 @@ :ivar children: children of the node :type children: dict with name to node mapping :ivar cli_element: CLIElement that this parameter is mapped to. + :ivar required: Whether or not this parameter is required. + :type required: bool """ def __init__(self, kind='', name='', description='', value='', type_='', tags='', - restrictions='', supported_formats=''): + restrictions='', supported_formats='', required=False): """Initialize the object.""" self.kind = kind self.name = name @@ -76,6 +88,7 @@ self.parent = None # not set, usually a list self.children = {} self.cli_element = None + self.required = required def computePath(self, is_root=True, path=[]): """Compute path entry from parent links. @@ -110,8 +123,8 @@ def __str__(self): """Return string representation.""" t = (self.name, self.description, self.value, self.type_, self.tags, - self.supported_formats, self.children, self.path) - return 'ParametersNode(%s, %s, %s, %s, %s, %s, %s, path=%s)' % tuple(map(repr, t)) + self.supported_formats, self.children, self.path, self.required) + return 'ParametersNode(%s, %s, %s, %s, %s, %s, %s, path=%s, %s)' % tuple(map(repr, t)) def __repr__(self): """Return programmatic representation, same as __str__().""" @@ -194,13 +207,16 @@ # Create the top level Tool object. self.tool = Tool() self.result = self.tool + if not attrs.get('name'): + raise CTDFormatException('No attribute "name" in <tool> tag.') + self.tool.name = attrs.get('name') elif self.stack == ['tool', 'cli', 'clielement']: # Create a new CLIElement object for a <clieelement> tag. if not attrs.get('isList'): raise CTDFormatException('No attribute isList in <clielement>.') if attrs.get('optionIdentifier') is None: raise CTDFormatException('no attribute optionIdentifier in <clielement>.') - is_list = (attrs.get('isList') == 'false') + is_list = (attrs.get('isList') == 'true') option_identifier = attrs.get('optionIdentifier') self.tool.cli_elements.append(CLIElement(option_identifier=option_identifier, is_list=is_list)) elif self.stack == ['tool', 'cli', 'clielement', 'mapping']: @@ -221,19 +237,21 @@ node.parent = self.parameter_node self.parameter_node.children[name] = node self.parameter_node = node - elif self.stack[:2] == ['tool', 'PARAMETERS'] and self.stack[-1] == 'ITEM': - # Create a new item ParametersNode for the <ITEM> entry. + elif self.stack[:2] == ['tool', 'PARAMETERS'] and self.stack[-1] in ['ITEM', 'ITEMLIST']: + # Create a new item ParametersNode for the <ITEM>/<ITEMLIST> entry. if not attrs.get('name'): - raise CTDFormatException('no attribute name in <ITEM>') + raise CTDFormatException('no attribute name in <ITEM>/<ITEMLIST>') name = attrs.get('name') value = attrs.get('value') type_ = attrs.get('type') tags = attrs.get('tags') description = attrs.get('description') restrictions = attrs.get('restrictions') - supported_formats = attrs.get('supported_formats') + required = attrs.get('required') == 'true' + supported_formats = attrs.get('supported_formats', '') + kind = {'ITEM': 'item', 'ITEMLIST': 'itemlist'}[self.stack[-1]] child = ParametersNode( - kind='item', name=name, description=description, value=value, + kind=kind, name=name, description=description, value=value, type_=type_, tags=tags, supported_formats=supported_formats, restrictions=restrictions) self.parameter_node.children[name] = child @@ -248,9 +266,7 @@ def characters(self, content): """Handle characters in XML file.""" - if self.stack == ['tool', 'name']: - self.tool.name += content - elif self.stack == ['tool', 'executableName']: + if self.stack == ['tool', 'executableName']: self.tool.executable_name += content elif self.stack == ['tool', 'version']: self.tool.version += content @@ -299,7 +315,7 @@ def appendTag(self, tag, text='', args={}): """Append a tag to self.result with text content only or no content at all.""" e = xml.sax.saxutils.quoteattr - args_str = ' '.join('%s=%s' % (key, e(str(value))) for key, value in args.items()) + args_str = ' '.join('%s=%s' % (key, e(str(value))) for key, value in args.items() if value is not None) if args_str: args_str = ' '+ args_str vals = {'indent': self.indent(), @@ -330,14 +346,14 @@ def handleParameters(self, node): """Recursion for appending tags for ParametersNode.""" for pn in node.children.values(): - if pn.kind == 'item': + if pn.kind in ['item', 'itemlist']: args = {'name': pn.name, 'value': pn.value, 'type': pn.type_, 'description': pn.description, 'restrictions': pn.restrictions, 'tags': pn.tags} - self.appendTag('ITEM', args=args) + self.appendTag(pn.kind.upper(), args=args) else: # node.kind == 'node' args = {'name': pn.name, 'description': pn.description} @@ -375,7 +391,7 @@ self.closeTag('clielement') self.indent_level -= 1 self.closeTag('cli') - # <PARAMETERS>, <NODE>, <ITEM> group + # <PARAMETERS>, <NODE>, <ITEM>, <ITEMLIST> group self.openTag('PARAMETERS', args={'version': 1.4, 'xsi:noNamespaceSchemaLocation': 'http://open-ms.sourceforge.net/schemas/Param_1_4.xsd', 'xmlns:xsi': 'http://www.w3.org/2001/XMLSchema-instance'}) @@ -390,6 +406,34 @@ f.write(x) +class GalaxyCommandSnippet(object): + """Stores a snippet for the Galaxy <command> tag. + + Such a snippet consists of a list of text that will be concatenated using + space as the separator. + + Optionally, a condition can be given which will be pasted verbatimly into + an #if condition that will also be properly closed. As a bonus, the + snippet will be properly indented. + """ + + def __init__(self, words, condition=None, indent=4, level=1): + self.words = words + self.condition = condition + self.indent = indent + self.level = level + + def build(self): + res = [] + if self.condition: + res.append('#if %s' % self.condition) + res.append(' '.join(self.words)) + if self.condition: + res[-1] = ' ' * self.indent + res[-1] + res.append('#end if') + return '\n'.join([' ' * self.indent * self.level + l for l in res]) + + class GalaxyWriter(XMLWriter): """Write a Tool to the Galaxy format.""" @@ -424,12 +468,16 @@ def addInputParam(self, param_node): """Add a ParametersNode object if it is to go to <inputs>.""" - if param_node.tags and 'output file' in param_node.tags.split(','): + if param_node.type_ == 'output-file': return # Skip output files - if param_node.kind != 'item': + if param_node.kind not in ['item', 'itemlist']: return # Skip if not item. + if param_node.name.endswith('-file-ext'): + return # Skip if extension to override. args = {} - if param_node.tags and 'input file' in param_node.tags.split(','): + if param_node.tags and 'required' not in param_node.tags.split(','): + args['optional'] = 'true' # false would be default + if param_node.type_ == 'input-file': args['type'] = 'data' args['format'] = ','.join([x.replace('*', '').replace('.', '') for x in param_node.supported_formats.split(',')]) @@ -469,10 +517,12 @@ def addOutputParam(self, param_node): """Add a ParametersNode object if it is to go to <inputs>.""" - if not param_node.tags or not 'output file' in param_node.tags.split(','): + if param_node.type_ != 'output-file': return # Only add for output files. + if param_node.name.endswith('-file-ext'): + return # Skip if extension to override. args = {} - if '.' in param_node.supported_formats: + if '.' in param_node.supported_formats: args['format'] = param_node.supported_formats.split(',')[0].split('.')[-1] else: args['format'] = param_node.supported_formats.split(',')[0].split('*')[-1] @@ -482,18 +532,44 @@ def addCommandTag(self, tool): """Write <command> tag to self.result.""" - lst = [] + file_ext_elements = [] + # Process non-file-extension arguments. + snippets = [] for ce in tool.cli_elements: + if ce.param_node.name.endswith('-file-ext'): + file_ext_elements.append(ce) + continue # Skip -file-ext options. + # The name of the variable that is used. + var_name = '$' + ce.mapping_path.replace('-', '_').replace('.', '_') + # Check whether it is optional. + optional = bool(ce.param_node.tags and 'required' not in ce.param_node.tags.split(',')) + # Check whether it is a boolean. bool_param = False if ce.param_node.type_ == 'string' and ce.param_node.restrictions and \ sorted(ce.param_node.restrictions.split(',')) == ['false', 'true']: bool_param = True - if not bool_param and ce.option_identifier: - lst.append(ce.option_identifier) - # The path mapping is not ideal but should work OK. - lst.append('$' + ce.mapping_path.replace('-', '_').replace('.', '_')) - txt = [tool.executable_name] + lst - self.appendTag('command', text=' '.join(txt)) + # Get variable name. + val = '"' + var_name + '"' + # Build the snippet for the command. + if bool_param: + # The true value for boolean parameters is the argument itself. + snippets.append(GalaxyCommandSnippet([var_name])) + else: + condition = {True: var_name, False: None}.get(optional) + snippets.append(GalaxyCommandSnippet([ce.option_identifier, val], + condition=condition)) + # Process file extension arguments. + ext_overrides = [] + for ce in file_ext_elements: + if ce.option_identifier == '--write-ctd-file-ext': + continue # Skip special args. + # The name of the variable that is used. + var_name = ce.mapping_path[:-len('-file-ext')].replace('-', '_').replace('.', '_') + snippets.append(GalaxyCommandSnippet([ce.option_identifier, '${%s.ext}' % var_name], + condition='$%s' % var_name)) + # Finalize building the command line. + txt = GalaxyCommandSnippet([tool.executable_name]).build() + '\n' + '\n'.join([s.build() for s in snippets]) + self.appendTag('command', text=txt) def main():
--- a/gff_sort.sh Fri Jun 28 14:01:42 2013 -0400 +++ b/gff_sort.sh Mon Aug 12 09:58:57 2013 -0400 @@ -9,8 +9,8 @@ # -p sort by position (ref, start, end) -- default # The parameters that we will pass to sort. -SORT_POS_ARGS="-k 1,1 -k 2,2n -k 3,3n" -SORT_POS_ARGS_REV="-k 1,1r -k 2,2nr -k 3,3nr" +SORT_POS_ARGS="-k 1,1 -k 4,4n -k 5,5n" +SORT_POS_ARGS_REV="-k 1,1r -k 4,4nr -k 5,5nr" # The arguments will go here. SORT_BY=beginPos
--- a/ngs_roi/app.py Fri Jun 28 14:01:42 2013 -0400 +++ b/ngs_roi/app.py Mon Aug 12 09:58:57 2013 -0400 @@ -44,16 +44,9 @@ def __init__(self, args): self.args = args - def _mkLinks(self): - """Create symlink.""" - subprocess.call(['ln', '-s', self.args.in_file, self.args.in_file + '.roi']) - - def _rmLinks(self): - """Remove symlink.""" - subprocess.call(['rm', '-f', self.args.in_file + '.roi']) - def run(self): - cmd_args = ['-if', self.args.in_file + '.roi', + cmd_args = ['-if', self.args.in_file, + '--in-file-ext', 'roi', '-o', os.path.join(self.args.out_dir, 'thumbnail_'), '--max-rois', self.args.max_rois, '--max-value', self.args.max_value, @@ -67,10 +60,8 @@ #import pdb; pdb.set_trace() import sys print >>sys.stderr, 'Running %s' % ' '.join(cmd_args) - self._mkLinks() p = subprocess.Popen(cmd_args, stderr=subprocess.PIPE, stdout=subprocess.PIPE) res = p.wait() - self._rmLinks() if res: print 'ERROR', p.stdin, p.stderr return res
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/roi_feature_projection.ctd Mon Aug 12 09:58:57 2013 -0400 @@ -0,0 +1,77 @@ +<?xml version="1.0" encoding="UTF-8"?> +<tool name="RoiFeatureProjection" version="0.1" docurl="http://www.seqan.de" category="NGS ROI Analysis" > + <executableName>roi_feature_projection</executableName> + <description>Region Of Interest Projection.</description> + <manual>Compute the projection of a ROI file to regions from a BED or GFF file. The result is a ROI file where each interval from the BED/GFF/GTF file that overlapped with one input ROI file is a region of interest, with the coverage counts projected to the new region of interest. +</manual> + <cli> + <clielement optionIdentifier="--write-ctd-file-ext" isList="false"> + <mapping referenceName="roi_feature_projection.write-ctd-file-ext" /> + </clielement> + <clielement optionIdentifier="--quiet" isList="false"> + <mapping referenceName="roi_feature_projection.quiet" /> + </clielement> + <clielement optionIdentifier="--verbose" isList="false"> + <mapping referenceName="roi_feature_projection.verbose" /> + </clielement> + <clielement optionIdentifier="--very-verbose" isList="false"> + <mapping referenceName="roi_feature_projection.very-verbose" /> + </clielement> + <clielement optionIdentifier="--in-roi" isList="false"> + <mapping referenceName="roi_feature_projection.in-roi" /> + </clielement> + <clielement optionIdentifier="--in-roi-file-ext" isList="false"> + <mapping referenceName="roi_feature_projection.in-roi-file-ext" /> + </clielement> + <clielement optionIdentifier="--in-features" isList="false"> + <mapping referenceName="roi_feature_projection.in-features" /> + </clielement> + <clielement optionIdentifier="--in-features-file-ext" isList="false"> + <mapping referenceName="roi_feature_projection.in-features-file-ext" /> + </clielement> + <clielement optionIdentifier="--out-roi" isList="false"> + <mapping referenceName="roi_feature_projection.out-roi" /> + </clielement> + <clielement optionIdentifier="--out-roi-file-ext" isList="false"> + <mapping referenceName="roi_feature_projection.out-roi-file-ext" /> + </clielement> + <clielement optionIdentifier="--genome" isList="false"> + <mapping referenceName="roi_feature_projection.genome" /> + </clielement> + <clielement optionIdentifier="--genome-file-ext" isList="false"> + <mapping referenceName="roi_feature_projection.genome-file-ext" /> + </clielement> + <clielement optionIdentifier="--mode" isList="false"> + <mapping referenceName="roi_feature_projection.mode" /> + </clielement> + <clielement optionIdentifier="--strand-specific" isList="false"> + <mapping referenceName="roi_feature_projection.strand-specific" /> + </clielement> + <clielement optionIdentifier="--gff-type" isList="false"> + <mapping referenceName="roi_feature_projection.gff-type" /> + </clielement> + <clielement optionIdentifier="--gff-group-by" isList="false"> + <mapping referenceName="roi_feature_projection.gff-group-by" /> + </clielement> + </cli> + <PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> + <NODE name="roi_feature_projection" description="Region Of Interest Projection."> + <ITEM name="write-ctd-file-ext" value="" type="string" description="Override file extension for --write-ctd" required="false" advanced="true" /> + <ITEM name="quiet" value="false" type="string" description="Set verbosity to a minimum." restrictions="true,false" required="false" advanced="false" /> + <ITEM name="verbose" value="false" type="string" description="Enable verbose output." restrictions="true,false" required="false" advanced="false" /> + <ITEM name="very-verbose" value="false" type="string" description="Enable very verbose output." restrictions="true,false" required="false" advanced="false" /> + <ITEM name="in-roi" value="" type="input-file" description="ROI file to read." supported_formats="*.roi" required="true" advanced="false" /> + <ITEM name="in-roi-file-ext" value="" type="string" description="Override file extension for --in-roi" restrictions="roi" required="false" advanced="true" /> + <ITEM name="in-features" value="" type="input-file" description="BED, GFF, or GTF file to read." supported_formats="*.bed,*.gff,*.gtf" required="true" advanced="false" /> + <ITEM name="in-features-file-ext" value="" type="string" description="Override file extension for --in-features" restrictions="bed,gff,gtf" required="false" advanced="true" /> + <ITEM name="out-roi" value="" type="output-file" description="ROI file to write." supported_formats="*.roi" required="true" advanced="false" /> + <ITEM name="out-roi-file-ext" value="" type="string" description="Override file extension for --out-roi" restrictions="roi" required="false" advanced="true" /> + <ITEM name="genome" value="" type="input-file" description="Path to FASTA file with genome; optional. When given, this is used for computing the overall region's C+G content." supported_formats="*.fasta,*.fa" required="false" advanced="false" /> + <ITEM name="genome-file-ext" value="" type="string" description="Override file extension for --genome" restrictions="fasta,fa" required="false" advanced="true" /> + <ITEM name="mode" value="projection" type="string" description="The mode in which to combine the ROI and BED/GFF file. See section Combination Modes below for details." restrictions="intersection,projection,union,difference" required="false" advanced="false" /> + <ITEM name="strand-specific" value="false" type="string" description="Enable strand-specific mode if set." restrictions="true,false" required="false" advanced="false" /> + <ITEM name="gff-type" value="" type="string" description="The GFF/GTF record type (value of third column) to keep. Keep all if not set or input file type is not GFF/GTF." required="false" advanced="false" /> + <ITEM name="gff-group-by" value="" type="string" description="The GFF/GTF tag to use for grouping, e.g. "Parent", "transcript_id". No grouping if empty. When using the grouping feature, the --mode is automatically set to projection." required="false" advanced="false" /> + </NODE> + </PARAMETERS> +</tool>
--- a/roi_feature_projection.xml Fri Jun 28 14:01:42 2013 -0400 +++ b/roi_feature_projection.xml Mon Aug 12 09:58:57 2013 -0400 @@ -1,87 +1,52 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="roi_feature_projection" name="ROI Feature Projection"> - <description>Intersect ROIs with GFF/BED</description> - - <command> - <!-- First, create link for the input files --> - #if $roi_intersect_genome# ln -s ${roi_intersect_genome} ${roi_intersect_genome}.${roi_intersect_genome.ext}; #end if - #if $roi_intersect_in_roi# ln -s ${roi_intersect_in_roi} ${roi_intersect_in_roi}.${roi_intersect_in_roi.ext}; #end if - #if $roi_intersect_out_roi# touch ${roi_intersect_out_roi}; ln -s ${roi_intersect_out_roi} ${roi_intersect_out_roi}.roi; #end if - #if $roi_intersect_in_features # ln -s ${roi_intersect_in_features} ${roi_intersect_in_features}.${roi_intersect_in_features.ext}; #end if - - <!-- Call the feature projection on the links --> - roi_feature_projection $roi_intersect_strand_specific - --in-roi ${roi_intersect_in_roi}.${roi_intersect_in_roi.ext} - --in-features ${roi_intersect_in_features}.${roi_intersect_in_features.ext} - --out-roi ${roi_intersect_out_roi}.roi - --mode $roi_intersect_mode - #if $roi_intersect_genome# --genome ${roi_intersect_genome}.${roi_intersect_genome.ext} #end if - #if $verbosity # $verbosity #end if - #if $roi_intersect_gff_type # --gff-type $roi_intersect_gff_type #end if - #if $roi_intersect_gff_group_by# --gff-group-by $roi_intersect_gff_group_by #end if - ; - - <!-- Get rid of the links again --> - #if $roi_intersect_genome# rm -f ${roi_intersect_genome}.${roi_intersect_genome.ext}; #end if - #if $roi_intersect_in_roi# rm -f ${roi_intersect_in_roi}.${roi_intersect_in_roi.ext}; #end if - #if $roi_intersect_in_roi# rm -f ${roi_intersect_out_roi}.roi; #end if - #if $roi_intersect_in_features# rm -f ${roi_intersect_in_features}.${roi_intersect_in_features.ext}; #end if - </command> - - <!-- - Input Files and Parameters - --> +<tool id="roi_feature_projection" name="RoiFeatureProjection"> + <command>roi_feature_projection + $roi_feature_projection_quiet + $roi_feature_projection_verbose + $roi_feature_projection_very_verbose + --in-roi "$roi_feature_projection_in_roi" + --in-features "$roi_feature_projection_in_features" + --out-roi "$roi_feature_projection_out_roi" + --genome "$roi_feature_projection_genome" + --mode "$roi_feature_projection_mode" + $roi_feature_projection_strand_specific + --gff-type "$roi_feature_projection_gff_type" + --gff-group-by "$roi_feature_projection_gff_group_by" + #if $roi_feature_projection_in_roi + --in-roi-file-ext ${roi_feature_projection_in_roi.ext} + #end if + #if $roi_feature_projection_in_features + --in-features-file-ext ${roi_feature_projection_in_features.ext} + #end if + #if $roi_feature_projection_out_roi + --out-roi-file-ext ${roi_feature_projection_out_roi.ext} + #end if + #if $roi_feature_projection_genome + --genome-file-ext ${roi_feature_projection_genome.ext} + #end if</command> + <description>Region Of Interest Projection.</description> <inputs> - <param label="BED, GFF, or GTF file to read." type="data" name="roi_intersect_in_features" format="bed,gff,gtf" /> - <param label="ROI file to read." type="data" name="roi_intersect_in_roi" format="roi" /> - <param label="Path to FASTA file with genome; optional. When given, this is used for computing the overall region's C+G content." type="data" name="roi_intersect_genome" format="fasta,fa" optional="true" /> - - <param type="select" name="verbosity"> - <option value="--quiet">verbose</option> - <option value="" selected="true">normal</option> - <option value="--verbose">verbose</option> - <option value="--very-verbose">very verbose</option> - </param> - - <param type="text" name="roi_intersect_gff_type" value="" label="The GFF/GTF record type (value of third column) to keep. Keep all if not set or input file type is not GFF/GTF." /> - <param type="text" name="roi_intersect_gff_group_by" value="" label='The GFF/GTF tag to use for grouping, e.g. "Parent", "transcript_id". No grouping if empty. When using the grouping feature, the --mode is automatically set to projection.' /> - <param falsevalue="" truevalue="--strand-specific" type="boolean" name="roi_intersect_strand_specific" label="Enable strand-specific mode if set." /> - - <param type="select" name="roi_intersect_mode" value="projection" label="The mode in which to combine the ROI and BED/GFF file. See section Combination Modes below for details."> - <option value="projection" selected="true">projection</option> + <param label="BED, GFF, or GTF file to read." type="data" name="roi_feature_projection_in_features" format="bed,gff,gtf" /> + <param type="text" name="roi_feature_projection_gff_type" value="" label="The GFF/GTF record type (value of third column) to keep. Keep all if not set or input file type is not GFF/GTF." /> + <param falsevalue="" truevalue="--verbose" type="boolean" name="roi_feature_projection_verbose" label="Enable verbose output." /> + <param label="ROI file to read." type="data" name="roi_feature_projection_in_roi" format="roi" /> + <param falsevalue="" truevalue="--strand-specific" type="boolean" name="roi_feature_projection_strand_specific" label="Enable strand-specific mode if set." /> + <param falsevalue="" truevalue="--very-verbose" type="boolean" name="roi_feature_projection_very_verbose" label="Enable very verbose output." /> + <param falsevalue="" truevalue="--quiet" type="boolean" name="roi_feature_projection_quiet" label="Set verbosity to a minimum." /> + <param label="Path to FASTA file with genome; optional. When given, this is used for computing the overall region's C+G content." type="data" name="roi_feature_projection_genome" format="fasta,fa" /> + <param type="text" name="roi_feature_projection_gff_group_by" value="" label='The GFF/GTF tag to use for grouping, e.g. "Parent", "transcript_id". No grouping if empty. When using the grouping feature, the --mode is automatically set to projection.' /> + <param type="select" name="roi_feature_projection_mode" value="projection" label="The mode in which to combine the ROI and BED/GFF file. See section Combination Modes below for details."> <option value="intersection">intersection</option> + <option value="projection">projection</option> <option value="union">union</option> <option value="difference">difference</option> </param> </inputs> - - <!-- - Recognize errors by return code and not output to stderr. - --> - <outputs> - <data label="${roi_intersect_in_roi} & ${roi_intersect_in_features}" - name="roi_intersect_out_roi" format="roi" /> + <data label="ROI file to write." name="roi_feature_projection_out_roi" format="roi" /> </outputs> - - <!-- - Recognize errors by return code and not output to stderr. - --> <stdio> <exit_code range="1:" level="fatal" /> <exit_code range=":-1" level="fatal" /> </stdio> - - <!-- - Tool Help - --> - <help>No help yet.</help> - - <!-- - Dependencies - --> - <requirements> - <requirement type="python-module">Cheetah</requirement> - <requirement type="binary">roi_feature_projection</requirement> - </requirements> </tool>
--- a/roi_plot_9.sh Fri Jun 28 14:01:42 2013 -0400 +++ b/roi_plot_9.sh Mon Aug 12 09:58:57 2013 -0400 @@ -13,6 +13,9 @@ SORT_COL=0 REVERSE= +# Current directory. +DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" + helpme () { echo "host: ${HOST}" echo "Plot ROIs 9 per page to PDF with links to IGV." @@ -51,10 +54,10 @@ fi gawk -v fileName=${IN_FILE}.tmp.ps \ - -f plot.awk \ + -f ${DIR}/plot.awk \ ${USED_INFILE} |gnuplot 2> /dev/null gawk -v roiFile=${USED_INFILE} \ - -f ps2pswLinks.gawk \ + -f ${DIR}/ps2pswLinks.gawk \ ${IN_FILE}.tmp.ps > ${IN_FILE}.tmp.ln.ps ps2pdf ${IN_FILE}.tmp.ln.ps ${OUT_FILE} # rm ${IN_FILE}.tmp.ps @@ -62,3 +65,5 @@ if [ "x${IN_FILE##*.}" == "xgz" ]; then echo rm $USED_INFILE fi + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/roi_plot_thumbnails.ctd Mon Aug 12 09:58:57 2013 -0400 @@ -0,0 +1,73 @@ +<?xml version="1.0" encoding="UTF-8"?> +<tool name="RoiPlotThumbnails" version="0.1" docurl="http://www.seqan.de" category="NGS ROI Analysis" > + <executableName>roi_plot_thumbnails</executableName> + <description>Create plot grids for ROI file.</description> + <manual>Create PNG images with plot grids to OUT${i}.png from ROI records in IN.roi. +</manual> + <cli> + <clielement optionIdentifier="--write-ctd-file-ext" isList="false"> + <mapping referenceName="roi_plot_thumbnails.write-ctd-file-ext" /> + </clielement> + <clielement optionIdentifier="--verbose" isList="false"> + <mapping referenceName="roi_plot_thumbnails.verbose" /> + </clielement> + <clielement optionIdentifier="--vverbose" isList="false"> + <mapping referenceName="roi_plot_thumbnails.vverbose" /> + </clielement> + <clielement optionIdentifier="--input-file" isList="false"> + <mapping referenceName="roi_plot_thumbnails.input-file" /> + </clielement> + <clielement optionIdentifier="--input-file-file-ext" isList="false"> + <mapping referenceName="roi_plot_thumbnails.input-file-file-ext" /> + </clielement> + <clielement optionIdentifier="--output-prefix" isList="false"> + <mapping referenceName="roi_plot_thumbnails.output-prefix" /> + </clielement> + <clielement optionIdentifier="--output-prefix-file-ext" isList="false"> + <mapping referenceName="roi_plot_thumbnails.output-prefix-file-ext" /> + </clielement> + <clielement optionIdentifier="--max-rois" isList="false"> + <mapping referenceName="roi_plot_thumbnails.max-rois" /> + </clielement> + <clielement optionIdentifier="--max-value" isList="false"> + <mapping referenceName="roi_plot_thumbnails.max-value" /> + </clielement> + <clielement optionIdentifier="--num-cols" isList="false"> + <mapping referenceName="roi_plot_thumbnails.num-cols" /> + </clielement> + <clielement optionIdentifier="--num-rows" isList="false"> + <mapping referenceName="roi_plot_thumbnails.num-rows" /> + </clielement> + <clielement optionIdentifier="--plot-height" isList="false"> + <mapping referenceName="roi_plot_thumbnails.plot-height" /> + </clielement> + <clielement optionIdentifier="--plot-width" isList="false"> + <mapping referenceName="roi_plot_thumbnails.plot-width" /> + </clielement> + <clielement optionIdentifier="--border-width" isList="false"> + <mapping referenceName="roi_plot_thumbnails.border-width" /> + </clielement> + <clielement optionIdentifier="--spacing" isList="false"> + <mapping referenceName="roi_plot_thumbnails.spacing" /> + </clielement> + </cli> + <PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> + <NODE name="roi_plot_thumbnails" description="Create plot grids for ROI file."> + <ITEM name="write-ctd-file-ext" value="" type="string" description="Override file extension for --write-ctd" required="false" advanced="true" /> + <ITEM name="verbose" value="false" type="string" description="Verbose mode." restrictions="true,false" required="false" advanced="false" /> + <ITEM name="vverbose" value="false" type="string" description="Very verbose mode." restrictions="true,false" required="false" advanced="false" /> + <ITEM name="input-file" value="" type="input-file" description="ROI to plot." supported_formats="*.roi" required="true" advanced="false" /> + <ITEM name="input-file-file-ext" value="" type="string" description="Override file extension for --input-file" restrictions="roi" required="false" advanced="true" /> + <ITEM name="output-prefix" value="" type="output-file" description="Prefix of output file." required="true" advanced="false" /> + <ITEM name="output-prefix-file-ext" value="" type="string" description="Override file extension for --output-prefix" required="false" advanced="true" /> + <ITEM name="max-rois" value="20000" type="int" description="Maximal number of plots to create (0 for all)." restrictions="0:" required="false" advanced="false" /> + <ITEM name="max-value" value="0" type="int" description="Fix maximal y value. 0 for no limit.." restrictions="0:" required="false" advanced="false" /> + <ITEM name="num-cols" value="40" type="int" description="Number of plots in one row." restrictions="1:" required="false" advanced="false" /> + <ITEM name="num-rows" value="50" type="int" description="Number of plots in one column." restrictions="1:" required="false" advanced="false" /> + <ITEM name="plot-height" value="30" type="int" description="Height of one plot in px." restrictions="1:" required="false" advanced="false" /> + <ITEM name="plot-width" value="30" type="int" description="Width of one plot in px." restrictions="1:" required="false" advanced="false" /> + <ITEM name="border-width" value="0" type="int" description="Border width." restrictions="0:" required="false" advanced="false" /> + <ITEM name="spacing" value="2" type="int" description="Space between plots." required="false" advanced="false" /> + </NODE> + </PARAMETERS> +</tool>
--- a/roi_plot_thumbnails.xml Fri Jun 28 14:01:42 2013 -0400 +++ b/roi_plot_thumbnails.xml Mon Aug 12 09:58:57 2013 -0400 @@ -17,24 +17,6 @@ #if $ucsc_org # --ucsc-org $ucsc_org #end if #if $ucsc_db # --ucsc-db $ucsc_db #end if #if $ucsc_chr_prefix # --ucsc-chr-prefix "$ucsc_chr_prefix" #end if - - && - - ln -s ${input} ${input}.${input.ext} - - ; - - roi_plot_thumbnails -if $input -o "${out_file.files_path}/thumbnail_" - #if $max_rois # --max-rois $max_rois #end if - #if $num_rows # --num-rows $num_rows #end if - #if $num_cols # --num-cols $num_cols #end if - #if $plot_height # --plot-height $plot_height #end if - #if $plot_width # --plot-width $plot_width #end if - #if $max_value # --max-value $max_value #end if - - ; - - rm -f ${input}.${input.ext} </command> <inputs> <param name="input" format="roi" type="data" label="ROI file to generate statistics for."/>