December 2011 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: dan: UCSC BAM display will now pass the pairEndsByName attribute. Closes #455.
by Bitbucket 08 Dec '11

08 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/af24105e47a9/ changeset: af24105e47a9 user: dan date: 2011-12-08 22:25:08 summary: UCSC BAM display will now pass the pairEndsByName attribute. Closes #455. affected #: 1 file diff -r d93edf2dc43612e38a9e7aafac4d50fba60ae647 -r af24105e47a9966566ad92833f0990805da69ac3 display_applications/ucsc/bam.xml --- a/display_applications/ucsc/bam.xml +++ b/display_applications/ucsc/bam.xml @@ -12,6 +12,6 @@ <url>${ucsc_link}db=${qp($bam_file.dbkey)}&hgt.customText=${qp($track.url)}</url><param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" /><param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" /> - <param type="template" name="track" viewable="True">track type="bam" name="${bam_file.name.replace( '\\', '\\\\' ).replace( '"', '\\"' )}" bigDataUrl="${bam_file.url}" db="${bam_file.dbkey}"</param> + <param type="template" name="track" viewable="True">track type="bam" name="${bam_file.name.replace( '\\', '\\\\' ).replace( '"', '\\"' )}" bigDataUrl="${bam_file.url}" db="${bam_file.dbkey}" pairEndsByName="."</param></dynamic_links></display> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Allow tools with zero inputs. Resolves #463.
by Bitbucket 08 Dec '11

08 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d93edf2dc436/ changeset: d93edf2dc436 user: dan date: 2011-12-08 20:26:34 summary: Allow tools with zero inputs. Resolves #463. affected #: 2 files diff -r 0639c7b530774aea53776cc207b39cee22a5499a -r d93edf2dc43612e38a9e7aafac4d50fba60ae647 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -386,6 +386,16 @@ self.config_file = config_file self.tool_dir = os.path.dirname( config_file ) self.app = app + #setup initial attribute values + self.inputs = odict() + self.inputs_by_page = list() + self.display_by_page = list() + self.action = '/tool_runner/index' + self.target = 'galaxy_main' + self.method = 'post' + self.check_values = True + self.nginx_upload = False + self.input_required = False # Define a place to keep track of all input parameters. These # differ from the inputs dictionary in that inputs can be page # elements like conditionals, but input_params are basic form @@ -565,11 +575,12 @@ """ # Load parameters (optional) input_elem = root.find("inputs") + enctypes = set() if input_elem: # Handle properties of the input form - self.check_values = util.string_as_bool( input_elem.get("check_values", "true") ) - self.nginx_upload = util.string_as_bool( input_elem.get( "nginx_upload", "false" ) ) - self.action = input_elem.get( 'action', '/tool_runner/index' ) + self.check_values = util.string_as_bool( input_elem.get("check_values", self.check_values ) ) + self.nginx_upload = util.string_as_bool( input_elem.get( "nginx_upload", self.nginx_upload ) ) + self.action = input_elem.get( 'action', self.action ) # If we have an nginx upload, save the action as a tuple instead of # a string. The actual action needs to get url_for run to add any # prefixes, and we want to avoid adding the prefix to the @@ -582,13 +593,9 @@ 'hidden POST parameters' ) self.action = (self.app.config.nginx_upload_path + '?nginx_redir=', urllib.unquote_plus(self.action)) - self.target = input_elem.get( "target", "galaxy_main" ) - self.method = input_elem.get( "method", "post" ) + self.target = input_elem.get( "target", self.target ) + self.method = input_elem.get( "method", self.method ) # Parse the actual parameters - self.inputs = odict() - self.inputs_by_page = list() - self.display_by_page = list() - enctypes = set() # Handle multiple page case pages = input_elem.findall( "page" ) for page in ( pages or [ input_elem ] ): @@ -596,22 +603,24 @@ self.inputs_by_page.append( inputs ) self.inputs.update( inputs ) self.display_by_page.append( display ) - self.display = self.display_by_page[0] - self.npages = len( self.inputs_by_page ) - self.last_page = len( self.inputs_by_page ) - 1 - self.has_multiple_pages = bool( self.last_page ) - # Determine the needed enctype for the form - if len( enctypes ) == 0: - self.enctype = "application/x-www-form-urlencoded" - elif len( enctypes ) == 1: - self.enctype = enctypes.pop() - else: - raise Exception, "Conflicting required enctypes: %s" % str( enctypes ) + else: + self.inputs_by_page.append( self.inputs ) + self.display_by_page.append( None ) + self.display = self.display_by_page[0] + self.npages = len( self.inputs_by_page ) + self.last_page = len( self.inputs_by_page ) - 1 + self.has_multiple_pages = bool( self.last_page ) + # Determine the needed enctype for the form + if len( enctypes ) == 0: + self.enctype = "application/x-www-form-urlencoded" + elif len( enctypes ) == 1: + self.enctype = enctypes.pop() + else: + raise Exception, "Conflicting required enctypes: %s" % str( enctypes ) # Check if the tool either has no parameters or only hidden (and # thus hardcoded) parameters. FIXME: hidden parameters aren't # parameters at all really, and should be passed in a different # way, making this check easier. - self.input_required = False for param in self.inputs.values(): if not isinstance( param, ( HiddenToolParameter, BaseURLToolParameter ) ): self.input_required = True @@ -943,7 +952,7 @@ return False # This is probably the best bet for detecting external web tools # right now - if self.action != "/tool_runner/index": + if self.tool_type.startswith( 'data_source' ): return False # HACK: upload is (as always) a special case becuase file parameters # can't be persisted. diff -r 0639c7b530774aea53776cc207b39cee22a5499a -r d93edf2dc43612e38a9e7aafac4d50fba60ae647 templates/root/tool_menu.mako --- a/templates/root/tool_menu.mako +++ b/templates/root/tool_menu.mako @@ -13,7 +13,7 @@ <div class="toolTitleNoSection"> %endif <% - if tool.input_required: + if not tool.tool_type.startswith( 'data_source' ): link = h.url_for( controller='tool_runner', tool_id=tool.id ) else: link = h.url_for( tool.action, ** tool.get_static_param_values( t ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Email action on job failure, resolves bb issue #600. Fail/cleanup logic condensation.
by Bitbucket 08 Dec '11

08 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0639c7b53077/ changeset: 0639c7b53077 user: dannon date: 2011-12-08 18:08:53 summary: Email action on job failure, resolves bb issue #600. Fail/cleanup logic condensation. affected #: 1 file diff -r 5e211b535425ba3ea80723153043be21446230d7 -r 0639c7b530774aea53776cc207b39cee22a5499a lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -443,7 +443,7 @@ job = self.get_job() self.sa_session.refresh( job ) # if the job was deleted, don't fail it - if not job.state == model.Job.states.DELETED: + if not job.state == job.states.DELETED: # Check if the failure is due to an exception if exception: # Save the traceback immediately in case we generate another @@ -474,15 +474,18 @@ dataset.extension = 'data' self.sa_session.add( dataset ) self.sa_session.flush() - job.state = model.Job.states.ERROR + job.state = job.states.ERROR job.command_line = self.command_line job.info = message self.sa_session.add( job ) self.sa_session.flush() + #Perform email action even on failure. + for pja in [x for x in job.post_job_actions if x.action_type == "EmailAction"]: + ActionBox.execute(self.app, self.sa_session, pja.post_job_action, job) # If the job was deleted, call tool specific fail actions (used for e.g. external metadata) and clean up if self.tool: self.tool.job_failed( self, message, exception ) - if self.app.config.cleanup_job == 'always': + if self.app.cleanup_job == 'always' or (self.app.config.cleanup_job == 'onsuccess' and job.state == job.states.DELETED): self.cleanup() def change_state( self, state, info = False ): @@ -525,14 +528,9 @@ self.sa_session.expunge_all() job = self.get_job() # if the job was deleted, don't finish it - if job.state == job.states.DELETED: - if self.app.config.cleanup_job in ( 'always', 'onsuccess' ): - self.cleanup() - return - elif job.state == job.states.ERROR: - # Job was deleted by an administrator - self.fail( job.info ) - return + if job.state == job.states.DELETED or job.state == job.states.ERROR: + #ERROR at this point means the job was deleted by an administrator. + return self.fail( job.info ) if stderr: job.state = job.states.ERROR else: @@ -555,8 +553,7 @@ if os.path.exists( dataset_path.real_path ) and os.stat( dataset_path.real_path ).st_size > 0: log.warning( "finish(): %s not found, but %s is not empty, so it will be used instead" % ( dataset_path.false_path, dataset_path.real_path ) ) else: - self.fail( "Job %s's output dataset(s) could not be read" % job.id ) - return + return self.fail( "Job %s's output dataset(s) could not be read" % job.id ) job_context = ExpressionContext( dict( stdout = stdout, stderr = stderr ) ) job_tool = self.app.toolbox.tools_by_id.get( job.tool_id, None ) def in_directory( file, directory ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Do not allow public user names to be changed within the tool shed if the user has created a tool shed repository.
by Bitbucket 08 Dec '11

08 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5e211b535425/ changeset: 5e211b535425 user: greg date: 2011-12-08 17:49:52 summary: Do not allow public user names to be changed within the tool shed if the user has created a tool shed repository. affected #: 2 files diff -r 862d562e31670dd22a6bd575b2fa79328acabb4d -r 5e211b535425ba3ea80723153043be21446230d7 templates/user/info.mako --- a/templates/user/info.mako +++ b/templates/user/info.mako @@ -21,12 +21,28 @@ </div><div class="form-row"><label>Public name:</label> - <input type="text" name="username" size="40" value="${username}"/> - <div class="toolParamHelp" style="clear: both;"> - Your public name is an optional identifier that will be used to generate addresses for information - you share publicly. Public names must be at least four characters in length and contain only lower-case - letters, numbers, and the '-' character. - </div> + %if webapp == 'community': + ${username} + %if user.active_repositories: + <div class="toolParamHelp" style="clear: both;"> + You cannot change your public name after you have created a repository in this tool shed. + </div> + %else: + <div class="toolParamHelp" style="clear: both;"> + Your public name provides a means of identifying you publicly within this tool shed. Public + names must be at least four characters in length and contain only lower-case letters, numbers, + and the '-' character. You cannot change your public name after you have created a repository + in this tool shed. + </div> + %endif + %else: + <input type="text" name="username" size="40" value="${username}"/> + <div class="toolParamHelp" style="clear: both;"> + Your public name is an optional identifier that will be used to generate addresses for information + you share publicly. Public names must be at least four characters in length and contain only lower-case + letters, numbers, and the '-' character. + </div> + %endif </div><div class="form-row"><input type="submit" name="login_info_button" value="Save"/> diff -r 862d562e31670dd22a6bd575b2fa79328acabb4d -r 5e211b535425ba3ea80723153043be21446230d7 templates/user/register.mako --- a/templates/user/register.mako +++ b/templates/user/register.mako @@ -50,11 +50,20 @@ <div class="form-row"><label>Public name:</label><input type="text" name="username" size="40" value="${username}"/> - <div class="toolParamHelp" style="clear: both;"> - Your public name is an identifier that will be used to generate addresses for information - you share publicly. Public names must be at least four characters in length and contain only lower-case - letters, numbers, and the '-' character. - </div> + %if webapp == 'galaxy': + <div class="toolParamHelp" style="clear: both;"> + Your public name is an identifier that will be used to generate addresses for information + you share publicly. Public names must be at least four characters in length and contain only lower-case + letters, numbers, and the '-' character. + </div> + %else: + <div class="toolParamHelp" style="clear: both;"> + Your public name provides a means of identifying you publicly within this tool shed. Public + names must be at least four characters in length and contain only lower-case letters, numbers, + and the '-' character. You cannot change your public name after you have created a repository + in this tool shed. + </div> + %endif </div> %if trans.app.config.smtp_server: <div class="form-row"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Escape backslashes and quotes in name attributes for UCSC external display applications which use bigDataUrls. Remove no longer required strip_https attribute. Resolves #627.
by Bitbucket 08 Dec '11

08 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/862d562e3167/ changeset: 862d562e3167 user: dan date: 2011-12-08 17:44:22 summary: Escape backslashes and quotes in name attributes for UCSC external display applications which use bigDataUrls. Remove no longer required strip_https attribute. Resolves #627. affected #: 3 files diff -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca -r 862d562e31670dd22a6bd575b2fa79328acabb4d display_applications/ucsc/bam.xml --- a/display_applications/ucsc/bam.xml +++ b/display_applications/ucsc/bam.xml @@ -10,8 +10,8 @@ <filter>${dataset.dbkey in $builds}</filter><url>${ucsc_link}db=${qp($bam_file.dbkey)}&hgt.customText=${qp($track.url)}</url> - <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" strip_https="True" /> - <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" /> - <param type="template" name="track" viewable="True" strip_https="True">track type=bam name="${bam_file.name}" bigDataUrl=${bam_file.url} db=${bam_file.dbkey}</param> + <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" /> + <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" /> + <param type="template" name="track" viewable="True">track type="bam" name="${bam_file.name.replace( '\\', '\\\\' ).replace( '"', '\\"' )}" bigDataUrl="${bam_file.url}" db="${bam_file.dbkey}"</param></dynamic_links></display> diff -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca -r 862d562e31670dd22a6bd575b2fa79328acabb4d display_applications/ucsc/bigbed.xml --- a/display_applications/ucsc/bigbed.xml +++ b/display_applications/ucsc/bigbed.xml @@ -10,7 +10,7 @@ <filter>${dataset.dbkey in $builds}</filter><url>${ucsc_link}db=${qp($bigbed_file.dbkey)}&hgt.customText=${qp($track.url)}</url> - <param type="data" name="bigbed_file" url="galaxy_${DATASET_HASH}.bigbed" strip_https="True" /> - <param type="template" name="track" viewable="True" strip_https="True">track type=bigBed name="${bigbed_file.name}" bigDataUrl=${bigbed_file.url} db=${bigbed_file.dbkey}</param> + <param type="data" name="bigbed_file" url="galaxy_${DATASET_HASH}.bigbed" /> + <param type="template" name="track" viewable="True">track type="bigBed" name="${bigbed_file.name.replace( '\\', '\\\\' ).replace( '"', '\\"' )}" bigDataUrl="${bigbed_file.url}" db="${bigbed_file.dbkey}"</param></dynamic_links></display> diff -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca -r 862d562e31670dd22a6bd575b2fa79328acabb4d display_applications/ucsc/bigwig.xml --- a/display_applications/ucsc/bigwig.xml +++ b/display_applications/ucsc/bigwig.xml @@ -10,7 +10,7 @@ <filter>${dataset.dbkey in $builds}</filter><url>${ucsc_link}db=${qp($bigwig_file.dbkey)}&hgt.customText=${qp($track.url)}</url> - <param type="data" name="bigwig_file" url="galaxy_${DATASET_HASH}.bigwig" strip_https="True" /> - <param type="template" name="track" viewable="True" strip_https="True">track type=bigWig name="${bigwig_file.name}" bigDataUrl=${bigwig_file.url} db=${bigwig_file.dbkey}</param> + <param type="data" name="bigwig_file" url="galaxy_${DATASET_HASH}.bigwig" /> + <param type="template" name="track" viewable="True">track type="bigWig" name="${bigwig_file.name.replace( '\\', '\\\\' ).replace( '"', '\\"' )}" bigDataUrl="${bigwig_file.url}" db="${bigwig_file.dbkey}"</param></dynamic_links></display> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.
by Bitbucket 08 Dec '11

08 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4fbcfe913aea/ changeset: 4fbcfe913aea user: dan date: 2011-12-08 16:44:42 summary: Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610. affected #: 107 files diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_antigenic.xml --- a/tools/emboss_5/emboss_antigenic.xml +++ b/tools/emboss_5/emboss_antigenic.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: antigenic1" name="antigenic" version="5.0.0"><description>Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar.</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>antigenic -sequence $input1 -outfile $out_file1 -minlen $minlen -rformat2 $out_format1 -auto</command> + <command>antigenic -sequence '$input1' -outfile '$out_file1' -minlen '$minlen' -rformat2 '$out_format1' -auto</command><inputs><param format="data" name="input1" type="data"><label>On query</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_backtranseq.xml --- a/tools/emboss_5/emboss_backtranseq.xml +++ b/tools/emboss_5/emboss_backtranseq.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: backtranseq2" name="backtranseq" version="5.0.0"><description>Back translate a protein sequence</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>backtranseq -sequence $input1 -outfile $out_file1 -cfile $cfile -osformat2 $out_format1 -auto</command> + <command>backtranseq -sequence '$input1' -outfile '$out_file1' -cfile '$cfile' -osformat2 '$out_format1' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>On query</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_banana.xml --- a/tools/emboss_5/emboss_banana.xml +++ b/tools/emboss_5/emboss_banana.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: banana3" name="banana" version="5.0.0"><description>Bending and curvature plot in B-DNA</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>banana -sequence $input1 -outfile $out_file1 -graph none -auto</command> + <command>banana -sequence '$input1' -outfile '$out_file1' -graph none -auto</command><inputs><param format="data" name="input1" type="data"><label>On query</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_biosed.xml --- a/tools/emboss_5/emboss_biosed.xml +++ b/tools/emboss_5/emboss_biosed.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: biosed4" name="biosed" version="5.0.0"><description>Replace or delete sequence sections</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>biosed -sequence $input1 -outseq $out_file1 -target "$target" -replace "$replace" -osformat2 "$out_format1" -auto</command> + <command>biosed -sequence '$input1' -outseq '$out_file1' -target '$target' -replace '$replace' -osformat2 '$out_format1' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>On query</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_btwisted.xml --- a/tools/emboss_5/emboss_btwisted.xml +++ b/tools/emboss_5/emboss_btwisted.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: btwisted5" name="btwisted" version="5.0.0"><description>Calculates the twisting in a B-DNA sequence</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>btwisted -sequence $input1 -outfile $out_file1 -auto</command> + <command>btwisted -sequence '$input1' -outfile '$out_file1' -auto</command><inputs><param format="data" name="input1" type="data"><label>On query</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_cai.xml --- a/tools/emboss_5/emboss_cai.xml +++ b/tools/emboss_5/emboss_cai.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: cai6" name="cai" version="5.0.0"><description>CAI codon adaptation index</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>cai -seqall $input1 -outfile $out_file1 -cfile $cfile -auto</command> + <command>cai -seqall '$input1' -outfile '$out_file1' -cfile '$cfile' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>On query</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_cai_custom.xml --- a/tools/emboss_5/emboss_cai_custom.xml +++ b/tools/emboss_5/emboss_cai_custom.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: cai_custom6" name="cai custom" version="5.0.0"><description>CAI codon adaptation index using custom codon usage file</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>cai -seqall $input1 -outfile $out_file1 -cfile $input2 -auto</command> + <command>cai -seqall '$input1' -outfile '$out_file1' -cfile '$input2' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>On query</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_chaos.xml --- a/tools/emboss_5/emboss_chaos.xml +++ b/tools/emboss_5/emboss_chaos.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: chaos7" name="chaos" version="5.0.0"><description>Create a chaos game representation plot for a sequence</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command interpreter="perl">emboss_single_outputfile_wrapper.pl chaos -sequence $input1 -graph png -goutfile $out_file1 -auto</command> + <command interpreter="perl">emboss_single_outputfile_wrapper.pl chaos -sequence '$input1' -graph png -goutfile '$out_file1' -auto</command><inputs><param format="data" name="input1" type="data"><label>On query</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_charge.xml --- a/tools/emboss_5/emboss_charge.xml +++ b/tools/emboss_5/emboss_charge.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: charge8" name="charge" version="5.0.0"><description>Protein charge plot</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>charge -seqall $input1 -outfile $out_file1 -window $window -auto</command> + <command>charge -seqall '$input1' -outfile '$out_file1' -window '$window' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>On query</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_checktrans.xml --- a/tools/emboss_5/emboss_checktrans.xml +++ b/tools/emboss_5/emboss_checktrans.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: checktrans9" name="checktrans" version="5.0.0"><description>Reports STOP codons and ORF statistics of a protein</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>checktrans -sequence $input1 -outfile $out_file1 -outseq $out_file2 -osformat3 $out_format2 -outfeat $out_file3 -offormat4 $out_format3 -orfml $orfml -addlast $addlast -auto</command> + <command>checktrans -sequence '$input1' -outfile '$out_file1' -outseq '$out_file2' -osformat3 '$out_format2' -outfeat '$out_file3' -offormat4 '$out_format3' -orfml '$orfml' -addlast '$addlast' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>On query</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_chips.xml --- a/tools/emboss_5/emboss_chips.xml +++ b/tools/emboss_5/emboss_chips.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: chips10" name="chips" version="5.0.0"><description>Codon usage statistics</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>chips -seqall $input1 -outfile $out_file1 -sum $sum -auto</command> + <command>chips -seqall '$input1' -outfile '$out_file1' -sum '$sum' -auto</command><inputs><param format="data" name="input1" type="data"><label>On query</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_cirdna.xml --- a/tools/emboss_5/emboss_cirdna.xml +++ b/tools/emboss_5/emboss_cirdna.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: cirdna11" name="cirdna" version="5.0.0"><description>Draws circular maps of DNA constructs</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command interpreter="perl">emboss_single_outputfile_wrapper.pl cirdna -infile $input1 -graphout png -goutfile $out_file1 -auto</command> + <command interpreter="perl">emboss_single_outputfile_wrapper.pl cirdna -infile '$input1' -graphout png -goutfile '$out_file1' -auto</command><inputs><param format="data" name="input1" type="data"><label>On query</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_codcmp.xml --- a/tools/emboss_5/emboss_codcmp.xml +++ b/tools/emboss_5/emboss_codcmp.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: codcmp12" name="codcmp" version="5.0.0"><description>Codon usage table comparison</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>codcmp -first $cfile1 -second $cfile2 -outfile $out_file1 -auto</command> + <command>codcmp -first '$cfile1' -second '$cfile2' -outfile '$out_file1' -auto</command><inputs><param name="cfile1" type="select"><label>Codon Usage File 1</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_coderet.xml --- a/tools/emboss_5/emboss_coderet.xml +++ b/tools/emboss_5/emboss_coderet.xml @@ -1,8 +1,8 @@ <tool id="EMBOSS: coderet13" name="coderet" version="5.0.0"><description>Extract CDS, mRNA and translations from feature tables</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> -  - <command>coderet -seqall $input1 -outfile $out_file1 -auto</command> +  + <command>coderet -seqall '$input1' -outfile '$out_file1' -auto</command><inputs><param format="data" name="input1" type="data"><label>On query</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_compseq.xml --- a/tools/emboss_5/emboss_compseq.xml +++ b/tools/emboss_5/emboss_compseq.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: compseq14" name="compseq" version="5.0.0"><description>Count composition of dimer/trimer/etc words in a sequence</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>compseq -sequence $input1 -outfile $out_file1 -word $word -frame $frame -auto</command> + <command>compseq -sequence '$input1' -outfile '$out_file1' -word '$word' -frame '$frame' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>On query</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_cpgplot.xml --- a/tools/emboss_5/emboss_cpgplot.xml +++ b/tools/emboss_5/emboss_cpgplot.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: cpgplot15" name="cpgplot" version="5.0.0"><description>Plot CpG rich areas</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command interpreter="perl">emboss_cpgplot_wrapper.pl cpgplot -sequence $input1 -window $window -minlen $minlen -minpc $minpc -outfile $outfile -graph png -goutfile $goutfile -outfeat $outfeat -minoe $minoe -auto</command> + <command interpreter="perl">emboss_cpgplot_wrapper.pl cpgplot -sequence '$input1' -window '$window' -minlen '$minlen' -minpc '$minpc' -outfile '$outfile' -graph png -goutfile '$goutfile' -outfeat '$outfeat' -minoe '$minoe' -auto</command><inputs><param format="data" name="input1" type="data"><label>On query</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_cpgreport.xml --- a/tools/emboss_5/emboss_cpgreport.xml +++ b/tools/emboss_5/emboss_cpgreport.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: cpgreport16" name="cpgreport" version="5.0.0"><description>Reports all CpG rich regions</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>cpgreport -sequence $input1 -outfile $out_file1 -outfeat $out_file2 -offormat3 $out_format2 -score $score -auto</command> + <command>cpgreport -sequence '$input1' -outfile '$out_file1' -outfeat '$out_file2' -offormat3 '$out_format2' -score '$score' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>On query</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_cusp.xml --- a/tools/emboss_5/emboss_cusp.xml +++ b/tools/emboss_5/emboss_cusp.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: cusp17" name="cusp" version="5.0.0"><description>Create a codon usage table</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>cusp -sequence $input1 -outfile $out_file1 -auto</command> + <command>cusp -sequence '$input1' -outfile '$out_file1' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>On query</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_cutseq.xml --- a/tools/emboss_5/emboss_cutseq.xml +++ b/tools/emboss_5/emboss_cutseq.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: cutseq18" name="cutseq" version="5.0.0"><description>Removes a specified section from a sequence</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>cutseq -sequence $input1 -outseq $out_file1 -from $from -to $to -osformat2 $out_format1 -auto</command> + <command>cutseq -sequence '$input1' -outseq '$out_file1' -from '$from' -to '$to' -osformat2 '$out_format1' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>On query</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_dan.xml --- a/tools/emboss_5/emboss_dan.xml +++ b/tools/emboss_5/emboss_dan.xml @@ -1,8 +1,8 @@ <tool id="EMBOSS: dan19" name="dan" version="5.0.0"><description>Calculates DNA RNA/DNA melting temperature</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command interpreter="perl">emboss_single_outputfile_wrapper.pl dan -sequence $input1 -windowsize $window -goutfile $out_file1 -graph png -plot $plot1 -shiftincrement $shift -dnaconc $dnaconc - -saltconc $saltconc -product $product -formamide $formamide -mismatch $mismatch -prodlen $prodlen -thermo $thermo -temperature $temperature -rna $rna -outfile $out_file1 -auto</command> + <command interpreter="perl">emboss_single_outputfile_wrapper.pl dan -sequence '$input1' -windowsize '$window' -goutfile '$out_file1' -graph png -plot '$plot1' -shiftincrement '$shift' -dnaconc '$dnaconc' + -saltconc '$saltconc' -product '$product' -formamide '$formamide' -mismatch '$mismatch' -prodlen '$prodlen' -thermo '$thermo' -temperature '$temperature' -rna '$rna' -outfile '$out_file1' -auto</command><inputs><param format="data" name="input1" type="data"><label>On query</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_degapseq.xml --- a/tools/emboss_5/emboss_degapseq.xml +++ b/tools/emboss_5/emboss_degapseq.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: degapseq20" name="degapseq" version="5.0.0"><description>Removes gap characters from sequences</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>degapseq -sequence $input1 -outseq $out_file1 -osformat2 $out_format1 -auto</command> + <command>degapseq -sequence '$input1' -outseq '$out_file1' -osformat2 '$out_format1' -auto</command><inputs><param format="data" name="input1" type="data"><label>On query</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_descseq.xml --- a/tools/emboss_5/emboss_descseq.xml +++ b/tools/emboss_5/emboss_descseq.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: descseq21" name="descseq" version="5.0.0"><description>Alter the name or description of a sequence</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>descseq -sequence $input1 -outseq $out_file1 -name "$seqname" -description "$desc" -append $append -osformat2 $out_format1 -auto</command> + <command>descseq -sequence '$input1' -outseq '$out_file1' -name '$seqname' -description '$desc' -append '$append' -osformat2 '$out_format1' -auto</command><inputs><param format="data" name="input1" type="data"><label>On query</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_diffseq.xml --- a/tools/emboss_5/emboss_diffseq.xml +++ b/tools/emboss_5/emboss_diffseq.xml @@ -1,8 +1,8 @@ <tool id="EMBOSS: diffseq22" name="diffseq" version="5.0.0"><description>Find differences between nearly identical sequences</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>diffseq -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize $wordsize -globaldifferences $globaldifferences -rformat3 - $out_format1 -offormat4 $out_format2 -offormat5 $out_format3 -auto</command> + <command>diffseq -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -aoutfeat '$out_file2' -boutfeat '$out_file3' -wordsize '$wordsize' -globaldifferences '$globaldifferences' -rformat3 + '$out_format1' -offormat4 '$out_format2' -offormat5 '$out_format3' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequence 1</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_digest.xml --- a/tools/emboss_5/emboss_digest.xml +++ b/tools/emboss_5/emboss_digest.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: digest23" name="digest" version="5.0.0"><description>Protein proteolytic enzyme or reagent cleavage digest</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>digest -seqall $input1 -outfile $out_file1 -menu $menu -unfavoured $unfavoured -overlap $overlap -allpartials $allpartials -rformat2 $out_format1 -auto</command> + <command>digest -seqall '$input1' -outfile '$out_file1' -menu '$menu' -unfavoured '$unfavoured' -overlap '$overlap' -allpartials '$allpartials' -rformat2 '$out_format1' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_dotmatcher.xml --- a/tools/emboss_5/emboss_dotmatcher.xml +++ b/tools/emboss_5/emboss_dotmatcher.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: dotmatcher24" name="dotmatcher" version="5.0.0"><description>Displays a thresholded dotplot of two sequences</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command interpreter="perl">emboss_single_outputfile_wrapper.pl dotmatcher -asequence $input1 -bsequence $input2 -goutfile $out_file1 -windowsize $windowsize -threshold $threshold -graph png -xygraph png + <command interpreter="perl">emboss_single_outputfile_wrapper.pl dotmatcher -asequence '$input1' -bsequence '$input2' -goutfile '$out_file1' -windowsize '$windowsize' -threshold '$threshold' -graph png -xygraph png -auto</command><inputs><param format="data" name="input1" type="data"> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_dotpath.xml --- a/tools/emboss_5/emboss_dotpath.xml +++ b/tools/emboss_5/emboss_dotpath.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: dotpath25" name="dotpath" version="5.0.0"><description>Non-overlapping wordmatch dotplot of two sequences</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command interpreter="perl">emboss_single_outputfile_wrapper.pl dotpath -asequence $input1 -bsequence $input2 -goutfile $out_file1 -wordsize $wordsize -overlaps $overlaps -boxit $boxit -graph png + <command interpreter="perl">emboss_single_outputfile_wrapper.pl dotpath -asequence '$input1' -bsequence '$input2' -goutfile '$out_file1' -wordsize '$wordsize' -overlaps '$overlaps' -boxit '$boxit' -graph png -auto</command><inputs><param format="data" name="input1" type="data"> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_dottup.xml --- a/tools/emboss_5/emboss_dottup.xml +++ b/tools/emboss_5/emboss_dottup.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: dottup26" name="dottup" version="5.0.0"><description>Displays a wordmatch dotplot of two sequences</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command interpreter="perl">emboss_single_outputfile_wrapper.pl dottup -asequence $input1 -bsequence $input2 -goutfile $out_file1 -wordsize $wordsize -boxit $boxit -graph png -xygraph png -auto</command> + <command interpreter="perl">emboss_single_outputfile_wrapper.pl dottup -asequence '$input1' -bsequence '$input2' -goutfile '$out_file1' -wordsize '$wordsize' -boxit '$boxit' -graph png -xygraph png -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequence 1</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_dreg.xml --- a/tools/emboss_5/emboss_dreg.xml +++ b/tools/emboss_5/emboss_dreg.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: dreg27" name="dreg" version="5.0.0"><description>Regular expression search of a nucleotide sequence</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>dreg -sequence $input1 -outfile $out_file1 -pattern "$pattern" -raccshow3 "no" -rusashow3 "no" -rdesshow3 "no" -auto</command> + <command>dreg -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -raccshow3 'no' -rusashow3 'no' -rdesshow3 'no' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequence 1</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_einverted.xml --- a/tools/emboss_5/emboss_einverted.xml +++ b/tools/emboss_5/emboss_einverted.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: einverted28" name="einverted" version="5.0.0"><description>Finds DNA inverted repeats</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>einverted -sequence $input1 -outfile $out_file1 -gap $gap -threshold $threshold -match $match -mismatch $mismatch -maxrepeat $maxrepeat -auto</command> + <command>einverted -sequence '$input1' -outfile '$out_file1' -gap '$gap' -threshold '$threshold' -match '$match' -mismatch '$mismatch' -maxrepeat '$maxrepeat' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>On query</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_epestfind.xml --- a/tools/emboss_5/emboss_epestfind.xml +++ b/tools/emboss_5/emboss_epestfind.xml @@ -1,8 +1,8 @@ <tool id="EMBOSS: epestfind29" name="epestfind" version="5.0.0"><description>Finds PEST motifs as potential proteolytic cleavage sites</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command interpreter="perl">emboss_single_outputfile_wrapper.pl epestfind -sequence $input1 -goutfile $ofile2 -outfile $ofile1 -window $window -order $order -potential $potential -poor $poor - -invalid $invalid -map $map -graph png -auto</command> + <command interpreter="perl">emboss_single_outputfile_wrapper.pl epestfind -sequence '$input1' -goutfile '$ofile2' -outfile '$ofile1' -window '$window' -order '$order' -potential '$potential' -poor '$poor' + -invalid '$invalid' -map '$map' -graph png -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_equicktandem.xml --- a/tools/emboss_5/emboss_equicktandem.xml +++ b/tools/emboss_5/emboss_equicktandem.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: equicktandem31" name="equicktandem" version="5.0.0"><description>Finds tandem repeats</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>equicktandem -sequence $input1 -outfile $out_file1 -origfile $ofile2 -maxrepeat $maxrepeat -threshold $threshold -rformat2 $out_format1 -auto</command> + <command>equicktandem -sequence '$input1' -outfile '$out_file1' -origfile '$ofile2' -maxrepeat '$maxrepeat' -threshold '$threshold' -rformat2 '$out_format1' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_est2genome.xml --- a/tools/emboss_5/emboss_est2genome.xml +++ b/tools/emboss_5/emboss_est2genome.xml @@ -1,8 +1,8 @@ <tool id="EMBOSS: est2genome32" name="est2genome" version="5.0.0"><description>Align EST and genomic DNA sequences</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>est2genome -estsequence $input1 -genomesequence $input2 -outfile $out_file1 -match $match -mismatch $mismatch -gappenalty $gappenalty -intronpenalty $intronpenalty -splicepenalty - $splicepenalty -minscore $minscore -reverse $reverse -splice $splice -mode $mode -best $best -shuffle $shuffle -seed $seed -align $align -width $width -auto</command> + <command>est2genome -estsequence '$input1' -genomesequence '$input2' -outfile '$out_file1' -match '$match' -mismatch '$mismatch' -gappenalty '$gappenalty' -intronpenalty '$intronpenalty' -splicepenalty + ''$splice'penalty' -minscore '$minscore' -reverse '$reverse' -splice '$splice' -mode '$mode' -best '$best' -shuffle '$shuffle' -seed '$seed' -align '$align' -width '$width' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>EST sequence(s)</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_etandem.xml --- a/tools/emboss_5/emboss_etandem.xml +++ b/tools/emboss_5/emboss_etandem.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: etandem33" name="etandem" version="5.0.0"><description>Looks for tandem repeats in a nucleotide sequence</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>etandem -sequence $input1 -outfile $out_file1 -origfile $ofile2 -minrepeat $minrepeat -maxrepeat $maxrepeat -threshold $threshold -mismatch $mismatch -uniform $uniform -rformat2 $out_format1 -auto</command> + <command>etandem -sequence '$input1' -outfile '$out_file1' -origfile '$ofile2' -minrepeat '$minrepeat' -maxrepeat '$maxrepeat' -threshold '$threshold' -mismatch '$mismatch' -uniform '$uniform' -rformat2 '$out_format1' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_extractfeat.xml --- a/tools/emboss_5/emboss_extractfeat.xml +++ b/tools/emboss_5/emboss_extractfeat.xml @@ -2,8 +2,8 @@ <description>Extract features from a sequence</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>extractfeat -sequence $input1 -outseq $out_file1 -before $before -after $after -source "$source" -type "$type" -sense $sense -minscore $minscore -maxscore $maxscore -tag "$tag" -value - "$value" -join $join -featinname $featinname -describe "$describe" -osformat2 $out_format1 -auto</command> + <command>extractfeat -sequence '$input1' -outseq '$out_file1' -before '$before' -after '$after' -source '$source' -type '$type' -sense '$sense' -minscore '$minscore' -maxscore '$maxscore' -tag '$tag' -value + '$value' -join '$join' -featinname '$featinname' -describe '$describe' -osformat2 '$out_format1' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_extractseq.xml --- a/tools/emboss_5/emboss_extractseq.xml +++ b/tools/emboss_5/emboss_extractseq.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: extractseq35" name="extractseq" version="5.0.0"><description>Extract regions from a sequence</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>extractseq -sequence $input1 -outseq $out_file1 -regions $regions -separate $separate -osformat2 $out_format1 -auto</command> + <command>extractseq -sequence '$input1' -outseq '$out_file1' -regions '$regions' -separate '$separate' -osformat2 '$out_format1' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_freak.xml --- a/tools/emboss_5/emboss_freak.xml +++ b/tools/emboss_5/emboss_freak.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: freak36" name="freak" version="5.0.0"><description>Residue/base frequency table or plot</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>freak -seqall $input1 -outfile $out_file1 -window $window -letters $letters -graph png -step $step -auto</command> + <command>freak -seqall '$input1' -outfile '$out_file1' -window '$window' -letters '$letters' -graph png -step '$step' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_fuzznuc.xml --- a/tools/emboss_5/emboss_fuzznuc.xml +++ b/tools/emboss_5/emboss_fuzznuc.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: fuzznuc37" name="fuzznuc" version="5.0.1"><description>Nucleic acid pattern search</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>fuzznuc -sequence $input1 -outfile $out_file1 -pattern '$pattern' -pmismatch $mismatch -complement $complement -rformat2 $out_format1 -auto</command> + <command>fuzznuc -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -pmismatch '$mismatch' -complement '$complement' -rformat2 '$out_format1' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_fuzzpro.xml --- a/tools/emboss_5/emboss_fuzzpro.xml +++ b/tools/emboss_5/emboss_fuzzpro.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: fuzzpro38" name="fuzzpro" version="5.0.0"><description>Protein pattern search</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>fuzzpro -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -rformat2 $out_format1 -auto</command> + <command>fuzzpro -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -pmismatch '$mismatch' -rformat2 '$out_format1' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_fuzztran.xml --- a/tools/emboss_5/emboss_fuzztran.xml +++ b/tools/emboss_5/emboss_fuzztran.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: fuzztran39" name="fuzztran" version="5.0.0"><description>Protein pattern search after translation</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>fuzztran -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -frame $frame -table $table -rformat2 $out_format1 -auto</command> + <command>fuzztran -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -pmismatch '$mismatch' -frame '$frame' -table '$table' -rformat2 '$out_format1' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_garnier.xml --- a/tools/emboss_5/emboss_garnier.xml +++ b/tools/emboss_5/emboss_garnier.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: garnier40" name="garnier" version="5.0.0"><description>Predicts protein secondary structure</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>garnier -sequence $input1 -outfile $out_file1 -idc $idc -rformat2 $out_format1 -auto</command> + <command>garnier -sequence '$input1' -outfile '$out_file1' -idc '$idc' -rformat2 '$out_format1' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_geecee.xml --- a/tools/emboss_5/emboss_geecee.xml +++ b/tools/emboss_5/emboss_geecee.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: geecee41" name="geecee" version="5.0.0"><description>Calculates fractional GC content of nucleic acid sequences</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>geecee -sequence $input1 -outfile $out_file1 -auto</command> + <command>geecee -sequence '$input1' -outfile '$out_file1' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_getorf.xml --- a/tools/emboss_5/emboss_getorf.xml +++ b/tools/emboss_5/emboss_getorf.xml @@ -1,8 +1,8 @@ <tool id="EMBOSS: getorf42" name="getorf" version="5.0.0"><description>Finds and extracts open reading frames (ORFs)</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>getorf -sequence $input1 -outseq $out_file1 -table $table -minsize $minsize -maxsize $maxsize -find $find -methionine $methionine -circular $circular -reverse $reverse -flanking $flanking - -osformat2 $out_format1 -auto</command> + <command>getorf -sequence '$input1' -outseq '$out_file1' -table '$table' -minsize '$minsize' -maxsize '$maxsize' -find '$find' -methionine '$methionine' -circular '$circular' -reverse '$reverse' -flanking '$flanking' + -osformat2 '$out_format1' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_helixturnhelix.xml --- a/tools/emboss_5/emboss_helixturnhelix.xml +++ b/tools/emboss_5/emboss_helixturnhelix.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: helixturnhelix43" name="helixturnhelix" version="5.0.0"><description>Report nucleic acid binding motifs</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>helixturnhelix -sequence $input1 -outfile $out_file1 -mean $mean -sd $sd -minsd $minsd -eightyseven $eightyseven -rformat2 $out_format1 -auto</command> + <command>helixturnhelix -sequence '$input1' -outfile '$out_file1' -mean '$mean' -sd '$sd' -minsd '$minsd' -eightyseven '$eightyseven' -rformat2 '$out_format1' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_hmoment.xml --- a/tools/emboss_5/emboss_hmoment.xml +++ b/tools/emboss_5/emboss_hmoment.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: hmoment44" name="hmoment" version="5.0.0"><description>Hydrophobic moment calculation</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>hmoment -seqall $input1 -outfile $out_file1 -window $window -aangle $aangle -graph png -auto</command> + <command>hmoment -seqall '$input1' -outfile '$out_file1' -window '$window' -aangle '$aangle' -graph png -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_iep.xml --- a/tools/emboss_5/emboss_iep.xml +++ b/tools/emboss_5/emboss_iep.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: iep45" name="iep" version="5.0.0"><description>Calculates the isoelectric point of a protein</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>iep -sequence $input1 -outfile $out_file1 -step $step -amino $amino -graph png -termini $termini -auto</command> + <command>iep -sequence '$input1' -outfile '$out_file1' -step '$step' -amino '$amino' -graph png -termini '$termini' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_infoseq.xml --- a/tools/emboss_5/emboss_infoseq.xml +++ b/tools/emboss_5/emboss_infoseq.xml @@ -2,8 +2,8 @@ <description>Displays some simple information about sequences</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>infoseq -sequence $input1 -outfile $out_file1 -html $html_out1 -heading $heading -usa $usa -name $disname -accession $accession -gi $gi -version $version -type $type -length $length -pgc - $pgc -description $description -auto</command> + <command>infoseq -sequence '$input1' -outfile '$out_file1' -html '$html_out1' -heading '$heading' -usa '$usa' -name '$disname' -accession '$accession' -gi '$gi' -version '$version' -type '$type' -length '$length' -pgc + '$pgc' -description '$description' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_isochore.xml --- a/tools/emboss_5/emboss_isochore.xml +++ b/tools/emboss_5/emboss_isochore.xml @@ -1,8 +1,8 @@ <tool id="EMBOSS: isochore47" name="isochore" version="5.0.0"><description>Plots isochores in large DNA sequences</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command interpreter="perl">emboss_single_outputfile_wrapper.pl isochore -sequence $input1 -outfile $ofile2 -goutfile $ofile1 -graph png -window $window -shift $shift -auto</command> -  + <command interpreter="perl">emboss_single_outputfile_wrapper.pl isochore -sequence '$input1' -outfile '$ofile2' -goutfile '$ofile1' -graph png -window '$window' -shift '$shift' -auto</command> + <inputs><param format="fasta" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_lindna.xml --- a/tools/emboss_5/emboss_lindna.xml +++ b/tools/emboss_5/emboss_lindna.xml @@ -2,9 +2,9 @@ <description>Draws linear maps of DNA constructs</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>lindna -infile $input1 -graphout png -goutfile $out_file1 -ruler $ruler -blocktype $blocktype -maxgroups $maxgroups -maxlabels $maxlabels -intersymbol $intersymbol -intercolour $intercolour - -interticks $interticks -gapsize $gapsize -ticklines $ticklines -textheight $textheight -textlength $textlength -margin $margin -tickheight $tickheight -blockheight $blockheight -rangeheight - $rangeheight -gapgroup $gapgroup -postext $postext -auto</command> + <command>lindna -infile '$input1' -graphout png -goutfile '$out_file1' -ruler '$ruler' -blocktype '$blocktype' -maxgroups '$maxgroups' -maxlabels '$maxlabels' -intersymbol '$intersymbol' -intercolour '$intercolour' + -interticks '$interticks' -gapsize '$gapsize' -ticklines '$ticklines' -textheight '$textheight' -textlength '$textlength' -margin '$margin' -tickheight '$tickheight' -blockheight '$blockheight' -rangeheight + '$rangeheight' -gapgroup '$gapgroup' -postext '$postext' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_marscan.xml --- a/tools/emboss_5/emboss_marscan.xml +++ b/tools/emboss_5/emboss_marscan.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: marscan49" name="marscan" version="5.0.0"><description>Finds MAR/SAR sites in nucleic sequences</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>marscan -sequence $input1 -outfile $out_file1 -rformat2 $out_format1 -auto</command> + <command>marscan -sequence '$input1' -outfile '$out_file1' -rformat2 '$out_format1' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_maskfeat.xml --- a/tools/emboss_5/emboss_maskfeat.xml +++ b/tools/emboss_5/emboss_maskfeat.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: maskfeat50" name="maskfeat" version="5.0.0"><description>Mask off features of a sequence</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>maskfeat -sequence $input1 -outseq $out_file1 -type "$type" -tolower $tolower -maskchar "$maskchar" -osformat2 $out_format1 -auto</command> + <command>maskfeat -sequence '$input1' -outseq '$out_file1' -type '$type' -tolower '$tolower' -maskchar '$maskchar' -osformat2 '$out_format1' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_maskseq.xml --- a/tools/emboss_5/emboss_maskseq.xml +++ b/tools/emboss_5/emboss_maskseq.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: maskseq51" name="maskseq" version="5.0.0"><description>Mask off regions of a sequence</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>maskseq -sequence $input1 -outseq $out_file1 -regions "$regions" -tolower $tolower -maskchar "$maskchar" -osformat2 $out_format1 -auto</command> + <command>maskseq -sequence '$input1' -outseq '$out_file1' -regions '$regions' -tolower '$tolower' -maskchar '$maskchar' -osformat2 '$out_format1' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_matcher.xml --- a/tools/emboss_5/emboss_matcher.xml +++ b/tools/emboss_5/emboss_matcher.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: matcher52" name="matcher" version="5.0.0"><description>Finds the best local alignments between two sequences</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>matcher -asequence $input1 -bsequence $input2 -outfile $out_file1 -alternatives $alternatives -gapopen $gapopen -gapextend $gapextend -aformat3 $out_format1 -auto</command> + <command>matcher -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -alternatives '$alternatives' -gapopen '$gapopen' -gapextend '$gapextend' -aformat3 '$out_format1' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequence 1</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_megamerger.xml --- a/tools/emboss_5/emboss_megamerger.xml +++ b/tools/emboss_5/emboss_megamerger.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: megamerger53" name="megamerger" version="5.0.0"><description>Merge two large overlapping nucleic acid sequences</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>megamerger -asequence $input1 -bsequence $input2 -outseq $out_file1 -outfile $out_file2 -wordsize $wordsize -prefer $prefer -osformat3 $out_format1 -auto</command> + <command>megamerger -asequence '$input1' -bsequence '$input2' -outseq '$out_file1' -outfile '$out_file2' -wordsize '$wordsize' -prefer '$prefer' -osformat3 '$out_format1' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequence 1</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_merger.xml --- a/tools/emboss_5/emboss_merger.xml +++ b/tools/emboss_5/emboss_merger.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: merger54" name="merger" version="5.0.0"><description>Merge two overlapping nucleic acid sequences</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>merger -asequence $input1 -bsequence $input2 -outseq $out_file1 -outfile $out_file2 -gapopen $gapopen -gapextend $gapextend -osformat4 $out_format1 -aformat3 $out_format2 -auto</command> + <command>merger -asequence '$input1' -bsequence '$input2' -outseq '$out_file1' -outfile '$out_file2' -gapopen '$gapopen' -gapextend '$gapextend' -osformat4 '$out_format1' -aformat3 '$out_format2' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequence 1</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_msbar.xml --- a/tools/emboss_5/emboss_msbar.xml +++ b/tools/emboss_5/emboss_msbar.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: msbar55" name="msbar" version="5.0.0"><description>Mutate sequence beyond all recognition</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>msbar -sequence $input1 -outseq $out_file1 -count $count -point $point -block $block -codon $codon -inframe $inframe -minimum $minimum -maximum $maximum -osformat2 $out_format1 + <command>msbar -sequence '$input1' -outseq '$out_file1' -count '$count' -point '$point' -block '$block' -codon '$codon' -inframe '$inframe' -minimum '$minimum' -maximum '$maximum' -osformat2 '$out_format1' -auto</command><inputs><param format="fasta" name="input1" type="data"> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_needle.xml --- a/tools/emboss_5/emboss_needle.xml +++ b/tools/emboss_5/emboss_needle.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: needle56" name="needle" version="5.0.0"><description>Needleman-Wunsch global alignment</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>needle -asequence $input1 -bsequence $input2 -outfile $out_file1 -gapopen $gapopen -gapextend $gapextend -brief $brief -aformat3 $out_format1 -auto</command> + <command>needle -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -gapopen '$gapopen' -gapextend '$gapextend' -brief '$brief' -aformat3 '$out_format1' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Sequence 1</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_newcpgreport.xml --- a/tools/emboss_5/emboss_newcpgreport.xml +++ b/tools/emboss_5/emboss_newcpgreport.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: newcpgreport57" name="newcpgreport" version="5.0.0"><description>Report CpG rich areas</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>newcpgreport -sequence $input1 -window $window -shift $shift -minlen $minlen -minpc $minpc -outfile $out_file1 -minoe $minoe -auto</command> + <command>newcpgreport -sequence '$input1' -window '$window' -shift '$shift' -minlen '$minlen' -minpc '$minpc' -outfile '$out_file1' -minoe '$minoe' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_newcpgseek.xml --- a/tools/emboss_5/emboss_newcpgseek.xml +++ b/tools/emboss_5/emboss_newcpgseek.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: newcpgseek58" name="newcpgseek" version="5.0.0"><description>Reports CpG rich region</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>newcpgseek -sequence $input1 -outfile $out_file1 -score $score -auto</command> + <command>newcpgseek -sequence '$input1' -outfile '$out_file1' -score '$score' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_newseq.xml --- a/tools/emboss_5/emboss_newseq.xml +++ b/tools/emboss_5/emboss_newseq.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: newseq59" name="newseq" version="5.0.0"><description>Type in a short new sequence</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>newseq -outseq $out_file1 -name "$seqname" -description "$description" -type $type -sequence "$sequence" -osformat5 $out_format1 -auto</command> + <command>newseq -outseq '$out_file1' -name '$seqname' -description '$description' -type '$type' -sequence '$sequence' -osformat5 '$out_format1' -auto</command><inputs><param name="seqname" size="10" type="text" value=""><label>Name of of the sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_noreturn.xml --- a/tools/emboss_5/emboss_noreturn.xml +++ b/tools/emboss_5/emboss_noreturn.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: noreturn60" name="noreturn" version="5.0.0"><description>Removes carriage return from ASCII files</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>noreturn -infile $input1 -outfile $out_file1 -system $system -auto</command> + <command>noreturn -infile '$input1' -outfile '$out_file1' -system '$system' -auto</command><inputs><param format="data" name="input1" type="data"><label>On query</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_notseq.xml --- a/tools/emboss_5/emboss_notseq.xml +++ b/tools/emboss_5/emboss_notseq.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: notseq61" name="notseq" version="5.0.0"><description>Exclude a set of sequences and write out the remaining ones</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>notseq -sequence $input1 -outseq $out_file1 -exclude "$exclude" -osformat3 $out_format1 -auto</command> + <command>notseq -sequence '$input1' -outseq '$out_file1' -exclude '$exclude' -osformat3 '$out_format1' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>On query</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_nthseq.xml --- a/tools/emboss_5/emboss_nthseq.xml +++ b/tools/emboss_5/emboss_nthseq.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: nthseq62" name="nthseq" version="5.0.0"><description>Writes one sequence from a multiple set of sequences</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>nthseq -sequence $input1 -outseq $out_file1 -number $number -osformat2 $out_format1 -auto</command> + <command>nthseq -sequence '$input1' -outseq '$out_file1' -number '$number' -osformat2 '$out_format1' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_octanol.xml --- a/tools/emboss_5/emboss_octanol.xml +++ b/tools/emboss_5/emboss_octanol.xml @@ -2,8 +2,8 @@ <description>Displays protein hydropathy</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command interpreter="perl">emboss_single_outputfile_wrapper.pl octanol -sequence $input1 -graph png -goutfile $out_file1 -width $width -octanolplot $octanolplot -interfaceplot $interfaceplot - -differenceplot $differenceplot -auto</command> + <command interpreter="perl">emboss_single_outputfile_wrapper.pl octanol -sequence '$input1' -graph png -goutfile '$out_file1' -width '$width' -octanolplot '$octanolplot' -interfaceplot '$interfaceplot' + -differenceplot '$differenceplot' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_oddcomp.xml --- a/tools/emboss_5/emboss_oddcomp.xml +++ b/tools/emboss_5/emboss_oddcomp.xml @@ -2,7 +2,7 @@ <description>Find protein sequence regions with a biased composition</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>oddcomp -sequence $input1 -infile $input2 -outfile $out_file1 -window $window -ignorebz $ignorebz -auto</command> + <command>oddcomp -sequence '$input1' -infile '$input2' -outfile '$out_file1' -window '$window' -ignorebz '$ignorebz' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_palindrome.xml --- a/tools/emboss_5/emboss_palindrome.xml +++ b/tools/emboss_5/emboss_palindrome.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: palindrome65" name="palindrome" version="5.0.0"><description>Looks for inverted repeats in a nucleotide sequence</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>palindrome -sequence $input1 -outfile $out_file1 -minpallen $minpallen -maxpallen $maxpallen -gaplimit $gaplimit -nummismatches $nummismatches -overlap $overlap -auto</command> + <command>palindrome -sequence '$input1' -outfile '$out_file1' -minpallen '$minpallen' -maxpallen '$maxpallen' -gaplimit '$gaplimit' -nummismatches '$nummismatches' -overlap '$overlap' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_pasteseq.xml --- a/tools/emboss_5/emboss_pasteseq.xml +++ b/tools/emboss_5/emboss_pasteseq.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: pasteseq66" name="pasteseq" version="5.0.0"><description>Insert one sequence into another</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>pasteseq -asequence $input2 -bsequence $input1 -outseq $out_file1 -pos $pos -osformat3 $out_format1 -auto</command> + <command>pasteseq -asequence '$input2' -bsequence '$input1' -outseq '$out_file1' -pos '$pos' -osformat3 '$out_format1' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Main sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_patmatdb.xml --- a/tools/emboss_5/emboss_patmatdb.xml +++ b/tools/emboss_5/emboss_patmatdb.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: patmatdb67" name="patmatdb" version="5.0.0"><description>Search a protein sequence with a motif</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>patmatdb -sequence $input1 -outfile $out_file1 -motif "$motif" -rformat3 $out_format1 -auto</command> + <command>patmatdb -sequence '$input1' -outfile '$out_file1' -motif '$motif' -rformat3 '$out_format1' -auto</command><inputs><param format="data" name="input1" type="data"><label>Main sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_pepcoil.xml --- a/tools/emboss_5/emboss_pepcoil.xml +++ b/tools/emboss_5/emboss_pepcoil.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: pepcoil68" name="pepcoil" version="5.0.0"><description>Predicts coiled coil regions</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>pepcoil -sequence $input1 -outfile $out_file1 -window $window -coil $coil -frame $frame -other $other -auto</command> + <command>pepcoil -sequence '$input1' -outfile '$out_file1' -window '$window' -coil '$coil' -frame '$frame' -other '$other' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_pepinfo.xml --- a/tools/emboss_5/emboss_pepinfo.xml +++ b/tools/emboss_5/emboss_pepinfo.xml @@ -2,7 +2,7 @@ <description>Plots simple amino acid properties in parallel</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepinfo -sequence $input1 -outfile $out_file1 -goutfile $out_file2 -graph png -hwindow $hwindow $plot_type -auto</command> + <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepinfo -sequence '$input1' -outfile '$out_file1' -goutfile '$out_file2' -graph png -hwindow '$hwindow' '$plot_type' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_pepnet.xml --- a/tools/emboss_5/emboss_pepnet.xml +++ b/tools/emboss_5/emboss_pepnet.xml @@ -2,7 +2,7 @@ <description>Displays proteins as a helical net</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>pepnet -sequence $input1 -graph png -goutfile $out_file1 -squares $squares -diamonds $diamonds -octags $octags -amphipathic $amphipathic -auto</command> + <command>pepnet -sequence '$input1' -graph png -goutfile '$out_file1' -squares '$squares' -diamonds '$diamonds' -octags '$octags' -amphipathic '$amphipathic' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_pepstats.xml --- a/tools/emboss_5/emboss_pepstats.xml +++ b/tools/emboss_5/emboss_pepstats.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: pepstats71" name="pepstats" version="5.0.0"><description>Protein statistics</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>pepstats -sequence $input1 -outfile $out_file1 -termini $termini -auto</command> + <command>pepstats -sequence '$input1' -outfile '$out_file1' -termini '$termini' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_pepwheel.xml --- a/tools/emboss_5/emboss_pepwheel.xml +++ b/tools/emboss_5/emboss_pepwheel.xml @@ -2,8 +2,8 @@ <description>Shows protein sequences as helices</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepwheel -sequence $input1 -graph png -goutfile $out_file1 -squares $squares -diamonds $diamonds -octags $octags -amphipathic - $amphipathic -steps $steps -turns $turns -wheel $wheel -auto</command> + <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepwheel -sequence '$input1' -graph png -goutfile '$out_file1' -squares '$squares' -diamonds '$diamonds' -octags '$octags' -amphipathic + '$amphipathic' -steps '$steps' -turns '$turns' -wheel '$wheel' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_pepwindow.xml --- a/tools/emboss_5/emboss_pepwindow.xml +++ b/tools/emboss_5/emboss_pepwindow.xml @@ -2,7 +2,7 @@ <description>Displays protein hydropathy</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepwindow -sequence $input1 -graph png -goutfile $out_file1 -length $length -auto</command> + <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepwindow -sequence '$input1' -graph png -goutfile '$out_file1' -length '$length' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_pepwindowall.xml --- a/tools/emboss_5/emboss_pepwindowall.xml +++ b/tools/emboss_5/emboss_pepwindowall.xml @@ -2,7 +2,7 @@ <description>Displays protein hydropathy of a set of sequences</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepwindowall -sequence $input1 -graph png -goutfile $out_file1 -length $length -auto</command> + <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepwindowall -sequence '$input1' -graph png -goutfile '$out_file1' -length '$length' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_plotcon.xml --- a/tools/emboss_5/emboss_plotcon.xml +++ b/tools/emboss_5/emboss_plotcon.xml @@ -2,7 +2,7 @@ <description>Plot quality of conservation of a sequence alignment</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command interpreter="perl">emboss_single_outputfile_wrapper.pl plotcon -sequences $input1 -graph png -goutfile $out_file1 -winsize $winsize -auto</command> + <command interpreter="perl">emboss_single_outputfile_wrapper.pl plotcon -sequences '$input1' -graph png -goutfile '$out_file1' -winsize '$winsize' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_plotorf.xml --- a/tools/emboss_5/emboss_plotorf.xml +++ b/tools/emboss_5/emboss_plotorf.xml @@ -2,7 +2,7 @@ <description>Plot potential open reading frames</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command interpreter="perl">emboss_single_outputfile_wrapper.pl plotorf -sequence $input1 -graph png -goutfile $out_file1 -start $start -stop $stop -auto</command> + <command interpreter="perl">emboss_single_outputfile_wrapper.pl plotorf -sequence '$input1' -graph png -goutfile '$out_file1' -start '$start' -stop '$stop' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_polydot.xml --- a/tools/emboss_5/emboss_polydot.xml +++ b/tools/emboss_5/emboss_polydot.xml @@ -2,8 +2,8 @@ <description>Displays all-against-all dotplots of a set of sequences</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command interpreter="perl">emboss_single_outputfile_wrapper.pl polydot -sequence $input1 -graph png -goutfile $output2 -outfeat $output1 -wordsize $wordsize -boxit $boxit -dumpfeat yes -gap - $gap -auto</command> + <command interpreter="perl">emboss_single_outputfile_wrapper.pl polydot -sequence '$input1' -graph png -goutfile '$output2' -outfeat '$output1' -wordsize '$wordsize' -boxit '$boxit' -dumpfeat yes -gap + '$gap' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_preg.xml --- a/tools/emboss_5/emboss_preg.xml +++ b/tools/emboss_5/emboss_preg.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: preg78" name="preg" version="5.0.0"><description>Regular expression search of a protein sequence</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>preg -sequence $input1 -outfile $out_file1 -pattern "$pattern" -auto</command> + <command>preg -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequence 1</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_prettyplot.xml --- a/tools/emboss_5/emboss_prettyplot.xml +++ b/tools/emboss_5/emboss_prettyplot.xml @@ -2,9 +2,9 @@ <description>Displays aligned sequences, with colouring and boxing</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>prettyplot -sequences $input1 -graph png -goutfile $out_file1 -residuesperline $residuesperline -resbreak $resbreak -ccolours $ccolours -cidentity $cidentity -csimilarity $csimilarity - -cother $cother -docolour $docolour -gtitle $title -pair $pair -identity $identity -box $box -boxcol $boxcol -boxcolval $boxcolval -name $name -maxnamelen $maxnamelen -number $number -listoptions - $listoptions -consensus $consensus -collision $collision -alternative $alternative -showscore $showscore -portrait $portrait -auto</command> + <command>prettyplot -sequences '$input1' -graph png -goutfile '$out_file1' -residuesperline '$residuesperline' -resbreak '$resbreak' -ccolours '$ccolours' -cidentity '$cidentity' -csimilarity '$csimilarity' + -cother '$cother' -docolour '$docolour' -gtitle '$title' -pair '$pair' -identity '$identity' -box '$box' -boxcol '$box'col -boxcolval '$box'colval -name '$name' -maxnamelen '$maxnamelen' -number '$number' -listoptions + '$listoptions' -consensus '$consensus' -collision '$collision' -alternative '$alternative' -showscore '$showscore' -portrait '$portrait' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_prettyseq.xml --- a/tools/emboss_5/emboss_prettyseq.xml +++ b/tools/emboss_5/emboss_prettyseq.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: prettyseq80" name="prettyseq" version="5.0.0"><description>Output sequence with translated ranges</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>prettyseq -sequence $input1 -outfile $out_file1 -ruler $ruler -plabel $plabel -nlabel $nlabel -width $width -auto</command> + <command>prettyseq -sequence '$input1' -outfile '$out_file1' -ruler '$ruler' -plabel '$plabel' -nlabel '$nlabel' -width '$width' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_primersearch.xml --- a/tools/emboss_5/emboss_primersearch.xml +++ b/tools/emboss_5/emboss_primersearch.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: primersearch81" name="primersearch" version="5.0.0"><description>Searches DNA sequences for matches with primer pairs</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>primersearch -seqall $input1 -infile $input2 -outfile $out_file1 -mismatchpercent $mismatchpercent -auto</command> + <command>primersearch -seqall '$input1' -infile '$input2' -outfile '$out_file1' -mismatchpercent '$mismatchpercent' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Main sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_revseq.xml --- a/tools/emboss_5/emboss_revseq.xml +++ b/tools/emboss_5/emboss_revseq.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: revseq82" name="revseq" version="5.0.0"><description>Reverse and complement a sequence</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>revseq -sequence $input1 -outseq $out_file1 -reverse $reverse -complement $complement -osformat2 $out_format1 -auto</command> + <command>revseq -sequence '$input1' -outseq '$out_file1' -reverse '$reverse' -complement '$complement' -osformat2 '$out_format1' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_seqmatchall.xml --- a/tools/emboss_5/emboss_seqmatchall.xml +++ b/tools/emboss_5/emboss_seqmatchall.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: seqmatchall83" name="seqmatchall" version="5.0.0"><description>All-against-all comparison of a set of sequences</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>seqmatchall -sequence $input1 -outfile $out_file1 -wordsize $wordsize -aformat2 $out_format1 -auto</command> + <command>seqmatchall -sequence '$input1' -outfile '$out_file1' -wordsize '$wordsize' -aformat2 '$out_format1' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_seqret.xml --- a/tools/emboss_5/emboss_seqret.xml +++ b/tools/emboss_5/emboss_seqret.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: seqret84" name="seqret" version="5.0.0"><description>Reads and writes sequences</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>seqret -sequence $input1 -outseq $out_file1 -feature $feature -firstonly $firstonly -osformat2 $out_format1 -auto</command> + <command>seqret -sequence '$input1' -outseq '$out_file1' -feature '$feature' -firstonly '$firstonly' -osformat2 '$out_format1' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_showfeat.xml --- a/tools/emboss_5/emboss_showfeat.xml +++ b/tools/emboss_5/emboss_showfeat.xml @@ -2,9 +2,9 @@ <description>Show features of a sequence</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>showfeat -sequence $input1 -outfile $out_file1 -matchsource "$matchsource" -matchtype "$matchtype" -matchtag "$matchtag" -matchvalue "$matchvalue" -sort $sort -annotation "$annotation" -id - $id -description "$description" -scale "$scale" -width "$width" -collapse $collapse -forward $forward -reverse $reverse -unknown $unknown -strand $strand -source $source -position $position -type - $type -tags $tags -values $values -stricttags $stricttags -html $html_out1 -auto</command> + <command>showfeat -sequence '$input1' -outfile '$out_file1' -matchsource '$matchsource' -matchtype '$matchtype' -matchtag '$matchtag' -matchvalue '$matchvalue' -sort '$sort' -annotation '$annotation' -id + '$id' -description '$description' -scale '$scale' -width '$width' -collapse '$collapse' -forward '$forward' -reverse '$reverse' -unknown '$unknown' -strand '$strand' -source '$source' -position '$position' -type + '$type' -tags '$tags' -values '$values' -stricttags '$stricttags' -html '$html_out1' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_shuffleseq.xml --- a/tools/emboss_5/emboss_shuffleseq.xml +++ b/tools/emboss_5/emboss_shuffleseq.xml @@ -2,7 +2,7 @@ <description>Shuffles a set of sequences maintaining composition</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>shuffleseq -sequence $input1 -outseq $out_file1 -shuffle "$shuffle" -osformat2 $out_format1 -auto</command> + <command>shuffleseq -sequence '$input1' -outseq '$out_file1' -shuffle '$shuffle' -osformat2 '$out_format1' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_sigcleave.xml --- a/tools/emboss_5/emboss_sigcleave.xml +++ b/tools/emboss_5/emboss_sigcleave.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: sigcleave88" name="sigcleave" version="5.0.0"><description>Reports protein signal cleavage sites</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>sigcleave -sequence $input1 -outfile $out_file1 -minweight "$minweight" -prokaryote $prokaryote -rformat2 $out_format1 -auto</command> + <command>sigcleave -sequence '$input1' -outfile '$out_file1' -minweight '$minweight' -prokaryote '$prokaryote' -rformat2 '$out_format1' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_sirna.xml --- a/tools/emboss_5/emboss_sirna.xml +++ b/tools/emboss_5/emboss_sirna.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: sirna89" name="sirna" version="5.0.0"><description>Finds siRNA duplexes in mRNA</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>sirna -sequence $input1 -outfile $ofile1 -outseq $ofile2 -poliii $poliii -aa $aa -tt $tt -polybase $polybase -context $context -rformat2 $out_format1 -osformat3 $out_format2 + <command>sirna -sequence '$input1' -outfile '$ofile1' -outseq '$ofile2' -poliii '$poliii' -aa '$aa' -tt '$tt' -polybase '$polybase' -context '$context' -rformat2 '$out_format1' -osformat3 '$out_format2' -auto</command><inputs><param format="fasta" name="input1" type="data"> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_sixpack.xml --- a/tools/emboss_5/emboss_sixpack.xml +++ b/tools/emboss_5/emboss_sixpack.xml @@ -2,8 +2,8 @@ <description>Display a DNA sequence with 6-frame translation and ORFs</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>sixpack -sequence $input1 -outfile $ofile1 -outseq $ofile2 -table $table -firstorf $firstorf -lastorf $lastorf -mstart $mstart -reverse $reverse -orfminsize $orfminsize -uppercase - "$uppercase" -number $number -width "$width" -length "$length" -margin "$margin" -name $disp_name -description $description -offset "$offset" -html $html_out1 -osformat $out_format2 -auto</command> + <command>sixpack -sequence '$input1' -outfile '$ofile1' -outseq '$ofile2' -table '$table' -firstorf '$firstorf' -lastorf '$lastorf' -mstart '$mstart' -reverse '$reverse' -orfminsize '$orfminsize' -uppercase + '$uppercase' -number '$number' -width '$width' -length '$length' -margin '$margin' -name '$disp_name' -description '$description' -offset '$offset' -html '$html_out1' -osformat '$out_format2' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_skipseq.xml --- a/tools/emboss_5/emboss_skipseq.xml +++ b/tools/emboss_5/emboss_skipseq.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: skipseq91" name="skipseq" version="5.0.0"><description>Reads and writes sequences, skipping first few</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>skipseq -sequence $input1 -outseq $out_file1 -skip "$skip" -feature $feature -osformat2 $out_format1 -auto</command> + <command>skipseq -sequence '$input1' -outseq '$out_file1' -skip '$skip' -feature '$feature' -osformat2 '$out_format1' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_splitter.xml --- a/tools/emboss_5/emboss_splitter.xml +++ b/tools/emboss_5/emboss_splitter.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: splitter92" name="splitter" version="5.0.0"><description>Split a sequence into (overlapping) smaller sequences</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>splitter -sequence $input1 -outseq $out_file1 -size "$size" -overlap "$overlap" -addoverlap $addoverlap -osformat2 $out_format1 -auto</command> + <command>splitter -sequence '$input1' -outseq '$out_file1' -size '$size' -overlap '$overlap' -addoverlap '$addoverlap' -osformat2 '$out_format1' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_supermatcher.xml --- a/tools/emboss_5/emboss_supermatcher.xml +++ b/tools/emboss_5/emboss_supermatcher.xml @@ -2,8 +2,8 @@ <description>Match large sequences against one or more other sequences</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>supermatcher -asequence $input1 -bsequence $input2 -gapopen "$gapopen" -gapextend "$gapextend" -width "$width" -wordlen "$wordlen" -outfile $ofile1 -errorfile $ofile2 -aformat3 - $out_format1 -auto</command> + <command>supermatcher -asequence '$input1' -bsequence '$input2' -gapopen '$gapopen' -gapextend '$gapextend' -width '$width' -wordlen '$wordlen' -outfile '$ofile1' -errorfile '$ofile2' -aformat3 + '$out_format1' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Large sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_syco.xml --- a/tools/emboss_5/emboss_syco.xml +++ b/tools/emboss_5/emboss_syco.xml @@ -2,7 +2,7 @@ <description>Synonymous codon usage Gribskov statistic plot</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command interpreter="perl">emboss_single_outputfile_wrapper.pl syco -sequence $input1 -graph png -goutfile $ofile1 -outfile $ofile2 -cfile $cfile -window "$window" -uncommon $uncommon -minimum "$minimum" + <command interpreter="perl">emboss_single_outputfile_wrapper.pl syco -sequence '$input1' -graph png -goutfile '$ofile1' -outfile '$ofile2' -cfile '$cfile' -window '$window' -uncommon '$uncommon' -minimum '$minimum' -auto</command><inputs><param format="fasta" name="input1" type="data"> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_tcode.xml --- a/tools/emboss_5/emboss_tcode.xml +++ b/tools/emboss_5/emboss_tcode.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: tcode97" name="tcode" version="5.0.0"><description>Fickett TESTCODE statistic to identify protein-coding DNA</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>tcode -sequence $input1 -outfile $out_file1 -window "$window" -step "$step" -rformat $out_format1 -auto</command> + <command>tcode -sequence '$input1' -outfile '$out_file1' -window '$window' -step '$step' -rformat '$out_format1' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_textsearch.xml --- a/tools/emboss_5/emboss_textsearch.xml +++ b/tools/emboss_5/emboss_textsearch.xml @@ -1,8 +1,8 @@ <tool id="EMBOSS: textsearch98" name="textsearch" version="5.0.0"><description>Search sequence documentation. Slow, use SRS and Entrez!</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>textsearch -sequence $input1 -outfile $out_file1 -pattern "$pattern" -casesensitive -heading $heading -usa $usa -accession $accession -name $search_name -description $description -html - $html_out1 -auto</command> + <command>textsearch -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -casesensitive -heading '$heading' -usa '$usa' -accession '$accession' -name '$search_name' -description '$description' -html + '$html_out1' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_tmap.xml --- a/tools/emboss_5/emboss_tmap.xml +++ b/tools/emboss_5/emboss_tmap.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: tmap99" name="tmap" version="5.0.0"><description>Displays membrane spanning regions</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command interpreter="perl">emboss_single_outputfile_wrapper.pl tmap -sequences $input1 -outfile $out_file1 -goutfile $out_file2 -graph png -rformat $out_format1 -auto</command> + <command interpreter="perl">emboss_single_outputfile_wrapper.pl tmap -sequences '$input1' -outfile '$out_file1' -goutfile '$out_file2' -graph png -rformat '$out_format1' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_tranalign.xml --- a/tools/emboss_5/emboss_tranalign.xml +++ b/tools/emboss_5/emboss_tranalign.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: tranalign100" name="tranalign" version="5.0.0"><description>Align nucleic coding regions given the aligned proteins</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>tranalign -asequence $input1 -bsequence $input2 -outseq $out_file1 -table $table -osformat3 $out_format1 -auto</command> + <command>tranalign -asequence '$input1' -bsequence '$input2' -outseq '$out_file1' -table '$table' -osformat3 '$out_format1' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Nucleic Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_transeq.xml --- a/tools/emboss_5/emboss_transeq.xml +++ b/tools/emboss_5/emboss_transeq.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: transeq101" name="transeq" version="5.0.0"><description>Translate nucleic acid sequences</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>transeq -sequence $input1 -outseq $out_file1 -frame $frame -table $table -regions "$regions" -trim $trim -clean $clean -alternative $alternative -osformat2 $out_format1 -auto</command> + <command>transeq -sequence '$input1' -outseq '$out_file1' -frame '$frame' -table '$table' -regions '$regions' -trim '$trim' -clean '$clean' -alternative '$alternative' -osformat2 '$out_format1' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_trimest.xml --- a/tools/emboss_5/emboss_trimest.xml +++ b/tools/emboss_5/emboss_trimest.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: trimest102" name="trimest" version="5.0.0"><description>Trim poly-A tails off EST sequences</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>trimest -sequence $input1 -outseq $out_file1 -minlength "$minlength" -mismatches "$mismatches" -reverse $reverse -tolower $tolower -fiveprime $fiveprime -osformat2 $out_format1 + <command>trimest -sequence '$input1' -outseq '$out_file1' -minlength '$minlength' -mismatches '$mismatches' -reverse '$reverse' -tolower '$tolower' -fiveprime '$fiveprime' -osformat2 '$out_format1' -auto</command><inputs><param format="fasta" name="input1" type="data"> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_trimseq.xml --- a/tools/emboss_5/emboss_trimseq.xml +++ b/tools/emboss_5/emboss_trimseq.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: trimseq103" name="trimseq" version="5.0.0"><description>Trim ambiguous bits off the ends of sequences</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>trimseq -sequence $input1 -outseq $out_file1 -window "$window" -percent "$percent" -strict $strict -star $star -left $left -right $right -osformat2 $out_format1 -auto</command> + <command>trimseq -sequence '$input1' -outseq '$out_file1' -window '$window' -percent '$percent' -strict '$strict' -star '$star' -left '$left' -right '$right' -osformat2 '$out_format1' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_twofeat.xml --- a/tools/emboss_5/emboss_twofeat.xml +++ b/tools/emboss_5/emboss_twofeat.xml @@ -1,9 +1,9 @@ <tool id="EMBOSS: twofeat104" name="twofeat" version="5.0.0"><description>Finds neighbouring pairs of features in sequences</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>twofeat -sequence $input1 -outfile $out_file1 -atype "$atype" -btype "$btype" -minrange "$minrange" -maxrange "$maxrange" -asource "$asource" -asense $asense -aminscore "$aminscore" - -amaxscore "$amaxscore" -atag "$atag" -avalue "$avalue" -bsource "$bsource" -bsense "$bsense" -bminscore "$bminscore" -bmaxscore "$bmaxscore" -btag "$btag" -bvalue "$bvalue" -overlap $overlap - -rangetype $rangetype -sense $sense -order $order -twoout $twoout -typeout "$typeout" -rformat2 $out_format1 -auto</command> + <command>twofeat -sequence '$input1' -outfile '$out_file1' -atype '$atype' -btype '$btype' -minrange '$minrange' -maxrange '$maxrange' -asource '$asource' -asense '$asense' -aminscore '$aminscore' + -amaxscore '$amaxscore' -atag '$atag' -avalue '$avalue' -bsource '$bsource' -bsense '$bsense' -bminscore '$bminscore' -bmaxscore '$bmaxscore' -btag '$btag' -bvalue '$bvalue' -overlap '$overlap' + -rangetype '$rangetype' -sense '$sense' -order '$order' -twoout '$twoout' -typeout '$typeout' -rformat2 '$out_format1' -auto</command><inputs><param format="data" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_union.xml --- a/tools/emboss_5/emboss_union.xml +++ b/tools/emboss_5/emboss_union.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: union105" name="union" version="5.0.0"><description>Reads sequence fragments and builds one sequence</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>union -sequence $input1 -outseq $out_file1 -osformat2 $out_format1 -auto</command> + <command>union -sequence '$input1' -outseq '$out_file1' -osformat2 '$out_format1' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_vectorstrip.xml --- a/tools/emboss_5/emboss_vectorstrip.xml +++ b/tools/emboss_5/emboss_vectorstrip.xml @@ -1,8 +1,8 @@ <tool id="EMBOSS: vectorstrip106" name="vectorstrip" version="5.0.0"><description>Strips out DNA between a pair of vector sequences</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>vectorstrip -sequence $input1 -vectorsfile $input2 -outseq $ofile1 -outfile $ofile2 -vectorfile yes -mismatch "$mismatch" -besthits $besthits -linkera "$linkera" -linkerb - "$linkerb" -osformat4 $out_format1 -auto</command> + <command>vectorstrip -sequence '$input1' -vectorsfile '$input2' -outseq '$ofile1' -outfile '$ofile2' -vectorfile yes -mismatch '$mismatch' -besthits '$besthits' -linkera '$linkera' -linkerb + '$linkerb' -osformat4 '$out_format1' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Sequences</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_water.xml --- a/tools/emboss_5/emboss_water.xml +++ b/tools/emboss_5/emboss_water.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: water107" name="water" version="5.0.0"><description>Smith-Waterman local alignment</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>water -asequence $input1 -bsequence $input2 -outfile $out_file1 -gapopen "$gapopen" -gapextend "$gapextend" -brief $brief -aformat3 $out_format1 -auto</command> + <command>water -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -gapopen '$gapopen' -gapextend '$gapextend' -brief '$brief' -aformat3 '$out_format1' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Sequence 1</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_wobble.xml --- a/tools/emboss_5/emboss_wobble.xml +++ b/tools/emboss_5/emboss_wobble.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: wobble108" name="wobble" version="5.0.0"><description>Wobble base plot</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command interpreter="perl">emboss_single_outputfile_wrapper.pl wobble -sequence $input1 -graph png -goutfile $ofile1 -outfile $ofile2 -window "$window" -bases "$bases" -auto</command> + <command interpreter="perl">emboss_single_outputfile_wrapper.pl wobble -sequence '$input1' -graph png -goutfile '$ofile1' -outfile '$ofile2' -window '$window' -bases '$bases' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_wordcount.xml --- a/tools/emboss_5/emboss_wordcount.xml +++ b/tools/emboss_5/emboss_wordcount.xml @@ -1,7 +1,7 @@ <tool id="EMBOSS: wordcount109" name="wordcount" version="5.0.0"><description>Counts words of a specified size in a DNA sequence</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>wordcount -sequence $input1 -outfile $out_file1 -wordsize "$wordsize" -auto</command> + <command>wordcount -sequence '$input1' -outfile '$out_file1' -wordsize '$wordsize' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Sequence</label> diff -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe -r 4fbcfe913aea8a637dafe2bbbfe0287d62c5feca tools/emboss_5/emboss_wordmatch.xml --- a/tools/emboss_5/emboss_wordmatch.xml +++ b/tools/emboss_5/emboss_wordmatch.xml @@ -1,8 +1,8 @@ <tool id="EMBOSS: wordmatch110" name="wordmatch" version="5.0.0"><description>Finds all exact matches of a given size between 2 sequences</description><requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <command>wordmatch -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize "$wordsize" -aformat3 $out_format1 -offormat4 $out_format2 - -offormat5 $out_format3 -auto</command> + <command>wordmatch -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -aoutfeat '$out_file2' -boutfeat '$out_file3' -wordsize '$wordsize' -aformat3 '$out_format1' -offormat4 '$out_format2' + -offormat5 '$out_format3' -auto</command><inputs><param format="fasta" name="input1" type="data"><label>Sequence 1</label> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Trackster: standardize tile cache creation and size.
by Bitbucket 08 Dec '11

08 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c9eb9bb6f6b1/ changeset: c9eb9bb6f6b1 user: jgoecks date: 2011-12-08 15:00:47 summary: Trackster: standardize tile cache creation and size. affected #: 1 file diff -r e07f3bb09b89ad8803a4fe92e838e5914dd4a29a -r c9eb9bb6f6b1949a6885ea6637f06173b0b2eefe static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -374,8 +374,7 @@ DATA_CANNOT_RUN_TOOL = "Tool cannot be rerun: ", DATA_LOADING = "Loading data...", DATA_OK = "Ready for display", - CACHED_TILES_FEATURE = 10, - CACHED_TILES_LINE = 5, + TILE_CACHE_SIZE = 10, DATA_CACHE_SIZE = 20; /** @@ -2779,6 +2778,7 @@ this.filters_available = false; this.filters_visible = false; this.tool = (tool_dict !== undefined && obj_length(tool_dict) > 0 ? new Tool(this, tool_dict) : undefined); + this.tile_cache = new Cache(TILE_CACHE_SIZE); if (this.header_div) { // @@ -3173,8 +3173,6 @@ TiledTrack.call(this, "Composite Track", view, container); this.drawables = drawables; this.enabled = true; - // HACK: tile cache should be (but is not) set up in TiledTrack or earlier. - this.tile_cache = new Cache(CACHED_TILES_FEATURE); }; extend(CompositeTiledTrack.prototype, TiledTrack.prototype, { init: function() { @@ -3211,7 +3209,6 @@ this.data_url = reference_url; this.data_url_extra_params = {dbkey: view.dbkey}; this.data_manager = new ReferenceTrackDataManager(DATA_CACHE_SIZE, this, false); - this.tile_cache = new Cache(CACHED_TILES_LINE); }; extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, { build_header_div: function() {}, @@ -3262,7 +3259,6 @@ this.hda_ldda = hda_ldda; this.dataset_id = dataset_id; this.original_dataset_id = dataset_id; - this.tile_cache = new Cache(CACHED_TILES_LINE); this.left_offset = 0; // Define track configuration @@ -3447,7 +3443,6 @@ this.summary_draw_height = 30; this.inc_slots = {}; this.start_end_dct = {}; - this.tile_cache = new Cache(CACHED_TILES_FEATURE); this.left_offset = 200; // this.painter = painters.LinkedFeaturePainter; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: enable tracks to share data managers.
by Bitbucket 07 Dec '11

07 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e07f3bb09b89/ changeset: e07f3bb09b89 user: jgoecks date: 2011-12-07 21:50:58 summary: Trackster: enable tracks to share data managers. affected #: 1 file diff -r 841d163852cb799a5e11fbd3e29136275dd4516e -r e07f3bb09b89ad8803a4fe92e838e5914dd4a29a static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -1553,7 +1553,7 @@ view.overview_close.show(); view.resize_window(); }; - this.overview_drawable.init(); + view.overview_drawable.request_draw(); view.has_changes = true; }, /** Close and reset overview. */ @@ -2524,7 +2524,7 @@ * -------> ReadTrack * -------> VcfTrack */ -var Track = function(name, view, container, prefs, data_url, data_query_wait) { +var Track = function(name, view, container, prefs, data_manager, data_url, data_query_wait) { // For now, track's container is always view. Drawable.call(this, name, view, container, {}, "draghandle"); @@ -2535,9 +2535,7 @@ this.data_url_extra_params = {} this.data_query_wait = (data_query_wait ? data_query_wait : DEFAULT_DATA_QUERY_WAIT); this.dataset_check_url = converted_datasets_state_url; - - if (!Track.id_counter) { Track.id_counter = 0; } - this.id = Track.id_counter++; + this.data_manager = (data_manager ? data_manager : new DataManager(DATA_CACHE_SIZE, this)); // // Create content div, which is where track is displayed. @@ -2700,7 +2698,6 @@ track.enabled = false; track.tile_cache.clear(); track.data_manager.clear(); - track.initial_canvas = undefined; track.content_div.css("height", "auto"); /* if (!track.content_div.text()) { @@ -2767,8 +2764,8 @@ predraw_init: function() {} }); -var TiledTrack = function(name, view, container, prefs, filters_list, tool_dict) { - Track.call(this, name, view, container, prefs); +var TiledTrack = function(name, view, container, prefs, filters_list, tool_dict, data_manager) { + Track.call(this, name, view, container, prefs, data_manager); var track = this, view = track.view; @@ -2803,10 +2800,15 @@ }; extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, { /** - * Returns a copy of the track. + * Returns a copy of the track. The copy uses the same data manager so that the tracks can share data. */ - copy: function(container) { - return new this.constructor(this.name, this.view, container, this.hda_ldda, this.dataset_id, this.prefs, this.filters, this.tool); + copy: function(container) { + // Create copy. + var new_track = new this.constructor(this.name, this.view, container, this.hda_ldda, this.dataset_id, this.prefs, + this.filters, this.tool, this.data_manager); + // Misc. init and return. + new_track.enabled = this.enabled; + return new_track; }, /** * Convert track to JSON object. @@ -3247,11 +3249,11 @@ } }); -var LineTrack = function (name, view, container, hda_ldda, dataset_id, prefs) { +var LineTrack = function (name, view, container, hda_ldda, dataset_id, prefs, filters, tool, data_manager) { var track = this; this.display_modes = ["Histogram", "Line", "Filled", "Intensity"]; this.mode = "Histogram"; - TiledTrack.call( this, name, view, container, prefs ); + TiledTrack.call(this, name, view, container, prefs, filters, tool, data_manager); this.min_height_px = 16; this.max_height_px = 400; @@ -3260,7 +3262,6 @@ this.hda_ldda = hda_ldda; this.dataset_id = dataset_id; this.original_dataset_id = dataset_id; - this.data_manager = new DataManager(DATA_CACHE_SIZE, this); this.tile_cache = new Cache(CACHED_TILES_LINE); this.left_offset = 0; @@ -3400,7 +3401,7 @@ } }); -var FeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters, tool) { +var FeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters, tool, data_manager) { // // Preinitialization: do things that need to be done before calling Track and TiledTrack // initialization code. @@ -3411,7 +3412,7 @@ // // Initialization. // - TiledTrack.call(this, name, view, container, prefs, filters, tool); + TiledTrack.call(this, name, view, container, prefs, filters, tool, data_manager); // Define and restore track configuration. this.config = new DrawableConfig( { @@ -3447,7 +3448,6 @@ this.inc_slots = {}; this.start_end_dct = {}; this.tile_cache = new Cache(CACHED_TILES_FEATURE); - this.data_manager = new DataManager(DATA_CACHE_SIZE, this); this.left_offset = 200; // this.painter = painters.LinkedFeaturePainter; @@ -3810,8 +3810,8 @@ } }); -var VcfTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters, tool) { - FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters, tool); +var VcfTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters, tool, data_manager) { + FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters, tool, data_manager); this.config = new DrawableConfig( { track: this, @@ -3837,8 +3837,8 @@ extend(VcfTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype); -var ReadTrack = function (name, view, container, hda_ldda, dataset_id, prefs, filters) { - FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters); +var ReadTrack = function (name, view, container, hda_ldda, dataset_id, prefs, filters, data_manager) { + FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters, data_manager); var block_color = get_random_color(), Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Trackster: (a) bug fixes and refactoring and (b) prepartion for composite tracks.
by Bitbucket 07 Dec '11

07 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/841d163852cb/ changeset: 841d163852cb user: jgoecks date: 2011-12-07 17:31:51 summary: Trackster: (a) bug fixes and refactoring and (b) prepartion for composite tracks. affected #: 5 files diff -r b729f8f23f7aeb2c3005f6b260af5a49c38ac230 -r 841d163852cb799a5e11fbd3e29136275dd4516e static/images/fugue/layers-stack-bw.png Binary file static/images/fugue/layers-stack-bw.png has changed diff -r b729f8f23f7aeb2c3005f6b260af5a49c38ac230 -r 841d163852cb799a5e11fbd3e29136275dd4516e static/images/fugue/layers-stack.png Binary file static/images/fugue/layers-stack.png has changed diff -r b729f8f23f7aeb2c3005f6b260af5a49c38ac230 -r 841d163852cb799a5e11fbd3e29136275dd4516e static/june_2007_style/blue/trackster.css --- a/static/june_2007_style/blue/trackster.css +++ b/static/june_2007_style/blue/trackster.css @@ -57,6 +57,8 @@ .param-row{margin-top:0.2em;margin-left:1em;} .param-label{float:left;font-weight:bold;padding-top:0.2em;} .menu-button{margin:0px 4px 0px 4px;} +.layers-stack{background:transparent url(../images/fugue/layers-stack-bw.png) no-repeat;} +.layers-stack:hover{background:transparent url(../images/fugue/layers-stack.png) no-repeat;} .chevron-expand{background:transparent url(../images/fugue/chevron-expand-bw.png) no-repeat;} .chevron-expand:hover{background:transparent url(../images/fugue/chevron-expand.png) no-repeat;} .settings-icon{background:transparent url(../images/fugue/gear-bw.png) no-repeat;} diff -r b729f8f23f7aeb2c3005f6b260af5a49c38ac230 -r 841d163852cb799a5e11fbd3e29136275dd4516e static/june_2007_style/trackster.css.tmpl --- a/static/june_2007_style/trackster.css.tmpl +++ b/static/june_2007_style/trackster.css.tmpl @@ -298,6 +298,12 @@ .menu-button { margin: 0px 4px 0px 4px; } +.layers-stack { + background: transparent url(../images/fugue/layers-stack-bw.png) no-repeat; +} +.layers-stack:hover { + background:transparent url(../images/fugue/layers-stack.png) no-repeat; +} .chevron-expand { background: transparent url(../images/fugue/chevron-expand-bw.png) no-repeat; } diff -r b729f8f23f7aeb2c3005f6b260af5a49c38ac230 -r 841d163852cb799a5e11fbd3e29136275dd4516e static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -376,7 +376,7 @@ DATA_OK = "Ready for display", CACHED_TILES_FEATURE = 10, CACHED_TILES_LINE = 5, - CACHED_DATA = 5; + DATA_CACHE_SIZE = 20; /** * Round a number to a given number of decimal places. @@ -769,6 +769,13 @@ extend(Drawable.prototype, { init: function() {}, + can_draw: function() { + if (this.enabled && this.content_visible) { + return true; + } + + return false; + }, request_draw: function() {}, _draw: function() {}, to_json: function() {}, @@ -950,6 +957,19 @@ }; extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype, { + /* + action_icons_def: [ + // Create composite track from group's tracks. + { + name: "composite-icon", + title: "Show composite track", + css_class: "layers-stack", + on_click_fn: function(group) { + group.show_composite_track(); + } + } + ].concat(Drawable.prototype.action_icons_def), + */ build_container_div: function() { return $("<div/>").addClass("group").attr("id", "group_" + this.id).appendTo(this.container.content_div); }, @@ -959,14 +979,24 @@ this.name_div = $("<div/>").addClass("track-name").text(this.name).appendTo(header_div); return header_div; }, - hide_contents : function () { + hide_contents: function () { this.content_div.hide(); }, - show_contents : function() { + show_contents: function() { // Show the contents div and labels (if present) this.content_div.show(); // Request a redraw of the content this.request_draw(); + }, + update_icons: function() { + // TODO: only show icon for compositing if all tracks are the same type. + }, + /** + * Show composite track using group's tracks. + */ + show_composite_track: function() { + this.composite_track = new CompositeTiledTrack(this.drawables, this.view, this); + this.composite_track.request_draw(); } }); @@ -2532,7 +2562,7 @@ name: "overview_icon", title: "Set as overview", css_class: "overview-icon", - on_click_fn: function() { + on_click_fn: function(track) { track.view.set_overview(track); } }, @@ -2573,6 +2603,12 @@ // Remove track. Drawable.prototype.action_icons_def[2] ], + can_draw: function() { + if ( this.dataset_id && Drawable.prototype.can_draw.call(this) ) { + return true; + } + return false; + }, build_container_div: function () { return $("<div/>").addClass('track').attr("id", "track_" + this.id).css("position", "relative"); }, @@ -2807,7 +2843,7 @@ // // Show/hide filter icon. // - if (track.filters_available > 0) { + if (track.filters_available) { track.action_icons.filters_icon.show(); } else { @@ -2855,15 +2891,7 @@ * can manage drawing. */ _draw: function(force, clear_after) { - if (!this.enabled) { return; } - - // TODO: There should probably be a general way to disable content drawing - // for all drawables. However the button to toggle this is currently - // only present for Track instances. - if (!this.content_visible) { return; } - - // HACK: ReferenceTrack can draw without dataset ID, but other tracks cannot. - if ( !(this instanceof ReferenceTrack) && (!this.dataset_id) ) { return; } + if ( !this.can_draw() ) { return; } var low = this.view.low, high = this.view.high, @@ -3136,6 +3164,38 @@ } }); +/** + * A tiled track composed of multiple other tracks. + */ +var CompositeTiledTrack = function(drawables, view, container) { + TiledTrack.call(this, "Composite Track", view, container); + this.drawables = drawables; + this.enabled = true; + // HACK: tile cache should be (but is not) set up in TiledTrack or earlier. + this.tile_cache = new Cache(CACHED_TILES_FEATURE); +}; +extend(CompositeTiledTrack.prototype, TiledTrack.prototype, { + init: function() { + console.log("initing CompositeTiledTrack"); + this.enabled = true; + }, + can_draw: Drawable.prototype.can_draw, + draw_helper: function(force, width, tile_index, resolution, parent_element, w_scale, drawn_tiles, more_tile_data) { + // Check tile cache, if found show existing tile in correct position + var + key = this._gen_tile_cache_key(width, w_scale, tile_index), + tile = ( force ? undefined : this.tile_cache.get(key) ); + if (tile) { + this.show_tile(tile, parent_element, w_scale); + return tile; + } + + // TODO: Try to build tile. + + return tile; + } +}); + var ReferenceTrack = function (view) { TiledTrack.call(this, "reference", view, { content_div: view.top_labeltrack }, {}); @@ -3148,7 +3208,7 @@ this.content_div.css("border", "none"); this.data_url = reference_url; this.data_url_extra_params = {dbkey: view.dbkey}; - this.data_manager = new ReferenceTrackDataManager(CACHED_DATA, this, false); + this.data_manager = new ReferenceTrackDataManager(DATA_CACHE_SIZE, this, false); this.tile_cache = new Cache(CACHED_TILES_LINE); }; extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, { @@ -3157,6 +3217,7 @@ // Enable by default because there should always be data when drawing track. this.enabled = true; }, + can_draw: Drawable.prototype.can_draw, /** * Draw ReferenceTrack tile. */ @@ -3199,7 +3260,7 @@ this.hda_ldda = hda_ldda; this.dataset_id = dataset_id; this.original_dataset_id = dataset_id; - this.data_manager = new DataManager(CACHED_DATA, this); + this.data_manager = new DataManager(DATA_CACHE_SIZE, this); this.tile_cache = new Cache(CACHED_TILES_LINE); this.left_offset = 0; @@ -3386,7 +3447,7 @@ this.inc_slots = {}; this.start_end_dct = {}; this.tile_cache = new Cache(CACHED_TILES_FEATURE); - this.data_manager = new DataManager(20, this); + this.data_manager = new DataManager(DATA_CACHE_SIZE, this); this.left_offset = 200; // this.painter = painters.LinkedFeaturePainter; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Bugfix for the previous commit.
by Bitbucket 06 Dec '11

06 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b729f8f23f7a/ changeset: b729f8f23f7a user: natefoo date: 2011-12-06 19:01:03 summary: Bugfix for the previous commit. affected #: 3 files diff -r 5f044d41a8a74af74f36d020206f9807c55f0d34 -r b729f8f23f7aeb2c3005f6b260af5a49c38ac230 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -700,7 +700,7 @@ util.umask_fix_perms( path, self.app.config.umask, 0666, self.app.config.gid ) self.sa_session.flush() log.debug( 'job %d ended' % self.job_id ) - if self.app.config.cleanup_job in ( 'always', 'onsuccess' ): + if self.app.config.cleanup_job == 'always' or ( not stderr and self.app.config.cleanup_job == 'onsuccess' ): self.cleanup() def cleanup( self ): diff -r 5f044d41a8a74af74f36d020206f9807c55f0d34 -r b729f8f23f7aeb2c3005f6b260af5a49c38ac230 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -290,7 +290,7 @@ log.exception("Job wrapper finish method failed") # clean up the drm files - if self.app.config.cleanup_job == "always" or ( not stderr and self.app.config.cleanup_job == "onsuccess" )): + if self.app.config.cleanup_job == "always" or ( not stderr and self.app.config.cleanup_job == "onsuccess" ): self.cleanup( ( ofile, efile, job_file ) ) def fail_job( self, drm_job_state ): diff -r 5f044d41a8a74af74f36d020206f9807c55f0d34 -r b729f8f23f7aeb2c3005f6b260af5a49c38ac230 lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -519,7 +519,7 @@ pbs_job_state.job_wrapper.fail("Unable to finish job", exception=True) # clean up the pbs files - if self.app.config.cleanup_job == "always" or ( not stderr and self.app.config.cleanup_job == "onsuccess" )): + if self.app.config.cleanup_job == "always" or ( not stderr and self.app.config.cleanup_job == "onsuccess" ): self.cleanup( ( ofile, efile, job_file ) ) def fail_job( self, pbs_job_state ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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