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commit/galaxy-central: dan: UCSC BAM display will now pass the pairEndsByName attribute. Closes #455.
by Bitbucket 08 Dec '11
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_${DATASET_HASH}.bam.bai" metadata="bam_index" /><!-- UCSC expects index file to exist as bam_file_name.bai -->
- <param type="template" name="track" viewable="True">track type="bam" name="${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/
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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/
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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
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/
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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
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/
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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
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 $builds}</filter><!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --><url>${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" /><!-- UCSC expects index file to exist as bam_file_name.bai -->
- <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_${DATASET_HASH}.bam.bai" metadata="bam_index" /><!-- UCSC expects index file to exist as bam_file_name.bai -->
+ <param type="template" name="track" viewable="True">track type="bam" name="${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 $builds}</filter><!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --><url>${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 $builds}</filter><!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --><url>${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/
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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
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 -osformat2 $out_format1 -cds $cds -mrna $mrna -translation $translation -auto</command>-->
- <command>coderet -seqall $input1 -outfile $out_file1 -auto</command>
+ <!-- <command>coderet -seqall '$input1' -outfile '$out_file1' -osformat2 '$out_format1' -cds '$cds' -mrna '$mrna' -translation '$translation' -auto</command>-->
+ <command>coderet -seqall '$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 @@
<!-- tool tested with documentation, functional test not designed due to empty files resulting from test input sequences --><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 @@
<!-- info contains file information always --><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 -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>
+ <!-- <command interpreter="perl">emboss_single_outputfile_wrapper.pl isochore -sequence '$input1' -goutfile '$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 @@
<!-- tool produces memory error in ajmem.c --><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 @@
<!-- graphics output with filename, no functional tests added --><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 @@
<!-- output contains file location info, commented out functional tests --><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 @@
<!-- puts file info in output files --><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 @@
<!-- graphical output file with path information --><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 @@
<!-- produces png file --><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 @@
<!-- produces png file --><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 @@
<!-- produces png file --><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 @@
<!-- produces png file --><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 @@
<!-- produces png file output --><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 @@
<!-- produces png file, not added functional tests --><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 @@
<!-- produces png output with file name --><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 @@
<!-- tool gives memory errors --><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 @@
<!-- produces random outputs each time --><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 @@
<!-- tool adds file description and timestamp to output data --><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 @@
<!-- puts file information in output report --><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 @@
<!-- graphics output --><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/
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commit/galaxy-central: jgoecks: Trackster: standardize tile cache creation and size.
by Bitbucket 08 Dec '11
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/
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commit/galaxy-central: jgoecks: Trackster: enable tracks to share data managers.
by Bitbucket 07 Dec '11
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/
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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
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/
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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/
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