Mercurial > repos > jjohnson > mothur_toolsuite
changeset 25:bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
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--- a/mothur/lib/galaxy/datatypes/metagenomics.py Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/lib/galaxy/datatypes/metagenomics.py Wed May 16 12:28:44 2012 -0500 @@ -18,13 +18,42 @@ from galaxy import util from galaxy.datatypes.images import Html + log = logging.getLogger(__name__) ## Mothur Classes -class Otu( Tabular ): +class Otu( Text ): file_ext = 'otu' + MetadataElement( name="columns", default=0, desc="Number of columns", readonly=True, visible=True, no_value=0 ) + MetadataElement( name="labels", default=[], desc="Label Names", readonly=True, visible=True, no_value=[] ) + def __init__(self, **kwd): + Text.__init__( self, **kwd ) + def set_meta( self, dataset, overwrite = True, **kwd ): + if dataset.has_data(): + label_names = set() + ncols = 0 + data_lines = 0 + comment_lines = 0 + try: + fh = open( dataset.file_name ) + for line in fh: + fields = line.strip().split('\t') + if len(fields) >= 2: + data_lines += 1 + ncols = max(ncols,len(fields)) + label_names.add(fields[0]) + else: + comment_lines += 1 + # Set the discovered metadata values for the dataset + dataset.metadata.data_lines = data_lines + dataset.metadata.columns = ncols + dataset.metadata.labels = [] + dataset.metadata.labels += label_names + dataset.metadata.labels.sort() + finally: + fh.close() def sniff( self, filename ): """ @@ -63,10 +92,25 @@ class OtuList( Otu ): file_ext = 'list' + def __init__(self, **kwd): + Otu.__init__( self, **kwd ) + def init_meta( self, dataset, copy_from=None ): + Otu.init_meta( self, dataset, copy_from=copy_from ) + def set_meta( self, dataset, overwrite = True, **kwd ): + Otu.set_meta(self,dataset, overwrite = True, **kwd ) + """ + # too many columns to be stored in metadata + if dataset != None and dataset.metadata.columns > 2: + for i in range(2,dataset.metadata.columns): + dataset.metadata.column_types[i] = 'str' + """ class Sabund( Otu ): file_ext = 'sabund' - + def __init__(self, **kwd): + Otu.__init__( self, **kwd ) + def init_meta( self, dataset, copy_from=None ): + Otu.init_meta( self, dataset, copy_from=copy_from ) def sniff( self, filename ): """ Determines whether the file is a otu (operational taxonomic unit) format @@ -108,33 +152,71 @@ class Rabund( Sabund ): file_ext = 'rabund' + def __init__(self, **kwd): + Sabund.__init__( self, **kwd ) + def init_meta( self, dataset, copy_from=None ): + Sabund.init_meta( self, dataset, copy_from=copy_from ) class GroupAbund( Otu ): file_ext = 'grpabund' + MetadataElement( name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[] ) + def __init__(self, **kwd): + Otu.__init__( self, **kwd ) + # self.column_names[0] = ['label'] + # self.column_names[1] = ['group'] + # self.column_names[2] = ['count'] + """ + def init_meta( self, dataset, copy_from=None ): + Otu.init_meta( self, dataset, copy_from=copy_from ) + """ def init_meta( self, dataset, copy_from=None ): Otu.init_meta( self, dataset, copy_from=copy_from ) def set_meta( self, dataset, overwrite = True, skip=1, max_data_lines = 100000, **kwd ): # See if file starts with header line if dataset.has_data(): + label_names = set() + group_names = set() + data_lines = 0 + comment_lines = 0 + ncols = 0 try: fh = open( dataset.file_name ) line = fh.readline() - line = line.strip() - linePieces = line.split('\t') - if linePieces[0] == 'label' and linePieces[1] == 'Group': + fields = line.strip().split('\t') + ncols = max(ncols,len(fields)) + if fields[0] == 'label' and fields[1] == 'Group': skip=1 + comment_lines += 1 else: skip=0 + data_lines += 1 + label_names.add(fields[0]) + group_names.add(fields[1]) + for line in fh: + data_lines += 1 + fields = line.strip().split('\t') + ncols = max(ncols,len(fields)) + label_names.add(fields[0]) + group_names.add(fields[1]) + # Set the discovered metadata values for the dataset + dataset.metadata.data_lines = data_lines + dataset.metadata.columns = ncols + dataset.metadata.labels = [] + dataset.metadata.labels += label_names + dataset.metadata.labels.sort() + dataset.metadata.groups = [] + dataset.metadata.groups += group_names + dataset.metadata.groups.sort() + dataset.metadata.skip = skip finally: fh.close() - Otu.set_meta( self, dataset, overwrite, skip, max_data_lines, **kwd) + def sniff( self, filename, vals_are_int=False): """ Determines whether the file is a otu (operational taxonomic unit) Shared format label<TAB>group<TAB>count[<TAB>value(1..n)] The first line is column headings as of Mothur v 1.20 """ - log.info( "sniff GroupAbund vals_are_int %s" % vals_are_int) try: fh = open( filename ) count = 0 @@ -174,8 +256,10 @@ class SharedRabund( GroupAbund ): file_ext = 'shared' - - + def __init__(self, **kwd): + GroupAbund.__init__( self, **kwd ) + def init_meta( self, dataset, copy_from=None ): + GroupAbund.init_meta( self, dataset, copy_from=copy_from ) def sniff( self, filename ): """ Determines whether the file is a otu (operational taxonomic unit) Shared format @@ -184,13 +268,15 @@ """ # return GroupAbund.sniff(self,filename,True) isme = GroupAbund.sniff(self,filename,True) - log.info( "is SharedRabund %s" % isme) return isme class RelAbund( GroupAbund ): file_ext = 'relabund' - + def __init__(self, **kwd): + GroupAbund.__init__( self, **kwd ) + def init_meta( self, dataset, copy_from=None ): + GroupAbund.init_meta( self, dataset, copy_from=copy_from ) def sniff( self, filename ): """ Determines whether the file is a otu (operational taxonomic unit) Relative Abundance format @@ -199,7 +285,6 @@ """ # return GroupAbund.sniff(self,filename,False) isme = GroupAbund.sniff(self,filename,False) - log.info( "is RelAbund %s" % isme) return isme class SecondaryStructureMap(Tabular): @@ -346,8 +431,21 @@ class DistanceMatrix( Text ): file_ext = 'dist' """Add metadata elements""" - MetadataElement( name="sequence_count", default=0, desc="Number of sequences", readonly=False, optional=True, no_value=0 ) + MetadataElement( name="sequence_count", default=0, desc="Number of sequences", readonly=True, visible=True, optional=True, no_value='?' ) + + def init_meta( self, dataset, copy_from=None ): + Text.init_meta( self, dataset, copy_from=copy_from ) + def set_meta( self, dataset, overwrite = True, skip = 0, **kwd ): + Text.set_meta(self, dataset,overwrite = overwrite, skip = skip, **kwd ) + try: + fh = open( dataset.file_name ) + line = fh.readline().strip().strip() + dataset.metadata.sequence_count = int(line) + except Exception, e: + log.warn("DistanceMatrix set_meta %s" % e) + finally: + fh.close() class LowerTriangleDistanceMatrix(DistanceMatrix): file_ext = 'lower.dist' @@ -355,6 +453,9 @@ """Initialize secondary structure map datatype""" DistanceMatrix.__init__( self, **kwd ) + def init_meta( self, dataset, copy_from=None ): + DistanceMatrix.init_meta( self, dataset, copy_from=copy_from ) + def sniff( self, filename ): """ Determines whether the file is a lower-triangle distance matrix (phylip) format @@ -396,17 +497,13 @@ fh.close() return False -class SquareDistanceMatrix(DistanceMatrix,Tabular): +class SquareDistanceMatrix(DistanceMatrix): file_ext = 'square.dist' - sequence_count = -1 def __init__(self, **kwd): - """Initialize secondary structure map datatype""" - Tabular.__init__( self, **kwd ) + DistanceMatrix.__init__( self, **kwd ) def init_meta( self, dataset, copy_from=None ): - Text.init_meta( self, dataset, copy_from=copy_from ) - def set_meta( self, dataset, overwrite = True, skip = None, **kwd ): - dataset.metadata.sequences = 0 + DistanceMatrix.init_meta( self, dataset, copy_from=copy_from ) def sniff( self, filename ): """ @@ -460,7 +557,8 @@ Tabular.__init__( self, **kwd ) self.column_names = ['Sequence','Sequence','Distance'] self.column_types = ['str','str','float'] - self.comment_lines = 1 + def set_meta( self, dataset, overwrite = True, skip = None, **kwd ): + Tabular.set_meta(self, dataset,overwrite = overwrite, skip = skip, **kwd ) def sniff( self, filename ): """ @@ -522,19 +620,30 @@ class Group(Tabular): file_ext = 'groups' + MetadataElement( name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[] ) def __init__(self, **kwd): - """Name file shows the relationship between a representative sequence(col 1) and the sequences it represents(col 2)""" + """Group file assigns sequence (col 1) to a group (col 2)""" Tabular.__init__( self, **kwd ) self.column_names = ['name','group'] self.columns = 2 + def set_meta( self, dataset, overwrite = True, skip = None, max_data_lines = None, **kwd ): + Tabular.set_meta(self, dataset, overwrite, skip, max_data_lines) + group_names = set() + try: + fh = open( dataset.file_name ) + for line in fh: + fields = line.strip().split('\t') + group_names.add(fields[1]) + dataset.metadata.groups = [] + dataset.metadata.groups += group_names + finally: + fh.close() -class Design(Tabular): +class Design(Group): file_ext = 'design' def __init__(self, **kwd): - """Name file shows the relationship between a group(col 1) and a grouping (col 2), providing a way to merge groups.""" - Tabular.__init__( self, **kwd ) - self.column_names = ['group','grouping'] - self.columns = 2 + """Design file shows the relationship between a group(col 1) and a grouping (col 2), providing a way to merge groups.""" + Group.__init__( self, **kwd ) class AccNos(Tabular): file_ext = 'accnos' @@ -634,8 +743,6 @@ Tabular.__init__( self, **kwd ) self.column_names = ['num','ten','twentyfive','fifty','seventyfive','ninetyfive','ninetynine'] self.column_types = ['int','float','float','float','float','float','float'] - def set_meta( self, dataset, overwrite = True, skip = None, **kwd ): - log.info( "Mothur Quantile set_meta %s" % kwd) def sniff( self, filename ): """ Determines whether the file is a quantiles tabular format for chimera analysis
--- a/mothur/tools/mothur/bin.seqs.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/bin.seqs.xml Wed May 16 12:28:44 2012 -0500 @@ -24,9 +24,8 @@ <param name="otu" type="data" format="list" label="list - OTU List"/> <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> <param name="group" type="data" format="group" optional="true" label="group - Sequences Name reference"/>
--- a/mothur/tools/mothur/classify.otu.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/classify.otu.xml Wed May 16 12:28:44 2012 -0500 @@ -67,9 +67,8 @@ </when> </conditional> <param name="label" type="select" label="label - OTU Labels" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> <param name="cutoff" type="integer" value="60" label="cutoff - Confindence percentage cutoff between 1 and 100">
--- a/mothur/tools/mothur/collect.shared.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/collect.shared.xml Wed May 16 12:28:44 2012 -0500 @@ -26,20 +26,14 @@ <param name="otu" type="data" format="shared" label="shared - OTU Shared"/> <param name="label" type="select" label="label - OTU Label filter" multiple="true"> <help>To filter: select labels to include</help> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/> - <filter type="unique_value" name="unq_lbl" column="0" /> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> <param name="groups" type="select" label="groups - Groups filter (uses all groups if none are selected)" multiple="true"> <help>To filter: select select at least 2 groups</help> - <options from_dataset="otu"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="otu" key="groups" /> </options> </param> <param name="calc" type="select" label="calc - Calculators (Uses defaults if none are selected)" multiple="true">
--- a/mothur/tools/mothur/collect.single.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/collect.single.xml Wed May 16 12:28:44 2012 -0500 @@ -37,10 +37,8 @@ <inputs> <param name="otu" type="data" format="list,rabund,sabund,shared" label="list,rabund,sabund,shared - OTU List"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="unique_value" name="unq_lbl" column="0" /> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
--- a/mothur/tools/mothur/consensus.seqs.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/consensus.seqs.xml Wed May 16 12:28:44 2012 -0500 @@ -35,9 +35,8 @@ <when value="yes"> <param name="list" type="data" format="list" label="list - OTU List"/> <param name="label" type="select" optional="true" label="label - OTU Labels" multiple="true"> - <options from_dataset="list"> - <column name="name" index="0"/> - <column name="value" index="0"/> + <options> + <filter type="data_meta" ref="list" key="labels" /> </options> </param> </when>
--- a/mothur/tools/mothur/corr.axes.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/corr.axes.xml Wed May 16 12:28:44 2012 -0500 @@ -38,19 +38,13 @@ <when value="shared"> <param name="otu" type="data" format="shared,relabund" label="shared or relabund - OTU Shared or Relabund"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/> - <filter type="unique_value" name="unq_lbl" column="0" /> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> <param name="groups" type="select" label="groups - Pairwise comparision groups" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="otu" key="groups" /> </options> </param> </when>
--- a/mothur/tools/mothur/count.groups.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/count.groups.xml Wed May 16 12:28:44 2012 -0500 @@ -32,10 +32,8 @@ <when value="groups"> <param name="groups" type="select" label="groups - Pick groups to include" multiple="true"> <help>All groups displayed if none are selected.</help> - <options from_dataset="group"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="group" key="groups" /> </options> </param> </when>
--- a/mothur/tools/mothur/count.seqs.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/count.seqs.xml Wed May 16 12:28:44 2012 -0500 @@ -23,10 +23,8 @@ <param name="group" type="data" format="groups" label="group - Group file for the tree"/> <param name="groups" type="select" label="groups - Groups to display" multiple="true"> <help>All groups displayed if none are selected.</help> - <options from_dataset="group"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="group" key="groups" /> </options> </param> </when>
--- a/mothur/tools/mothur/dist.shared.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/dist.shared.xml Wed May 16 12:28:44 2012 -0500 @@ -36,19 +36,13 @@ <!-- list,group or shared --> <param name="otu" type="data" format="shared" label="shared - OTU Shared"/> <param name="label" type="select" label="label - OTU Labels to calculate" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/> - <filter type="unique_value" name="unq_lbl" column="0" /> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> <param name="groups" type="select" label="groups - Groups to analyze" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="otu" key="groups" /> </options> </param> <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
--- a/mothur/tools/mothur/get.groups.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/get.groups.xml Wed May 16 12:28:44 2012 -0500 @@ -53,10 +53,8 @@ </param> <when value="groups"> <param name="groups" type="select" label="groups - Pick groups to include" multiple="true"> - <options from_dataset="group_in"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="group_in" key="groups" /> </options> </param> </when>
--- a/mothur/tools/mothur/get.otulist.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/get.otulist.xml Wed May 16 12:28:44 2012 -0500 @@ -22,9 +22,8 @@ <inputs> <param name="list_in" type="data" format="list" label="list - OTU List"/> <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="By default, uses all if none are selected."> - <options from_dataset="list_in"> - <column name="name" index="0"/> - <column name="value" index="0"/> + <options> + <filter type="data_meta" ref="list_in" key="labels" /> </options> </param> <param name="sort" type="select" label="sort - select the output format">
--- a/mothur/tools/mothur/get.oturep.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/get.oturep.xml Wed May 16 12:28:44 2012 -0500 @@ -65,18 +65,15 @@ <when value="yes"> <param name="group" type="data" format="groups" label="group - Group file for the OTU List"/> <param name="groups" type="select" label="groups - Group Selection (all used if none are selected)" multiple="true"> - <options from_dataset="group"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="group" key="groups" /> </options> </param> </when> </conditional> <!-- pick --> <param name="label" type="select" label="label - OTU Labels" multiple="true"> - <options from_dataset="otu_list"> - <column name="name" index="0"/> - <column name="value" index="0"/> + <options> + <filter type="data_meta" ref="otu_list" key="labels" /> </options> </param> <param name="sorted" type="select" label="sorted - Sort Sequences by">
--- a/mothur/tools/mothur/get.otus.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/get.otus.xml Wed May 16 12:28:44 2012 -0500 @@ -27,9 +27,8 @@ <param name="group_in" type="data" format="groups" label="group - Groups"/> <param name="list_in" type="data" format="list" label="list - OTU List"/> <param name="label" type="select" label="label - OTU Labels" > - <options from_dataset="list_in"> - <column name="name" index="0"/> - <column name="value" index="0"/> + <options> + <filter type="data_meta" ref="list_in" key="labels" /> </options> </param> <conditional name="groupnames"> @@ -40,10 +39,8 @@ <when value="groups"> <param name="groups" type="select" label="groups - Pick groups to include" multiple="true" force_select="true"> <help>At least one group must be selected</help> - <options from_dataset="group_in"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="group_in" key="groups" /> </options> </param> </when>
--- a/mothur/tools/mothur/get.rabund.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/get.rabund.xml Wed May 16 12:28:44 2012 -0500 @@ -18,9 +18,8 @@ <inputs> <param name="otu" type="data" format="list,sabund" label="list,sabund - List or Sabund"/> <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)"> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> <param name="sorted" type="boolean" checked="false" truevalue="--sorted=true" falsevalue="" label="sorted - sort by abundance"
--- a/mothur/tools/mothur/get.relabund.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/get.relabund.xml Wed May 16 12:28:44 2012 -0500 @@ -20,19 +20,13 @@ <param name="otu" type="data" format="shared" label="shared - OTU Shared" help="Use Make.shared to create a shared file from a list and a group file"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/> - <filter type="unique_value" name="unq_lbl" column="0" /> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="otu" key="groups" /> </options> </param> <param name="scale" type="select" label="scale - Scale by">
--- a/mothur/tools/mothur/get.sabund.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/get.sabund.xml Wed May 16 12:28:44 2012 -0500 @@ -17,9 +17,8 @@ <inputs> <param name="otu" type="data" format="list,rabund" label="list,rabund - List or Rabund"/> <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)"> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> </inputs>
--- a/mothur/tools/mothur/get.sharedseqs.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/get.sharedseqs.xml Wed May 16 12:28:44 2012 -0500 @@ -39,9 +39,8 @@ <param name="group" type="data" format="groups" label="group - "/> <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" help="By default all are included if no selection is made."> - <options from_dataset="list"> - <column name="name" index="0"/> - <column name="value" index="0"/> + <options> + <filter type="data_meta" ref="list" key="labels" /> </options> </param> <param name="fasta" type="data" format="fasta" optional="true" label="fasta - Dataset"/> @@ -55,19 +54,15 @@ <when value="all"/> <when value="unique"> <param name="groups" type="select" label="unique - Group to analyze" multiple="true"> - <options from_dataset="group"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="group" key="groups" /> </options> </param> </when> <when value="shared"> <param name="groups" type="select" label="shared - Groups to analyze" multiple="true"> - <options from_dataset="group"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="group" key="groups" /> </options> </param> </when>
--- a/mothur/tools/mothur/heatmap.bin.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/heatmap.bin.xml Wed May 16 12:28:44 2012 -0500 @@ -49,29 +49,21 @@ <when value="default"> <param name="otu" type="data" format="shared,relabund" label="shared,relabund - OTU List"/> <param name="groups" type="select" label="groups - Groups to condider" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="otu" key="groups" /> </options> </param> <param name="label" type="select" label="label - OTU Labels" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/> - <filter type="unique_value" name="unq_lbl" column="0" /> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> </when> <when value="no"> <param name="otu" type="data" format="list,rabund,sabund" label="list,rabund,sabund - OTU List"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="unique_value" name="unq_lbl" column="0" /> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> </when> @@ -79,17 +71,13 @@ <param name="otu" type="data" format="list,rabund,sabund" label="list,rabund,sabund - OTU List"/> <param name="otu_group" type="data" format="groups" label="group - Group file for the OTU List"/> <param name="groups" type="select" label="groups - Groups to include" multiple="true"> - <options from_dataset="otu_group"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="otu_group" key="groups" /> </options> </param> <param name="label" type="select" label="label - OTU Labels" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="unique_value" name="unq_lbl" column="0" /> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> </when>
--- a/mothur/tools/mothur/heatmap.sim.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/heatmap.sim.xml Wed May 16 12:28:44 2012 -0500 @@ -46,19 +46,13 @@ <when value="shared"> <param name="otu" type="data" format="shared" label="shared - OTU Shared"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/> - <filter type="unique_value" name="unq_lbl" column="0" /> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> <param name="groups" type="select" label="groups - Groups to include" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="otu" key="groups" /> </options> </param> <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
--- a/mothur/tools/mothur/indicator.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/indicator.xml Wed May 16 12:28:44 2012 -0500 @@ -29,19 +29,13 @@ <inputs> <param name="otu" type="data" format="shared,relabund" label="shared/relabund - Otu dataset"/> <param name="label" type="select" optional="true" label="label - OTU Labels" > - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/> - <filter type="unique_value" name="unq_lbl" column="0" /> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> <param name="groups" type="select" optional="true" label="groups - Pick groups to annalyze" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="otu" key="groups" /> </options> </param> <param name="tree" type="data" format="tree" optional="true" label="tree - A newick-formatted tree"
--- a/mothur/tools/mothur/libshuff.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/libshuff.xml Wed May 16 12:28:44 2012 -0500 @@ -27,10 +27,8 @@ <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> <param name="group" type="data" format="groups" label="group - Groups"/> <param name="groups" type="select" label="groups - Groups to condider" multiple="true"> - <options from_dataset="group"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="group" key="groups" /> </options> </param> <param name="iters" type="integer" value="10000" label="iters - Number of iterations to try (default 10000)"/>
--- a/mothur/tools/mothur/make.design.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/make.design.xml Wed May 16 12:28:44 2012 -0500 @@ -7,10 +7,8 @@ <repeat name="groupings" title="Grouping"> <param name="name" type="text" label="Name for a new combined grouping"/> <param name="groups" type="select" multiple="true" label="Select groups for to include in this grouping"> - <options from_dataset="source"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="source" key="groups" /> </options> </param> </repeat>
--- a/mothur/tools/mothur/make.shared.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/make.shared.xml Wed May 16 12:28:44 2012 -0500 @@ -29,16 +29,13 @@ <param name="group" type="data" format="groups" label="group - "/> <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" help="By default all are included if no selection is made."> - <options from_dataset="list"> - <column name="name" index="0"/> - <column name="value" index="0"/> + <options> + <filter type="data_meta" ref="list" key="labels" /> </options> </param> <param name="groups" type="select" label="groups - Groups to include" multiple="true"> - <options from_dataset="group"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="group" key="groups" /> </options> </param> <!--
--- a/mothur/tools/mothur/merge.groups.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/merge.groups.xml Wed May 16 12:28:44 2012 -0500 @@ -31,19 +31,13 @@ <param name="otu" type="data" format="shared" optional="true" label="shared - OTU Shared Dataset"/> <param name="group" type="data" format="groups" optional="true" label="group - Group Dataset"/> <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="otu" key="groups" /> </options> </param> <param name="label" type="select" label="label - Pick OTU Labels to include" optional="true" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/> - <filter type="unique_value" name="unq_lbl" column="0" /> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> <conditional name="design"> @@ -59,11 +53,8 @@ <repeat name="groupings" title="Grouping"> <param name="name" type="text" label="Name for a new combined grouping"/> <param name="groups" type="select" multiple="true" label="Select groups for to include in this grouping"> - <options from_dataset="otu"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="otu" key="groups" /> </options> </param> </repeat>
--- a/mothur/tools/mothur/metastats.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/metastats.xml Wed May 16 12:28:44 2012 -0500 @@ -31,28 +31,20 @@ <inputs> <param name="otu" type="data" format="shared" label="shared - OTU Shared"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/> - <filter type="unique_value" name="unq_lbl" column="0" /> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="otu" key="groups" /> </options> </param> <param name="design" type="data" format="tabular" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/> <param name="sets" type="select" label="sets - group sets to analyze" multiple="true"> - <options from_dataset="design"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="design" key="groups" /> </options> </param> <param name="iters" type="integer" value="1000" label="iters - Number of randomizations (default 1000)"/>
--- a/mothur/tools/mothur/normalize.shared.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/normalize.shared.xml Wed May 16 12:28:44 2012 -0500 @@ -27,19 +27,13 @@ <inputs> <param name="otu" type="data" format="shared,relabund" label="shared,relabund - OTU Shared or Relabund file"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/> - <filter type="unique_value" name="unq_lbl" column="0" /> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> <param name="groups" type="select" label="groups - Groups to include" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="otu" key="groups" /> </options> </param> <param name="norm" type="integer" value="0" label="norm - Number to normalize to (Uses default if < 1)"
--- a/mothur/tools/mothur/otu.association.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/otu.association.xml Wed May 16 12:28:44 2012 -0500 @@ -25,19 +25,13 @@ <inputs> <param name="otu" type="data" format="shared,relabund" label="shared,relabund - OTU Shared or Relabund file"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/> - <filter type="unique_value" name="unq_lbl" column="0" /> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> <param name="groups" type="select" label="groups - Groups to include" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="otu" key="groups" /> </options> </param> <param name="method" type="select" label="method - Normalization method">
--- a/mothur/tools/mothur/otu.hierarchy.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/otu.hierarchy.xml Wed May 16 12:28:44 2012 -0500 @@ -14,16 +14,13 @@ <inputs> <param name="list" type="data" format="list" label="list - OTU List"/> <param name="label1" type="select" label="label - OTU Label 1" > - <options from_dataset="list"> - <column name="name" index="0"/> - <column name="value" index="0"/> + <options> + <filter type="data_meta" ref="list" key="labels" /> </options> </param> <param name="label2" type="select" label="label - OTU Label 2" help="Must be different than Label 1"> - <options from_dataset="list"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="param_value" ref="label1" column="value" keep="false"/> + <options> + <filter type="data_meta" ref="list" key="labels" /> </options> </param> <param name="output" type="select" optional="true" label="output - display the names of the sequences in the otus or the otu numbers">
--- a/mothur/tools/mothur/parse.list.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/parse.list.xml Wed May 16 12:28:44 2012 -0500 @@ -18,9 +18,8 @@ <param name="group" type="data" format="groups" label="group - Sequences Name reference"/> <param name="label" type="select" optional="true" label="label - To filter: Select OTU Labels to include" multiple="true"> <help>All labels are included if none are selected</help> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> </inputs>
--- a/mothur/tools/mothur/parsimony.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/parsimony.xml Wed May 16 12:28:44 2012 -0500 @@ -25,10 +25,8 @@ <param name="group" type="data" format="groups" label="group - Group file for the tree"/> <param name="groups" type="select" label="groups - Groups to display" multiple="true" help="By default all are included if no selection is made."> - <options from_dataset="group"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="group" key="groups" /> </options> </param> <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference file for the tree"/>
--- a/mothur/tools/mothur/pca.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/pca.xml Wed May 16 12:28:44 2012 -0500 @@ -23,19 +23,13 @@ <inputs> <param name="otu" type="data" format="shared,relabund" label="shared,relabund - OTU Shared or Relabund file"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/> - <filter type="unique_value" name="unq_lbl" column="0" /> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="otu" key="groups" /> </options> </param> <param name="metric" type="boolean" truevalue="" falsevalue="--metric=False" checked="true" label="metric - Calculate pearson correlation coefficient" />
--- a/mothur/tools/mothur/phylo.diversity.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/phylo.diversity.xml Wed May 16 12:28:44 2012 -0500 @@ -40,10 +40,8 @@ <param name="group" type="data" format="groups" label="group - Group file for the tree"/> <param name="groups" type="select" label="groups - Groups to display" multiple="true"> <help>All groups displayed if none are selected.</help> - <options from_dataset="group"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="group" key="groups" /> </options> </param> </when>
--- a/mothur/tools/mothur/rarefaction.shared.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/rarefaction.shared.xml Wed May 16 12:28:44 2012 -0500 @@ -23,20 +23,14 @@ <inputs> <param name="otu" type="data" format="shared" label="shared - OTU Shared"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/> - <filter type="unique_value" name="unq_lbl" column="0" /> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> <param name="groups" type="select" label="groups - Groups to analyze" multiple="true"> <help>All groups will be analyzed by default if none are selected</help> - <options from_dataset="otu"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="otu" key="groups" /> <filter type="add_value" name="all" value="all" /> </options> </param>
--- a/mothur/tools/mothur/rarefaction.single.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/rarefaction.single.xml Wed May 16 12:28:44 2012 -0500 @@ -38,10 +38,8 @@ <inputs> <param name="otu" type="data" format="list,rabund,sabund,shared" label="list,rabund,sabund,shared - OTU List"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="unique_value" name="unq_lbl" column="0" /> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
--- a/mothur/tools/mothur/remove.groups.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/remove.groups.xml Wed May 16 12:28:44 2012 -0500 @@ -53,10 +53,8 @@ </param> <when value="groups"> <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true"> - <options from_dataset="group_in"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="group_in" key="groups" /> </options> </param> </when>
--- a/mothur/tools/mothur/remove.otus.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/remove.otus.xml Wed May 16 12:28:44 2012 -0500 @@ -27,9 +27,8 @@ <param name="group_in" type="data" format="groups" label="group - Groups"/> <param name="list_in" type="data" format="list" label="list - OTU List"/> <param name="label" type="select" label="label - OTU Labels" > - <options from_dataset="list_in"> - <column name="name" index="0"/> - <column name="value" index="0"/> + <options> + <filter type="data_meta" ref="list_in" key="labels" /> </options> </param> <conditional name="groupnames"> @@ -40,10 +39,8 @@ <when value="groups"> <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" force_select="true"> <help>At least one group must be selected</help> - <options from_dataset="group_in"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="group_in" key="groups" /> </options> </param> </when>
--- a/mothur/tools/mothur/remove.rare.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/remove.rare.xml Wed May 16 12:28:44 2012 -0500 @@ -47,20 +47,14 @@ <when value="shared"> <param name="otu" type="data" format="shared" label="shared - Otu dataset"/> <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="otu" key="groups" /> </options> </param> <param name="bygroup" type="boolean" truevalue="--bygroup=true" falsevalue="" checked="false" label="bygroup - Remove any OTU that has nseqs or fewer sequences across all groups"/> <param name="label" type="select" multiple="true" optional="true" label="label - OTU Labels" > - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/> - <filter type="unique_value" name="unq_lbl" column="0" /> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> </when> @@ -68,27 +62,21 @@ <param name="otu" type="data" format="list" label="list - Otu dataset"/> <param name="group" type="data" format="groups" label="group - Groups" /> <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" multiple="true"> - <options from_dataset="group"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="group" key="groups" /> </options> </param> <param name="label" type="select" multiple="false" optional="true" label="label - OTU Labels" > - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="unique_value" name="unq_lbl" column="0" /> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> </when> <when value="default"> <param name="otu" type="data" format="shared,list,rabund,sabund" label="shared,list,rabund,sabund - Otu dataset"/> <param name="label" type="select" multiple="true" optional="true" label="label - OTU Labels" > - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="unique_value" name="unq_lbl" column="0" /> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> </when>
--- a/mothur/tools/mothur/sens.spec.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/sens.spec.xml Wed May 16 12:28:44 2012 -0500 @@ -28,9 +28,8 @@ <param name="dist" type="data" format="dist" label="phylip,column - Distance Matrix"/> <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" help="By default all are included if no selection is made."> - <options from_dataset="list"> - <column name="name" index="0"/> - <column name="value" index="0"/> + <options> + <filter type="data_meta" ref="list" key="labels" /> </options> </param> <param name="precision" type="integer" value="100" optional="true" label="precision - Precision for rounding distance values"/>
--- a/mothur/tools/mothur/split.abund.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/split.abund.xml Wed May 16 12:28:44 2012 -0500 @@ -59,9 +59,8 @@ <when value="list"> <param name="input" type="data" format="list" label="list - OTU List"/> <param name="label" type="select" label="label - OTU Labels" multiple="true" help="Select OTU Labels to filter out all but selected labels"> - <options from_dataset="input"> - <column name="name" index="0"/> - <column name="value" index="0"/> + <options> + <filter type="data_meta" ref="input" key="labels" /> </options> </param> </when> @@ -76,10 +75,8 @@ <when value="yes"> <param name="group" type="data" format="groups" label="group - Group dataset"/> <param name="groups" type="select" label="groups - Group Selection (all used if none are selected)" multiple="true"> - <options from_dataset="group"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="group" key="groups" /> </options> </param> </when>
--- a/mothur/tools/mothur/split.groups.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/split.groups.xml Wed May 16 12:28:44 2012 -0500 @@ -21,10 +21,8 @@ <param name="name" type="data" format="names" label="name - Names to split by group" optional="true"/> <param name="group" type="data" format="groups" label="group - Groups"/> <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" multiple="true"> - <options from_dataset="group"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="group" key="groups" /> </options> </param> </inputs>
--- a/mothur/tools/mothur/sub.sample.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/sub.sample.xml Wed May 16 12:28:44 2012 -0500 @@ -88,10 +88,8 @@ <when value="yes"> <param name="group_in" type="data" format="groups" label="group - Groups"/> <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true"> - <options from_dataset="group_in"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="group_in" key="groups" /> </options> </param> <param name="persample" type="boolean" truevalue="--persample=true" falsevalue="" checked="false" label="persample - select subsample of the same size from each of the groups"/> @@ -109,56 +107,45 @@ <when value="yes"> <param name="group_in" type="data" format="groups" label="group - Groups"/> <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true"> - <options from_dataset="group_in"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="group_in" key="groups" /> </options> </param> <param name="persample" type="boolean" truevalue="--persample=true" falsevalue="" checked="false" label="persample - select subsample of the same size from each of the groups"/> </when> <!-- yes --> </conditional> <!-- use_group --> <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true"> - <options from_dataset="otu_in"> - <column name="name" index="0"/> - <column name="value" index="0"/> + <options> + <filter type="data_meta" ref="otu_in" key="labels" /> </options> </param> </when> <!-- list --> <when value="shared"> <param name="otu_in" type="data" format="shared" label="shared - OTU Shared"/> <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true"> - <options from_dataset="otu_in"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="otu_in" key="groups" /> </options> </param> <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true"> - <options from_dataset="otu_in"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/> - <filter type="unique_value" name="unq_lbl" column="0" /> + <options> + <filter type="data_meta" ref="otu_in" key="labels" /> </options> </param> </when> <!-- shared --> <when value="sabund"> <param name="otu_in" type="data" format="sabund" label="sabund - OTU Species Abundance"/> <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true"> - <options from_dataset="otu_in"> - <column name="name" index="0"/> - <column name="value" index="0"/> + <options> + <filter type="data_meta" ref="otu_in" key="labels" /> </options> </param> </when> <!-- sabund --> <when value="rabund"> <param name="otu_in" type="data" format="rabund" label="rabund - OTU Relative Abundance"/> <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true"> - <options from_dataset="otu_in"> - <column name="name" index="0"/> - <column name="value" index="0"/> + <options> + <filter type="data_meta" ref="otu_in" key="labels" /> </options> </param> </when> <!-- rabund -->
--- a/mothur/tools/mothur/summary.shared.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/summary.shared.xml Wed May 16 12:28:44 2012 -0500 @@ -24,19 +24,13 @@ <inputs> <param name="otu" type="data" format="shared" label="shared - OTU Shared"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/> - <filter type="unique_value" name="unq_lbl" column="0" /> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> <param name="groups" type="select" label="groups - Pairwise comparision groups" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="otu" key="groups" /> </options> </param> <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
--- a/mothur/tools/mothur/summary.single.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/summary.single.xml Wed May 16 12:28:44 2012 -0500 @@ -37,10 +37,8 @@ <inputs> <param name="otu" type="data" format="list,rabund,sabund,shared" label="list,rabund,sabund,shared - OTU List"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="unique_value" name="unq_lbl" column="0" /> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
--- a/mothur/tools/mothur/tree.shared.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/tree.shared.xml Wed May 16 12:28:44 2012 -0500 @@ -53,19 +53,13 @@ <param name="dist" type="data" format="shared" label="shared - OTU Shared"/> <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Create a new history dataset for each label and calculator"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> - <options from_dataset="dist"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/> - <filter type="unique_value" name="unq_lbl" column="0" /> + <options> + <filter type="data_meta" ref="dist" key="labels" /> </options> </param> <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> - <options from_dataset="dist"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="dist" key="groups" /> </options> </param> </when>
--- a/mothur/tools/mothur/unifrac.unweighted.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/unifrac.unweighted.xml Wed May 16 12:28:44 2012 -0500 @@ -31,10 +31,8 @@ <param name="group" type="data" format="groups" label="group - Group file for the tree"/> <param name="groups" type="select" label="groups - Select groups for pairwise comparisons" multiple="true"> <help></help> - <options from_dataset="group"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="group" key="groups" /> </options> </param> <param name="name" type="data" format="names" optional="true" label="name - Names file for the tree"/>
--- a/mothur/tools/mothur/unifrac.weighted.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/unifrac.weighted.xml Wed May 16 12:28:44 2012 -0500 @@ -30,10 +30,8 @@ <param name="group" type="data" format="groups" label="group - Group file for the tree"/> <param name="groups" type="select" label="groups - Select groups for pairwise comparisons" multiple="true"> <help></help> - <options from_dataset="group"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="group" key="groups" /> </options> </param> <param name="name" type="data" format="names" optional="true" label="name - Names file for the tree"/>
--- a/mothur/tools/mothur/venn.xml Wed Mar 28 15:45:03 2012 -0500 +++ b/mothur/tools/mothur/venn.xml Wed May 16 12:28:44 2012 -0500 @@ -52,19 +52,13 @@ <option value="sharedace">Shared Ace</option> </param> <param name="label" type="select" label="label - OTU Labels" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/> - <filter type="unique_value" name="unq_lbl" column="0" /> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/> - <filter type="unique_value" name="unq_grp" column="1" /> + <options> + <filter type="data_meta" ref="otu" key="groups" /> </options> </param> </when> @@ -79,9 +73,8 @@ <validator type="in_range" min="5" /> </param> <param name="label" type="select" label="label - OTU Labels" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> + <options> + <filter type="data_meta" ref="otu" key="labels" /> </options> </param> </when>