changeset 18:697156806162

Mothur - update for Mothur version 1.23.0

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mothur/tools/mothur/chimera.perseus.xml	Tue Jan 17 11:22:44 2012 -0600
@@ -0,0 +1,58 @@
+<tool id="mothur_chimera_perseus" name="Chimera.perseus" version="1.23.0" >
+ <description>Find putative chimeras using chimeraCheck</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  --cmd='chimera.perseus'
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.perseus\.chimeras?$:'$out_file
+  --outputdir='$logfile.extra_files_path'
+  --fasta=$fasta
+  --name=$name
+  #if $group.__str__ != "None" and len($group.__str__) > 0:
+   --group='$group'
+  #end if
+  #if $alpha.__str__ != '':
+   --alpha=$alpha
+  #end if
+  #if $beta.__str__ != '':
+   --beta=$beta
+  #end if
+  #if $cutoff.__str__ != '':
+   --cutoff=$cutoff
+  #end if
+  --processors=8
+ </command>
+ <inputs>
+  <param name="fasta" type="data" format="align" label="fasta - Candiate Aligned Sequences"/>
+  <param name="name" type="data" format="names" label="name - Names "/>
+  <param name="group" type="data" format="group" optional="true" label="group - Sequences Name reference"/>
+  <param name="alpha" type="float" value="-5.54" optional="true" label="alpha" help="The default is -5.54"/>
+  <param name="beta" type="float" value="0.33" optional="true" label="beta" help="The default is 0.33"/>
+  <param name="cutoff" type="float" value="0.50" optional="true" label="cutoff" help="The default is 0.50"/>
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format="tabular" name="out_file" label="${tool.name} on ${on_string}: perseus.chimeras" />
+ </outputs>
+ <requirements>
+  <requirement type="binary">mothur</requirement>
+ </requirements>
+ <tests>
+ </tests>
+ <help>
+**Mothur Overview**
+
+Mothur_, initiated by Dr. Patrick Schloss and his software development team
+in the Department of Microbiology and Immunology at The University of Michigan,
+provides bioinformatics for the microbial ecology community.
+
+.. _Mothur: http://www.mothur.org/wiki/Main_Page
+
+**Command Documenation**
+
+The chimera.perseus_ command reads a fasta and name file, and outputs potentially chimeric sequences.
+
+.. _chimera.perseus: http://www.mothur.org/wiki/Chimera.perseus
+
+
+ </help>
+</tool>

--- a/mothur/tools/mothur/get.oturep.xml	Tue Jan 17 11:08:15 2012 -0600
+++ b/mothur/tools/mothur/get.oturep.xml	Tue Jan 17 11:22:44 2012 -0600
@@ -1,4 +1,4 @@
-<tool id="mothur_get_oturep" name="Get.oturep" version="1.20.0"  force_history_refresh="True">
+<tool id="mothur_get_oturep" name="Get.oturep" version="1.23.0"  force_history_refresh="True">
  <description>Generate a fasta with a representative sequence for each OTU</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -9,7 +9,9 @@
    --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
    --new_datasets='^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.fasta)$:${fasta.ext}','^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.names)$:names'
   #end if
-  --fasta=$fasta
+  #if $fasta.__str__ != "None" and len($fasta.__str__) > 0:
+   --fasta=$fasta
+  #end if
   --list=$otu_list
   #if $input.source == 'column':
    --column=$input.dist
@@ -38,7 +40,6 @@
  </command>
  <inputs>
   <!-- get.relabund  relabund type should also work -->
-  <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/>
   <param name="otu_list" type="data" format="list" label="list - OTU List"/>
   <conditional name="input">
    <param name="source" type="select" label="Distance Matrix Format">
@@ -54,6 +55,7 @@
     <param name="name" type="data" format="names" optional="true" label="name - Names"/>
    </when>
   </conditional>
+  <param name="fasta" type="data" format="fasta" optional="true" label="fasta - Fasta"/>
   <conditional name="pick">
    <param name="type" type="select" label="Parse a group file into abundant and rare groups?" help="">
     <option value="no" selected="true">No</option>

--- a/mothur/tools/mothur/heatmap.sim.xml	Tue Jan 17 11:08:15 2012 -0600
+++ b/mothur/tools/mothur/heatmap.sim.xml	Tue Jan 17 11:22:44 2012 -0600
@@ -1,4 +1,4 @@
-<tool id="mothur_heatmap_sim" name="Heatmap.sim" version="1.20.0"  force_history_refresh="True">
+<tool id="mothur_heatmap_sim" name="Heatmap.sim" version="1.23.0"  force_history_refresh="True">
  <description>Generate a heatmap for pariwise similarity</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -32,6 +32,9 @@
   #elif $input.source == 'phylip':
    --phylip=$input.dist
   #end if
+  #if 100 > $fontsize > 0:
+   --fontsize=$fontsize
+  #end if
  </command>
  <inputs>
   <conditional name="input">
@@ -75,6 +78,7 @@
        <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/>
    </when>
   </conditional>
+  <param name="fontsize" type="integer" value="24" label="fontsize - Fontsize (default is 24)"/>
   <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each image"/>
  </inputs>
  <outputs>

--- a/mothur/tools/mothur/mothur_wrapper.py	Tue Jan 17 11:08:15 2012 -0600
+++ b/mothur/tools/mothur/mothur_wrapper.py	Tue Jan 17 11:22:44 2012 -0600
@@ -4,7 +4,7 @@
 http://www.mothur.org/
 
 Supports mothur version 
-mothur v.1.22.0
+mothur v.1.23.0
 
 Class encapsulating Mothur galaxy tool.
 Expect each invocation to include:
@@ -185,6 +185,7 @@
     cmd_dict['chimera.bellerophon'] = dict({'required' : ['fasta'], 'optional' : ['filter','correction','window','increment','processors']})
     cmd_dict['chimera.ccode'] = dict({'required' : ['fasta','reference'], 'optional' : ['filter','mask','window','numwanted','save','processors']})
     cmd_dict['chimera.check'] = dict({'required' : ['fasta','reference'], 'optional' : ['ksize','svg','name','increment','save','processors']})
+    cmd_dict['chimera.perseus'] = dict({'required' : ['fasta','name'], 'optional' : ['group','sigma']})
     cmd_dict['chimera.pintail'] = dict({'required' : ['fasta','reference'], 'optional' : ['conservation','quantile','filter','mask','window','increment','save','processors']})
     cmd_dict['chimera.slayer'] = dict({'required' : ['fasta','reference'], 'optional' : ['name','group','search','window','increment','match','mismatch','numwanted','parents','minsim','mincov','iters','minbs','minsnp','divergence','realign','split','blastlocation','save','processors']})
     cmd_dict['chimera.uchime'] = dict({'required' : ['fasta'], 'optional' : ['name','group','reference','abskew','chimealns','minh','mindiv','xn','dn','xa','chunks','minchunk','idsmoothwindow','minsmoothid','maxp','skipgaps','skipgaps2','minlen','maxlen','ucl','queryfract','processors']})
@@ -214,7 +215,7 @@
     cmd_dict['get.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','shared','taxonomy']})
     cmd_dict['get.lineage'] = dict({'required' : ['taxonomy','taxon'],'optional' : ['fasta','name','group','list','alignreport','dups']})
     cmd_dict['get.otulist'] = dict({'required' : ['list'], 'optional' : ['label','sort']})
-    cmd_dict['get.oturep'] = dict({'required' : ['fasta','list',['phylip','column']], 'optional' : ['name','label','group','groups','sorted','precision','cutoff','large','weighted']})
+    cmd_dict['get.oturep'] = dict({'required' : ['list',['phylip','column']], 'optional' : ['fasta','name','label','group','groups','sorted','precision','cutoff','large','weighted']})
     cmd_dict['get.otus'] = dict({'required' : ['group','list','label'], 'optional' : ['groups','accnos']})
     cmd_dict['get.rabund'] = dict({'required' : [['list','sabund']],'optional' : ['sorted','label']})
     cmd_dict['get.relabund'] = dict({'required' : ['shared'],'optional' : ['scale','label','groups']})
@@ -223,7 +224,7 @@
     cmd_dict['get.sharedseqs'] = dict({'required' : ['list','group'], 'optional' : ['label', 'unique', 'shared', 'output', 'fasta']})
     cmd_dict['hcluster'] = dict({'required' : [['column','phylip']] , 'optional' : ['name','method','cutoff','hard','precision','sorted','showabund','timing']})
     cmd_dict['heatmap.bin'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['label','groups','scale','sorted','numotu','fontsize']})
-    cmd_dict['heatmap.sim'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['calc','name','label','groups']})
+    cmd_dict['heatmap.sim'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['calc','name','label','groups','fontsize']})
     cmd_dict['homova'] = dict({'required' : ['phylip','design'] ,  'optional' : ['alpha','iters']})
     cmd_dict['indicator'] = dict({'required' : [['tree','design'],['shared','relabund']], 'optional' : ['groups','label','processors']})
     cmd_dict['libshuff'] = dict({'required' : ['phylip','group'],'optional' : ['groups','iters','form','sim','step','cutoff']})
@@ -245,7 +246,7 @@
     cmd_dict['pcoa'] = dict({'required' : ['phylip'], 'optional' : ['metric']})
     cmd_dict['phylo.diversity'] = dict({'required' : ['tree'],'optional' : ['group','name','groups','iters','freq','scale','rarefy','collect','summary','processors']})
     cmd_dict['phylotype'] = dict({'required' : ['taxonomy'],'optional' : ['name','cutoff','label']})
-    cmd_dict['pre.cluster'] = dict({'required' : ['fasta'],  'optional' : ['name','diffs','group']})
+    cmd_dict['pre.cluster'] = dict({'required' : ['fasta'],  'optional' : ['name','diffs','group','processors']})
     cmd_dict['rarefaction.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','iters','groups','jumble']})
     cmd_dict['rarefaction.single'] = dict({'required' : [['list', 'sabund', 'rabund', 'shared']], 'optional' : ['calc','abund','iters','label','freq','processors']})
     cmd_dict['remove.groups'] = dict({'required' : ['group'], 'optional' : ['groups','accnos','fasta','name','list','shared','taxonomy']})
@@ -254,7 +255,7 @@
     cmd_dict['remove.rare'] = dict({'required' : [['list','sabund','rabund','shared'],'nseqs'], 'optional' : ['group','groups','label','bygroup']})
     cmd_dict['remove.seqs'] = dict({'required' : ['accnos',['fasta','qfile','name','group','list','alignreport','taxonomy']], 'optional' : ['dups']})
     cmd_dict['reverse.seqs'] = dict({'required' : ['fasta']})
-    cmd_dict['screen.seqs'] = dict({'required' : ['fasta'],  'optional' : ['start','end','maxambig','maxhomop','minlength','maxlength','criteria','optimize','name','group','alignreport','processors']})
+    cmd_dict['screen.seqs'] = dict({'required' : ['fasta'],  'optional' : ['start','end','maxambig','maxhomop','minlength','maxlength','criteria','optimize','name','group','alignreport'''taxonomy','processors']})
     cmd_dict['sens.spec'] = dict({'required' : ['list',['column','phylip']] , 'optional' : ['label','cutoff','hard','precision']})
 
     cmd_dict['seq.error'] = dict({'required' : ['fasta','reference'] , 'optional' : ['name','qfile','report','ignorechimeras','threshold','processors']})
@@ -262,10 +263,12 @@
     cmd_dict['sffinfo'] = dict({'required' : [['sff','sfftxt']], 'optional' : ['fasta','qfile','trim','sfftxt','flow','accnos']})
 
     cmd_dict['shhh.flows'] = dict({'required' : [['flow','files']], 'optional' : ['lookup','maxiter','mindelta','cutoff','sigma','order','processors']})
+    cmd_dict['shhh.seqs'] = dict({'required' : [['fasta','files']], 'optional' : ['group','sigma','processors']})
 
     cmd_dict['split.abund'] = dict({'required' : ['fasta',['name','list']], 'optional' : ['cutoff','group','groups','label','accnos']})
     cmd_dict['split.groups'] = dict({'required' : ['fasta','group'], 'optional' : ['name','groups']})
     cmd_dict['sub.sample'] = dict({'required' : [['fasta','list','sabund','rabund','shared']], 'optional' : ['name','group','groups','label','size','persample']})
+    cmd_dict['summary.qual'] = dict({'required' : ['qfile'], 'optional' : ['name']})
     cmd_dict['summary.seqs'] = dict({'required' : ['fasta'], 'optional' : ['name','processors']})
     cmd_dict['summary.shared'] = dict({'required' : ['shared'], 'optional' : ['calc','label','groups','all','distance','processors']})
     cmd_dict['summary.single'] = dict({'required' : [['list','sabund','rabund','shared']], 'optional' : ['calc','abund','size','label','groupmode']})
@@ -276,7 +279,7 @@
     cmd_dict['unifrac.unweighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','processors']})
     cmd_dict['unifrac.weighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','processors']})
     cmd_dict['unique.seqs'] = dict({'required' : ['fasta'],  'optional' : ['name']})
-    cmd_dict['venn'] = dict({'required' : [['list','shared']], 'optional' : ['calc','label','groups','abund','nseqs','permute']})
+    cmd_dict['venn'] = dict({'required' : [['list','shared']], 'optional' : ['calc','label','groups','abund','nseqs','permute','fontsize']})
 
     parser = optparse.OptionParser()
     # Options for managing galaxy interaction

--- a/mothur/tools/mothur/pre.cluster.xml	Tue Jan 17 11:08:15 2012 -0600
+++ b/mothur/tools/mothur/pre.cluster.xml	Tue Jan 17 11:22:44 2012 -0600
@@ -1,4 +1,4 @@
-<tool id="mothur_pre_cluster" name="Pre.cluster" version="1.22.0">
+<tool id="mothur_pre_cluster" name="Pre.cluster" version="1.23.0">
  <description>Remove sequences due to pyrosequencing errors</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -7,6 +7,7 @@
   ## adds .precluster before the last extension to the input file
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.precluster.\2',$os.path.basename($fasta.__str__)) + ":'" + $fasta_out.__str__]
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.precluster.names',$os.path.basename($fasta.__str__)) + ":'" + $names_out.__str__]
+  #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.precluster.map',$os.path.basename($fasta.__str__)) + ":'" + $map_out.__str__]
   --cmd='pre.cluster'
   --outputdir='$logfile.extra_files_path'
   --fasta=$fasta
@@ -20,6 +21,7 @@
    --diffs=$diffs
   #end if
   --result=#echo ','.join($results)
+  --processors=8
  </command>
  <inputs>
   <param name="fasta" type="data" format="fasta" label="fasta - Sequence Fasta"/>
@@ -31,6 +33,7 @@
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
   <data format_source="fasta" name="fasta_out" label="${tool.name} on ${on_string}: precluster.fasta" />
   <data format="names" name="names_out" label="${tool.name} on ${on_string}: precluster.names" />
+  <data format="tabular" name="map_out" label="${tool.name} on ${on_string}: precluster.map" />
  </outputs>
  <requirements>
   <requirement type="binary">mothur</requirement>

--- a/mothur/tools/mothur/screen.seqs.xml	Tue Jan 17 11:08:15 2012 -0600
+++ b/mothur/tools/mothur/screen.seqs.xml	Tue Jan 17 11:22:44 2012 -0600
@@ -1,4 +1,4 @@
-<tool id="mothur_screen_seqs" name="Screen.seqs" version="1.20.0">
+<tool id="mothur_screen_seqs" name="Screen.seqs" version="1.23.0">
  <description>Screen sequences</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -50,6 +50,10 @@
    --alignreport=$input_alignreport
    #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input_alignreport.__str__)) + ":'" + $output_alignreport.__str__]
   #end if
+  #if $input_taxonomy != None and $input_taxonomy.__str__ != "None":
+   --taxonomy=$input_taxonomy
+   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input_taxonomy.__str__)) + ":'" + $output_taxonomy.__str__]
+  #end if
   --result=#echo ','.join($results)
   --processors=8
  </command>
@@ -74,6 +78,7 @@
   <param name="input_names" type="data" format="names" optional="true" label="name - Sequence Names to screen"/>
   <param name="input_groups" type="data" format="groups" optional="true" label="group - Groups to screen"/>
   <param name="input_alignreport" type="data" format="align.report" optional="true" label="alignreport - Align Report to screen"/>
+  <param name="input_taxonomy" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/>
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
@@ -91,6 +96,9 @@
   <data format="align.report" name="output_alignreport" label="${tool.name} on ${on_string}: align.report" >
    <filter>input_alignreport != None</filter>
   </data>
+  <data format="taxonomy" name="output_taxonomy" label="${tool.name} on ${on_string}: taxonomy" >
+   <filter>input_taxonomy != None</filter>
+  </data>
  </outputs>
  <requirements>
   <requirement type="binary">mothur</requirement>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mothur/tools/mothur/shhh.seqs.xml	Tue Jan 17 11:22:44 2012 -0600
@@ -0,0 +1,56 @@
+<tool id="mothur_shhh_seqs" name="Shhh.seqs" version="1.23.0">
+ <description>Denoise program (Quince SeqNoise)</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  #import re, os.path
+  --cmd='shhh.seqs'
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.shhh\.fasta$:'$shhh_fasta,'^\S+\.shhh\.names$:'$shhh_names,'^\S+\.shhh\.map$:'$shhh_map
+  --outputdir='$logfile.extra_files_path'
+  --fasta=$fasta
+  --name=$name
+  #if $group.__str__ != "None" and len($group.__str__) > 0:
+   --group=$group
+  #end if
+  #if $sigma.__str__ != '':
+   --sigma=$sigma 
+  #end if
+  --processors=8
+ </command>
+ <inputs>
+  <param name="fasta" type="data" format="fasta" label="fasta - Sequences" help=""/>
+  <param name="name" type="data" format="names" label="name - Sequences Name reference"/>
+  <param name="group" type="data" format="groups" optional="true" label="group - Sequences Name reference"/>
+  <param name="sigma" type="float" value="" optional="true" label="sigma" 
+         help="default .01">
+   <validator type="in_range" message="sigma between 0. and 1." min="0.0" max="1.0"/>
+  </param>
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format_source="fasta" name="shhh_fasta" label="${tool.name} on ${on_string}: shhh.fasta"/>
+  <data format_source="names" name="shhh_names" label="${tool.name} on ${on_string}: shhh.names"/>
+  <data format_source="txt" name="shhh_map" label="${tool.name} on ${on_string}: shhh.map"/>
+ </outputs>
+ <requirements>
+  <requirement type="binary">mothur</requirement>
+ </requirements>
+ <tests>
+ </tests>
+ <help>
+**mothur overview**
+
+Mothur_, initiated by Dr. Patrick Schloss and his software development team
+in the Department of Microbiology and Immunology at The University of Michigan,
+provides bioinformatics for the microbial ecology community.
+
+.. _Mothur: http://www.mothur.org/wiki/Main_Page
+
+**Command Documenation**
+
+The shhh.seqs_ command is a mothur-based rewrite of Chris Quince's sequence denoting program, SeqNoise.  Schloss prefers pre.cluster for this operation.
+
+.. _shhh.seqs: http://www.mothur.org/wiki/Shhh.seqs
+
+
+ </help>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mothur/tools/mothur/summary.qual.xml	Tue Jan 17 11:22:44 2012 -0600
@@ -0,0 +1,43 @@
+<tool id="mothur_summary_qual" name="Summary.qual" version="1.23.0">
+ <description>Summarize the quality scores</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  --cmd='summary.qual'
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.summary$:'$out_summary
+  --outputdir='$logfile.extra_files_path'
+  --qfile=$qfile
+  #if $name.__str__ != "None" and len($name.__str__) > 0:
+   --name=$name
+  #end if
+  ## --processors=8
+ </command>
+ <inputs>
+  <param name="qfile" type="data" format="qual" label="qfile - Sequence Quality file"/>
+  <param name="name" type="data" format="names" optional="true" label="name - Names" optional="true"/>
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format="summary" name="out_summary" label="${tool.name} on ${on_string}: summary" />
+ </outputs>
+ <requirements>
+  <requirement type="binary">mothur</requirement>
+ </requirements>
+ <tests>
+ </tests>
+ <help>
+**Mothur Overview**
+
+Mothur_, initiated by Dr. Patrick Schloss and his software development team 
+in the Department of Microbiology and Immunology at The University of Michigan,  
+provides bioinformatics for the microbial ecology community.
+
+.. _Mothur: http://www.mothur.org/wiki/Main_Page
+
+**Command Documenation**
+
+The summary.qual_ command reads a quality file and an optional name, and summarizes the quality information.
+
+.. _summary.qual: http://www.mothur.org/wiki/Summary.qual
+
+ </help>
+</tool>

--- a/mothur/tools/mothur/venn.xml	Tue Jan 17 11:08:15 2012 -0600
+++ b/mothur/tools/mothur/venn.xml	Tue Jan 17 11:22:44 2012 -0600
@@ -1,4 +1,4 @@
-<tool id="mothur_venn" name="Venn" version="1.20.0"  force_history_refresh="True">
+<tool id="mothur_venn" name="Venn" version="1.23.0"  force_history_refresh="True">
  <description>Generate Venn diagrams for groups </description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -33,7 +33,9 @@
    #if $input.abund >= 5:
      --abund='$input.abund'
    #end if
-
+  #end if
+  #if 100 > $fontsize > 0:
+   --fontsize=$fontsize
   #end if
  </command>
  <inputs>
@@ -86,6 +88,7 @@
   </conditional>
   <param name="nseqs" type="boolean" truevalue="--nseqs=true" falsevalue="" checked="false" label="nseqs - Output the number of sequences represented by the otus in the picture"/>
   <param name="permute" type="boolean" truevalue="--permute=true" falsevalue="" checked="false" label="permute - Create pictures with all possible 4-way permutations of groups"/>
+  <param name="fontsize" type="integer" value="24" label="fontsize - Fontsize (default is 24)"/>
   <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each image"/>
  </inputs>
  <outputs>