--- a/meme.xml	Sat Apr 09 08:34:02 2022 +0000
+++ b/meme.xml	Thu Aug 29 10:20:10 2024 +0000
@@ -1,12 +1,12 @@
-<tool id="meme_meme" name="MEME" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="meme_meme" name="MEME" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>- Multiple EM for Motif Elicitation</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
     <xrefs>
         <xref type="bio.tools">meme_meme</xref>
     </xrefs>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="requirements" />
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 @CHECK_NON_COMMERCIAL_USE@
 export TMPDIR=\${TMPDIR:-.};
@@ -81,15 +81,15 @@
 && mv '${html_outfile.files_path}/meme.xml' '${xml_outfile}'
     ]]></command>
     <inputs>
-        <param format="fasta" name="input1" type="data" label="Sequences"/>
+        <param name="input1" type="data" format="fasta" label="Sequences"/>
         <conditional name="options_type">
             <param name="options_type_selector" type="select" label="Options Configuration">
                 <option value="basic" selected="true">Basic</option>
                 <option value="advanced">Advanced</option>
             </param>
-            <when value="basic" />
+            <when value="basic"/>
             <when value="advanced">
-                <param name="sf" type="text" value="Galaxy FASTA Input" label="Name of sequence set" argument="-sf"/>
+                <param argument="-sf" type="text" value="Galaxy FASTA Input" label="Name of sequence set"/>
                 <conditional name="alphabet_type">
                     <param name="alphabet_type_selector" type="select" label="Sequence Alphabet">
                         <option value="protein">Protein</option>
@@ -97,7 +97,7 @@
                     </param>
                     <when value="protein">
                         <conditional name="prior_type">
-                            <param name="prior_type_selector" type="select" label="Choice of prior" argument="-prior">
+                            <param name="prior_type_selector" argument="-prior" type="select" label="Choice of prior">
                                 <option value="dirichlet">simple Dirichlet prior</option>
                                 <option value="dmix" selected="true">mixture of Dirichlets prior</option>
                                 <option value="mega">extremely low variance dmix</option>
@@ -105,45 +105,45 @@
                                 <option value="addone">add +1 to each observed count</option>
                             </param>
                             <when value="dirichlet">
-                                <param name="prior_b" type="float" value="0.01" label="strength of prior on model parameters" argument="-b"/>
-                                <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
+                                <param name="prior_b" argument="-b" type="float" value="0.01" label="strength of prior on model parameters"/>
+                                <param argument="-plib" type="data" format="txt" optional="True" label="Dirichlet prior file"/>
                             </when>
                             <when value="dmix">
-                                <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
-                                <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
+                                <param name="prior_b" argument="-b" type="float" value="0" label="strength of prior on model parameters"/>
+                                <param argument="-plib" type="data" format="txt" optional="True" label="Dirichlet prior file"/>
                             </when>
                             <when value="mega">
-                                <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
-                                <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
+                                <param name="prior_b" argument="-b" type="float" value="0" label="strength of prior on model parameters"/>
+                                <param argument="-plib" type="data" format="txt" optional="True" label="Dirichlet prior file"/>
                             </when>
                             <when value="megap">
-                                <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
-                                <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
+                                <param name="prior_b" argument="-b" type="float" value="0" label="strength of prior on model parameters"/>
+                                <param argument="-plib" type="data" format="txt" optional="True" label="Dirichlet prior file"/>
                             </when>
-                            <when value="addone" />
+                            <when value="addone"/>
                         </conditional>
                         <conditional name="spmap_type">
-                            <param name="spmap_type_selector" type="select" label="EM starting points" argument="-spmap">
+                            <param name="spmap_type_selector" argument="-spmap" type="select" label="EM starting points">
                                 <option value="uni">uni</option>
                                 <option value="pam" selected="true">pam</option>
                                 <option value="cons">Use starting point from string</option>
                             </param>
                             <when value="uni">
-                                <param name="spfuzz" type="float" value="0.5" label="Fuzziness of the mapping" argument="-spfuzz"/>
+                                <param argument="-spfuzz" type="float" value="0.5" label="Fuzziness of the mapping"/>
                             </when>
                             <when value="pam">
-                                <param name="spfuzz" type="integer" value="120" label="Fuzziness of the mapping" argument="-spfuzz"/>
+                                <param argument="-spfuzz" type="integer" value="120" label="Fuzziness of the mapping"/>
                             </when>
                             <when value="cons">
-                                <param name="cons" type="text" value="" label="Starting point from string" argument="-cons"/>
+                                <param argument="-cons" type="text" value="" label="Starting point from string"/>
                             </when>
                         </conditional>
                     </when>
                     <when value="dna">
-                        <param name="revcomp" label="Check reverse complement" type="boolean" truevalue="-revcomp" falsevalue="" checked="False"/>
-                        <param name="pal" label="Check for palindromes" type="boolean" truevalue="-pal" falsevalue="" checked="False"/>
+                        <param argument="-revcomp" type="boolean" truevalue="-revcomp" falsevalue="" checked="False" label="Check reverse complement"/>
+                        <param argument="-pal" type="boolean" truevalue="-pal" falsevalue="" checked="False" label="Check for palindromes"/>
                         <conditional name="prior_type">
-                            <param name="prior_type_selector" type="select" label="Sequence Alphabet" argument="-prior">
+                            <param name="prior_type_selector" argument="-prior" type="select" label="Sequence Alphabet">
                                 <option value="dirichlet" selected="true">simple Dirichlet prior</option>
                                 <option value="dmix">mixture of Dirichlets prior</option>
                                 <option value="mega">extremely low variance dmix</option>
@@ -151,50 +151,50 @@
                                 <option value="addone">add +1 to each observed count</option>
                             </param>
                             <when value="dirichlet">
-                                <param name="prior_b" type="float" value="0.01" label="strength of prior on model parameters" argument="-b"/>
-                                <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
+                                <param name="prior_b" argument="-b" type="float" value="0.01" label="strength of prior on model parameters"/>
+                                <param argument="-plib" type="data" format="txt" optional="True" label="Dirichlet prior file"/>
                             </when>
                             <when value="dmix">
-                                <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
-                                <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
+                                <param name="prior_b" argument="-b" type="float" value="0" label="strength of prior on model parameters"/>
+                                <param argument="-plib" type="data" format="txt" optional="True" label="Dirichlet prior file"/>
                             </when>
                             <when value="mega">
-                                <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
-                                <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
+                                <param name="prior_b" argument="-b" type="float" value="0" label="strength of prior on model parameters"/>
+                                <param argument="-plib" type="data" format="txt" optional="True" label="Dirichlet prior file"/>
                             </when>
                             <when value="megap">
-                                <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
-                                <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
+                                <param name="prior_b" argument="-b" type="float" value="0" label="strength of prior on model parameters"/>
+                                <param argument="-plib" type="data" format="txt" optional="True" label="Dirichlet prior file"/>
                             </when>
-                            <when value="addone" />
+                            <when value="addone"/>
                         </conditional>
                         <conditional name="spmap_type">
-                            <param name="spmap_type_selector" type="select" label="EM starting points" argument="-spmap">
+                            <param name="spmap_type_selector" argument="-spmap" type="select" label="EM starting points">
                                 <option value="uni" selected="true">uni</option>
                                 <option value="pam">pam</option>
                                 <option value="cons">Use starting point from string</option>
                             </param>
                             <when value="uni">
-                                <param name="spfuzz" type="float" value="0.5" label="Fuzziness of the mapping" argument="-spfuzz"/>
+                                <param argument="-spfuzz" type="float" value="0.5" label="Fuzziness of the mapping"/>
                             </when>
                             <when value="pam">
-                                <param name="spfuzz" type="integer" value="120" label="Fuzziness of the mapping" argument="-spfuzz"/>
+                                <param argument="-spfuzz" type="integer" value="120" label="Fuzziness of the mapping"/>
                             </when>
                             <when value="cons">
-                                <param name="cons" type="text" value="" label="Starting point from string" argument="-cons"/>
+                                <param argument="-cons" type="text" value="" label="Starting point from string"/>
                             </when>
                         </conditional>
                     </when>
                 </conditional>
-                <param name="nmotifs" type="integer" value="1" label="Number of different motifs to search" argument="-nmotifs" />
-                <param name="evt" type="float" value="inf" label="E-value to stop looking for motifs" argument="-evt"/>
+                <param argument="-nmotifs" type="integer" value="1" label="Number of different motifs to search"/>
+                <param argument="-evt" type="float" value="inf" label="E-value to stop looking for motifs"/>
                 <conditional name="mod_type">
-                    <param name="mod_type_selector" type="select" label="Expected motif distribution" argument="-mod">
+                    <param name="mod_type_selector" argument="-mod" type="select" label="Expected motif distribution">
                         <option value="oops">One Occurrence Per Sequence</option>
                         <option value="zoops" selected="true">Zero or One Occurrence Per Sequence</option>
                         <option value="anr">Any Number of Repetitions</option>
                     </param>
-                    <when value="oops" />
+                    <when value="oops"/>
                     <when value="zoops">
                         <conditional name="motif_occurrence_type">
                             <param name="motif_occurrence_type_selector" type="select" label="Number of motif occurrences">
@@ -202,13 +202,13 @@
                                 <option value="nsites">nsites</option>
                                 <option value="min_max_sites">min and max sites</option>
                             </param>
-                            <when value="default" />
+                            <when value="default"/>
                             <when value="nsites">
-                                <param name="nsites" type="integer" value="1" label="Search nsites number of occurrences" argument="-nsites"/>
+                                <param argument="-nsites" type="integer" value="1" label="Search nsites number of occurrences"/>
                             </when>
                             <when value="min_max_sites">
-                                <param name="minsites" type="integer" value="1" label="minsites" argument="-minsites"/>
-                                <param name="maxsites" type="integer" value="50" label="maxsites" argument="-maxsites"/>
+                                <param argument="-minsites" type="integer" value="1" label="minsites"/>
+                                <param argument="-maxsites" type="integer" value="50" label="maxsites"/>
                             </when>
                         </conditional>
                     </when>
@@ -219,29 +219,29 @@
                                 <option value="nsites">nsites</option>
                                 <option value="min_max_sites">min and max sites</option>
                             </param>
-                            <when value="default" />
+                            <when value="default"/>
                             <when value="nsites">
-                                <param name="nsites" type="integer" value="1" label="Search nsites number of occurrences" argument="-nsites"/>
+                                <param argument="-nsites" type="integer" value="1" label="Search nsites number of occurrences"/>
                             </when>
                             <when value="min_max_sites">
-                                <param name="minsites" type="integer" value="1" label="minsites" argument="-minsites"/>
-                                <param name="maxsites" type="integer" value="50" label="maxsites" argument="-maxsites"/>
+                                <param argument="-minsites" type="integer" value="1" label="minsites"/>
+                                <param argument="-maxsites" type="integer" value="50" label="maxsites"/>
                             </when>
                         </conditional>
                     </when>
                 </conditional>
-                <param name="wnsites" type="float" value="0.8" label="Weight on the prior on nsites" argument="-wnsites"/>
+                <param argument="-wnsites" type="float" value="0.8" label="Weight on the prior on nsites"/>
                 <conditional name="motif_width_type">
                     <param name="motif_width_type_selector" type="select" label="Motif width type">
                         <option value="exact">Exact width</option>
                         <option value="range" selected="true">Specify a range</option>
                     </param>
                     <when value="exact">
-                        <param name="width" type="integer" value="10" label="Width of motif to search" argument="-w"/>
+                        <param name="width" argument="-w" type="integer" value="10" label="Width of motif to search"/>
                     </when>
                     <when value="range">
-                        <param name="minw" type="integer" value="8" label="Min width of motif to search" argument="-minw"/>
-                        <param name="maxw" type="integer" value="50" label="Max width of motif to search" argument="-maxw"/>
+                        <param argument="-minw" type="integer" value="8" label="Min width of motif to search"/>
+                        <param argument="-maxw" type="integer" value="50" label="Max width of motif to search"/>
                     </when>
                 </conditional>
                 <conditional name="motif_trim_type">
@@ -249,31 +249,31 @@
                         <option value="nomatrim">No motif trim</option>
                         <option value="trim" selected="true">Trim motif</option>
                     </param>
-                    <when value="nomatrim" />
+                    <when value="nomatrim"/>
                     <when value="trim">
-                        <param name="wg" type="integer" value="11" label="Gap cost" argument="-wg"/>
-                        <param name="ws" type="integer" value="1" label="Space cost" argument="-ws"/>
-                        <param name="noendgaps" label="Do not penalize endgaps" type="boolean" truevalue="-noendgaps" falsevalue="" checked="False"/>
+                        <param argument="-wg" type="integer" value="11" label="Gap cost"/>
+                        <param argument="-ws" type="integer" value="1" label="Space cost"/>
+                        <param argument="-noendgaps" type="boolean" truevalue="-noendgaps" falsevalue="" checked="False" label="Do not penalize endgaps"/>
                     </when>
                 </conditional>
-                <param name="bfile" type="data" format="txt" optional="True" label="Background Model" argument="-bfile"/>
-                <param name="pspfile" type="data" format="txt" optional="True" label="Position-Specific Prior" argument="-psp"/>
-                <param name="maxiter" type="integer" value="50" label="Number of iterations of EM to run" argument="-maxiter"/>
-                <param name="distance" type="float" value="0.001" label="Convergence criterion" argument="-distance"/>
+                <param argument="-bfile" type="data" format="txt" optional="True" label="Background Model"/>
+                <param name="pspfile" argument="-psp" type="data" format="txt" optional="True" label="Position-Specific Prior"/>
+                <param argument="-maxiter" type="integer" value="50" label="Number of iterations of EM to run"/>
+                <param argument="-distance" type="float" value="0.001" label="Convergence criterion"/>
                 <conditional name="branching_type">
                     <param name="branching_type_selector" type="select" label="x-branching type">
                         <option value="x_branch">Perform x-branching</option>
                         <option value="no_x_branch" selected="true">No x-branching</option>
                     </param>
-                    <when value="no_x_branch" />
+                    <when value="no_x_branch"/>
                     <when value="x_branch">
-                        <param name="bfactor" type="integer" value="3" label="Number of iterations of branching" argument="-bfactor"/>
-                        <param name="heapsize" type="integer" value="64" label="Maximum number of heaps to use" argument="-heapsize"/>
+                        <param argument="-bfactor" type="integer" value="3" label="Number of iterations of branching"/>
+                        <param argument="-heapsize" type="integer" value="64" label="Maximum number of heaps to use"/>
                     </when>
                 </conditional>
             </when>
         </conditional>
-        <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False">
+        <param name="non_commercial_use" type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False" label="I certify that I am not using this tool for commercial purposes.">
             <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
         </param>
     </inputs>