# HG changeset patch
# User iuc
# Date 1740172961 0
# Node ID ef4a081bc97b74762d3dc901d1fa9446ae87c028
# Parent  8c29e3621475d8f538a4ab2a8a0f6042509b3aa0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit bb83e01055cde8c766c630bec27afd3402ad6c88

diff -r 8c29e3621475 -r ef4a081bc97b allegro.xml
--- a/allegro.xml	Sat Dec 09 06:39:42 2017 -0500
+++ b/allegro.xml	Fri Feb 21 21:22:41 2025 +0000
@@ -1,15 +1,18 @@
-<tool id="allegro" name="Allegro" version="@VER@.0" >
+<tool id="allegro" name="Allegro" version="@TOOL_VERSION@.1" profile="21.05">
     <description>Linkage and Haplotype analysis</description>
     <macros>
-        <token name="@VER@">2</token>
+        <token name="@TOOL_VERSION@">2</token>
         <xml name="macro_inputs" >
             <param name="inp_ped" value="pedin.21" />
             <param name="inp_dat" value="datain.21" />
             <param name="inp_map" value="map.21" />
         </xml>
     </macros>
+    <xrefs>
+        <xref type="bio.tools">allegro</xref>
+    </xrefs>
     <requirements>
-        <requirement type="package" version="@VER@">allegro</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">allegro</requirement>
     </requirements>
     <version_command><![CDATA[
     allegro 2>&1 | head -1 | awk -F' ' '{print $2}'
@@ -32,7 +35,7 @@
         #end if
 #elif $cond_haplotypes.opt_haplotypes.value == 'no'
     #if $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_type.value == 'defaults'
-MODEL $cond_haplotypes.section_linkage.extra_linkage_mptspt.value par ${opt_xlinked} het param.mpt ${out_fparam}
+MODEL $cond_haplotypes.section_linkage.extra_linkage_mptspt.value par $opt_xlinked het param.mpt ${out_fparam}
 
     #elif $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_type.value == 'allele_sharing'
 MODEL $cond_haplotypes.section_linkage.extra_linkage_mptspt.value $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_linexp.value $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_scoring.value $cond_haplotypes.section_linkage.cond_linktype.extra_weighting.value param.mpt ${out_linexp}
@@ -52,7 +55,7 @@
     #end if
 #end if
 
-#if $opt_xlinked.value == 'X'
+#if $opt_sexspecific
 SEXSPECIFIC on
 #end if
 
@@ -65,7 +68,11 @@
 
 
 #if $cond_sim.opt_sim.value == 'yes'
-SIMULATE $cond_sim.extra_sim_dloc $cond_sim.extra_sim_npre $cond_sim.extra_sim_rep $cond_sim.extra_sim_err $cond_sim.extra_sim_yield $cond_sim.extra_sim_het
+SIMULATE #slurp
+#if $cond_sim.extra_sim_dloc != ""
+dloc:$cond_sim.extra_sim_dloc #slurp
+#end if
+npre:$cond_sim.extra_sim_npre rep:$cond_sim.extra_sim_rep err:$cond_sim.extra_sim_err yield:$cond_sim.extra_sim_yield het:$cond_sim.extra_sim_het
 #end if
 
 MAXMEMORY 102400
@@ -140,7 +147,7 @@
                                     <param name="extra_linkage_par_pen" type="text" value="p0/p1/p2" label="Penetrance" />
                                 </when>
                             </conditional>
-                            <param name="extra_linkage_par_het" type="float" value="" label="HET Frequency (leave blank for dynamic)" />
+                            <param name="extra_linkage_par_het" type="float" value="" optional="true" label="HET Frequency (leave blank for dynamic)" />
                         </when>
                     </conditional>
 
@@ -196,7 +203,7 @@
             </param>
             <when value="no" />
             <when value="yes" >
-                <param name="extra_sim_dloc" type="float" value="" min="0" label="Disease Locus (cM). Leave blank for unlinked disease locus." />
+                <param name="extra_sim_dloc" type="float" value="" optional="true" min="0" label="Disease Locus (cM). Leave blank for unlinked disease locus." />
                 <param name="extra_sim_npre" type="integer" value="1" label="Number of prefiles to generate" />
                 <param name="extra_sim_rep" type="integer" value="1" label="How many times to repeat family pattern" />
                 <param name="extra_sim_err" type="float" value="0" min="0" label="Error Rate" />
@@ -209,52 +216,60 @@
     </inputs>
 
     <outputs>
-        <data name="out_ihaplo" format="allegro_haplo" label="${tool.name} on ${on_string}: Haplotypes" />
-        <data name="out_fparam" format="allegro_linkage" label="${tool.name} on ${on_string}: Linkage" />
+        <data name="out_ihaplo" format="allegro_ihaplo" label="${tool.name} on ${on_string}: Haplotypes" />
+        <data name="out_fparam" format="allegro_fparam" label="${tool.name} on ${on_string}: Linkage" />
         <data name="out_founder" format="allegro_descent" label="${tool.name} on ${on_string}: Descent" />
         <data name="out_linexp" format="txt" label="${tool.name} on ${on_string}: Linear Expression" />
         <data name="out_combined_cross" format="txt" label="${tool.name} on ${on_string}: Combined Crossovers" />
     </outputs>
 
     <tests>
-        <test><!-- Default Haplotypes -->
+        <!-- Default Haplotypes -->
+        <test>
             <expand macro="macro_inputs" />
-            
-            <param name="extra_linkage_type" value="classical" />
-            <param name="extra_linkage_mptspt" value="mpt" />
-            <param name="opt_haplotypes" value="yes" />
-
+            <conditional name="cond_haplotypes">
+                <param name="opt_haplotypes" value="yes" />
+            </conditional>
             <output name="out_ihaplo" >
                 <assert_contents>
                     <has_text_matching expression="1\s+206003\s+111\s+112(\s+[012])+" />
                 </assert_contents>
             </output>
         </test>
-        <test><!-- Linkage with custom steps-->
+        <!-- Linkage with custom steps-->
+        <test>
             <expand macro="macro_inputs" />
-            
-            <param name="extra_linkage_type" value="classical" />
-            <param name="extra_linkage_mptspt" value="mpt" />
-            <param name="extra_linkage_mptspt" value="mpt" />
-            <param name="extra_steps" value="3" />
-            <param name="extra_maxstep" value="30" />
-
-
+            <conditional name="cond_haplotypes">
+                <section name="section_linkage">
+                    <param name="extra_linkage_mptspt" value="mpt" />
+                    <conditional name="cond_linktype" >
+                        <param name="extra_linkage_type" value="classical" />
+                    </conditional>
+                    <conditional name="cond_steps" >
+                        <param name="extra_steps" value="3" />
+                    </conditional>
+                </section>
+            </conditional>
             <output name="out_fparam" >
                 <assert_contents>
                     <has_text_matching expression="1(\s+[-0-9.]+){2}\s+rs2822572" />
                 </assert_contents>
             </output>
         </test>
-        <test><!-- Single-point linear expression test with power weights -->
+        <!-- Single-point linear expression test with power weights -->
+        <test>
             <expand macro="macro_inputs" />
-            
-            <param name="extra_linkage_type" value="allele_sharing" />
-            <param name="extra_linkage_mptspt" value="spt" />
-            <param name="extra_linkage_linexp" value="lin" />
-            <param name="extra_linkage_scoring" value="homoz" />
-            <param name="extra_weighting" value="power:50" />
-                       
+            <conditional name="cond_haplotypes">
+                <section name="section_linkage">
+                    <param name="extra_linkage_mptspt" value="spt" />
+                    <conditional name="cond_linktype" >
+                        <param name="extra_linkage_type" value="allele_sharing" />
+                        <param name="extra_linkage_linexp" value="lin" />
+                        <param name="extra_linkage_scoring" value="homoz" />
+                        <param name="extra_weighting" value="power:0.5" />
+                    </conditional>
+                </section>
+            </conditional>
             <output name="out_fparam" >
                 <assert_contents>
                     <has_text_matching expression='(\-\d+\.\d+\s+)+rs2822696' />