# HG changeset patch
# User iuc
# Date 1539790990 14400
# Node ID d1c340a5664bd8cef6e09303e1f2e9f453d7cc0f
# Parent  288db50d1fb9a883aeb9c28b7bee7f7e5647e3ef
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91

diff -r 288db50d1fb9 -r d1c340a5664b iqtree.xml
--- a/iqtree.xml	Sat Nov 25 18:17:09 2017 -0500
+++ b/iqtree.xml	Wed Oct 17 11:43:10 2018 -0400
@@ -1,8 +1,9 @@
-<tool id="iqtree" name="IQ-TREE" version="1.5.5.1" >
+<tool id="iqtree" name="IQ-TREE" version="@TOOL_VERSION@.1" >
     <description>Phylogenomic / evolutionary tree construction from multiple sequences</description>
-    <requirements>
-        <requirement type="package" version="1.5.5">iqtree</requirement>
-    </requirements>
+    <macros>
+        <import>iqtree_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
     <command detect_errors='exit_code' ><![CDATA[
 iqtree
     -pre PREF
@@ -362,9 +363,8 @@
                 </conditional>
                 <param argument="-rcluster" type="integer" optional="true" label="Specify the percentage for the relaxed clustering algorithm (Lanfear et al., 2014)" help="This is similar to --rcluster-percent option of PartitionFinder. For example, with -rcluster 10 only the top 10% partition schemes are considered to save computations." />
                 <param argument="-mset" type="text" optional="true" label="Specify the name of a program (raxml, phyml or mrbayes) to restrict to only those models supported by the specified program" help="Alternatively, one can specify a comma-separated list of base models. For example, -mset WAG,LG,JTT will restrict model selection to WAG, LG, and JTT instead of all 18 AA models to save computations.">
-                    <sanitizer>
-                        <valid initial="string.ascii_uppercase,string.punctuation" />
-                    </sanitizer>
+                    <expand macro="sanitize_query"
+                    validinitial="string.ascii_uppercase,string.punctuation" />
                 </param>
                 <param argument="-msub" type="select" label="Specify either nuclear, mitochondrial, chloroplast or viral to restrict to those AA models designed for specified source." help="">
                     <option value="nuclear">nuclear</option>
@@ -373,14 +373,12 @@
                     <option value="viral">viral</option>
                 </param>
                 <param argument="-mfreq" type="text" optional="true" label="Specify a comma-separated list of frequency types for model selection" >
-                    <sanitizer>
-                        <valid initial="string.ascii_uppercase,string.digits,x,string.punctuation" />
-                    </sanitizer>
+                    <expand macro="sanitize_query"
+                    validinitial="string.ascii_uppercase,string.digits,x,string.punctuation" />
                 </param>
                 <param argument="-mrate" type="text" optional="true" label="Specify a comma-separated list of rate heterogeneity types for model selection">
-                    <sanitizer>
-                        <valid initial="string.ascii_uppercase,string.punctuation" />
-                    </sanitizer>
+                    <expand macro="sanitize_query"
+                    validinitial="string.ascii_uppercase,string.punctuation" />
                 </param>
                 <param argument="-cmin" type="integer" value="2" optional="true" label="Specify minimum number of categories for FreeRate model"/>
                 <param argument="-cmax" type="integer" value="10" optional="true" label="Specify maximum number of categories for FreeRate model"/>
@@ -391,9 +389,8 @@
                 </param>
                 <param argument="-mtree" type="boolean" truevalue="-mtree" falsevalue="" checked="false" label="Turn on full tree search for each model considered, to obtain more accurate result"/>
                 <param argument="-madd" type="text" optional="true" label="Specify a comma-separated list of mixture models to additionally consider for model selection" help="For example, -madd LG4M,LG4X to additionally include these two protein mixture models.">
-                    <sanitizer>
-                        <valid initial="string.ascii_uppercase,string.digits,string.punctuation" />
-                    </sanitizer>
+                    <expand macro="sanitize_query"
+                    validinitial="string.ascii_uppercase,string.digits,string.punctuation" />
                 </param>
                 <param argument="-mdef" type="data" format="txt" optional="true" label="Specify a NEXUS model file to define new models."/>
             </section>
@@ -402,15 +399,11 @@
             </section>
             <section name="rate_heterogeneity" expanded="False" title="Rate heterogeneity">
                 <param argument="-a" type="text" optional="true" label="Specify the Gamma shape parameter (default: estimate)">
-                    <sanitizer>
-                        <valid initial="string.printable" />
-                    </sanitizer>
+                    <expand macro="sanitize_query" />
                 </param>
                 <param argument="-gmedian" type="boolean" truevalue="-gmedian" falsevalue="" checked="false" label="Perform the median approximation for Gamma rate heterogeneity instead of the default mean approximation (Yang, 1994)"/>
                 <param argument="-i" type="text" optional="true" label="Specify the proportion of invariable sites (default: estimate)">
-                    <sanitizer>
-                        <valid initial="string.printable" />
-                    </sanitizer>
+                    <expand macro="sanitize_query" />
                 </param>
                 <param argument="--opt_gamma_inv" type="boolean" truevalue="--opt-gamma-inv" falsevalue="" checked="false" label="Perform more thorough estimation for +I+G model parameters"/>
                 <param argument="-wsr" type="boolean" truevalue="-wsr" falsevalue="" checked="false" label="Write per-site rates to .rate file"/>
@@ -500,9 +493,8 @@
         </section>
         <section name="miscellaneous_options" expanded="False" title="Miscellaneous options">
             <param argument="-fconst" type="text" optional="true" label="Specify a list of comma-separated integer numbers" help="The number of entries should be equal to the number of states in the model (e.g. 4 for DNA and 20 for protein). IQ-TREE will then add a number of constant sites accordingly. For example, -fconst 10,20,15,40 will add 10 constant sites of all A, 20 constant sites of all C, 15 constant sites of all G and 40 constant sites of all T into the alignment.">
-                <sanitizer>
-                    <valid initial="string.digits,string.punctuation" />
-                </sanitizer>
+                <expand macro="sanitize_query"
+                validinitial="string.digits,string.punctuation" />
             </param>
         </section>
     </inputs>
@@ -641,7 +633,7 @@
             </output>
         </test>
     </tests>
-    <help>
+    <help><![CDATA[
 IQ-TREE
 =======
 
@@ -922,7 +914,7 @@
 
 
 From this figure, the branching patterns within reptiles are poorly supported (e.g. **Sphenodon** with SH-aLRT: 39%, UFBoot: 51% and **Turtle** with SH-aLRT: 85%, UFBoot: 72%) as well as the phylogenetic position of **Seal** within mammals (SH-aLRT: 68.3%, UFBoot: 75%). Other branches appear to be well supported.
-    </help>
+    ]]></help>
     <citations>
         <citation type="doi">10.1093/molbev/msu300</citation>
         <citation type="doi">10.1093/molbev/mst024</citation>
diff -r 288db50d1fb9 -r d1c340a5664b iqtree_macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iqtree_macros.xml	Wed Oct 17 11:43:10 2018 -0400
@@ -0,0 +1,20 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.5.5</token>
+
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">iqtree</requirement>
+        </requirements>
+    </xml>
+
+    <xml name="sanitize_query" token_validinitial="string.printable">
+        <sanitizer>
+            <valid initial="@VALIDINITIAL@">
+                <remove value="&apos;" />
+            </valid>
+            <mapping initial="none">
+                <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
+            </mapping>
+       </sanitizer>
+    </xml>
+</macros>