diff stacks_populations.xml @ 6:e2db212d64ad draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"

--- a/stacks_populations.xml	Wed Sep 01 11:27:10 2021 +0000
+++ b/stacks_populations.xml	Thu Apr 14 09:21:25 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="stacks2_populations" name="Stacks2: populations" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
+<tool id="stacks2_populations" name="Stacks2: populations" profile="@PROFILE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>Calculate population-level summary statistics</description>
     <macros>
         <import>macros.xml</import>
@@ -119,8 +119,6 @@
 $populations_output.genepop
 $populations_output.structure
 $populations_output.radpainter
-##$populations_output.phase
-##$populations_output.fastphase
 $populations_output.plink
 $populations_output.hzar
 $populations_output.phylip
@@ -235,8 +233,6 @@
             <param argument="--genepop" truevalue="--genepop" falsevalue="" type="boolean" checked="false" label="Output results in GenePop Format"/>
             <param argument="--structure" truevalue="--structure" falsevalue="" type="boolean" checked="false" label="Output results in Structure Format"/>
             <param argument="--radpainter" truevalue="--radpainter" falsevalue="" type="boolean" checked="false" label="Output results in fineRADstructure/RADpainter format"/>
-            <!--<param argument="\-\-phase" truevalue="\-\-phase" falsevalue="" type="boolean" checked="false" label="Output genotypes in PHASE format"/>-->
-            <param argument="--fastphase" truevalue="--fastphase" falsevalue="" type="boolean" checked="false" label="Output genotypes in fastPHASE format"/>
             <param argument="--plink" truevalue="--plink" falsevalue="" type="boolean" checked="false" label="Output genotypes in PLINK format"/>
             <param argument="--hzar" truevalue="--hzar" falsevalue="" type="boolean" checked="false" label="Output genotypes in Hybrid Zone Analysis using R (HZAR) format."/>
             <param argument="--phylip" truevalue="--phylip" falsevalue="" type="boolean" checked="false" label="Output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction"/>
@@ -360,21 +356,21 @@
             </param>
             <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
             <param name="add_log" value="yes"/>
-            <param name="advanced_options|log_fst_comp" value="yes"/>
+            <param name="advanced_options|log_fst_comp" value="true"/>
             <param name="fstats_conditional|fstats" value="yes"/>
-            <param name="populations_output|fasta_loci" value="yes"/>
-            <param name="populations_output|fasta_samples" value="yes"/>
-            <param name="populations_output|fasta_samples_raw" value="yes"/>
-            <param name="populations_output|phylip" value="yes"/>
-            <param name="populations_output|phylip_var" value="yes"/>
-            <param name="populations_output|genepop" value="yes"/>
-            <param name="populations_output|vcf" value="yes"/>
-            <param name="populations_output|hzar" value="yes"/>
-            <param name="populations_output|plink" value="yes"/>
-            <param name="populations_output|structure" value="yes"/>
-            <param name="populations_output|radpainter" value="yes"/>
-            <param name="populations_output|treemix" value="yes"/>
-            <param name="populations_output|gtf" value="yes"/>
+            <param name="populations_output|fasta_loci" value="true"/>
+            <param name="populations_output|fasta_samples" value="true"/>
+            <param name="populations_output|fasta_samples_raw" value="true"/>
+            <param name="populations_output|phylip" value="true"/>
+            <param name="populations_output|phylip_var" value="true"/>
+            <param name="populations_output|genepop" value="true"/>
+            <param name="populations_output|vcf" value="true"/>
+            <param name="populations_output|hzar" value="true"/>
+            <param name="populations_output|plink" value="true"/>
+            <param name="populations_output|structure" value="true"/>
+            <param name="populations_output|radpainter" value="true"/>
+            <param name="populations_output|treemix" value="true"/>
+            <param name="populations_output|gtf" value="true"/>
             <assert_command>
                 <has_text text="--log-fst-comp"/>
             </assert_command>