diff macros.xml @ 3:eb784fa07f80 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"

--- a/macros.xml	Wed Jul 15 17:24:38 2020 -0400
+++ b/macros.xml	Tue Apr 27 09:31:18 2021 +0000
@@ -9,10 +9,9 @@
         </requirements>
     </xml>
 
-    <token name="@STACKS_VERSION@">2.53</token>
+    <token name="@STACKS_VERSION@">2.55</token>
     <token name="@WRAPPER_VERSION@">0</token>
-    <!-- fix to 18.01 since https://github.com/galaxyproject/galaxy/pull/7032 -->
-    <token name="@PROFILE@">18.01</token>
+    <token name="@PROFILE@">20.01</token>
 
     <xml name="citation">
         <citations>
@@ -67,6 +66,7 @@
         <option value="bsaHI">bsaHI</option>
         <option value="bspDI">bspDI</option>
         <option value="bstYI">bstYI</option>
+        <option value="btgI">btgI</option>
         <option value="cac8I">cac8I</option>
         <option value="claI">claI</option>
         <option value="csp6I">csp6I</option>
@@ -80,6 +80,7 @@
         <option value="hindIII">hindIII</option>
         <option value="hinP1I">hinP1I</option>
         <option value="hpaII">hpaII</option>
+        <option value="hpyCH4IV">hpyCH4IV</option>
         <option value="kpnI">kpnI</option>
         <option value="mluCI">mluCI</option>
         <option value="mseI">mseI</option>
@@ -88,10 +89,13 @@
         <option value="ncoI">ncoI</option>
         <option value="ndeI">ndeI</option>
         <option value="nheI">nheI</option>
+        <option value="ngoMIV">ngoMIV</option>
         <option value="nlaIII">nlaIII</option>
         <option value="notI">notI</option>
         <option value="nsiI">nsiI</option>
         <option value="nspI">nspI</option>
+        <option value="pacI">pacI</option>
+        <option value="pspXI">pspXI</option>
         <option value="pstI">pstI</option>
         <option value="rsaI">rsaI</option>
         <option value="sacI">sacI</option>
@@ -446,19 +450,19 @@
     <xml name="populations_output_full">
         <expand macro="populations_output_light"/>
 
-        <data format="txt" name="out_sql" label="${tool.name} @TOOLADD@ on ${on_string} Genotyping markers" from_work_dir="stacks_outputs/populations.sql.tsv">
+        <data format="txt" name="out_sql" label="${tool.name} on ${on_string} Genotyping markers" from_work_dir="stacks_outputs/populations.sql.tsv">
             <filter>genetic_map_options['map_type'] and genetic_map_options['map_format']</filter>
         </data>
 
         <!-- log_fst_comp populations.fst_summary.tsv populations.phistats_summary.tsv populations.phistats.tsv-->
         <data format="tabular" name="out_phistats" label="${tool.name} on ${on_string} Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats.tsv">
-            <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter>
+            <filter>fstats_conditional['fstats']=='yes' or kernel_smoothing['options_kernel']['kernel'] in ['--k', '--smooth-fstats']</filter>
         </data>
         <data format="tabular" name="out_phistats_sum" label="${tool.name} on ${on_string} Summary of Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats_summary.tsv">
-            <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter>
+            <filter>fstats_conditional['fstats']=='yes' or kernel_smoothing['options_kernel']['kernel'] in ['--k', '--smooth-fstats']</filter>
         </data>
         <data format="tabular" name="out_fststats_sum" label="${tool.name} on ${on_string} Summary of Fst statistics" from_work_dir="stacks_outputs/populations.fst_summary.tsv">
-            <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter>
+            <filter>fstats_conditional['fstats']=='yes' or kernel_smoothing['options_kernel']['kernel'] in ['--k', '--smooth-fstats']</filter>
         </data>
 
         <!-- fasta_loci populations.loci.fa
@@ -531,23 +535,28 @@
         <data format="tabular" name="out_treemix" label="${tool.name} on ${on_string} Treemix format" from_work_dir="stacks_outputs/populations.treemix">
             <filter>populations_output['treemix']</filter>
         </data>
+
+        <!-- gtf populations.treemix -->
+        <data format="gtf" name="out_gtf" label="${tool.name} on ${on_string} gtf" from_work_dir="stacks_outputs/populations.gtf">
+            <filter>populations_output['gtf']</filter>
+        </data>
     </xml>
 
     <!-- fastq output for kmer/clone-filter -->
-    <xml name="fastq_output_filter">
-        <data name="clean" format_source="fqinputs" label="${tool.name} on ${on_string}">
+    <xml name="fastq_output_filter" token_format="">
+        <data name="clean" format="@FORMAT@" label="${tool.name} on ${on_string}">
             <filter>input_type['input_type_select'] == 'single'</filter>
             <yield/>
         </data>
-        <collection name="clean_pair" type="paired" format_source="fqinputs" label="${tool.name} on ${on_string}">
+        <collection name="clean_pair" type="paired" format="@FORMAT@" label="${tool.name} on ${on_string}">
             <filter>input_type['input_type_select'] == 'paired'</filter>
             <yield/>
         </collection>
-        <data name="discarded" format_source="fqinputs" label="${tool.name} on ${on_string}: discarded reads">
+        <data name="discarded" format="@FORMAT@" label="${tool.name} on ${on_string}: discarded reads">
             <filter>capture and input_type['input_type_select'] == 'single'</filter>
             <yield/>
         </data>
-        <collection name="discarded_pair" format_source="fqinputs" type="paired" label="${tool.name} on ${on_string}: discarded reads">
+        <collection name="discarded_pair" format="@FORMAT@" type="paired" label="${tool.name} on ${on_string}: discarded reads">
             <filter>capture and input_type['input_type_select'] == 'paired'</filter>
             <yield/>
         </collection>