# HG changeset patch
# User iuc
# Date 1619516113 0
# Node ID 4f65e343ecdf23f69c9976c13df16e73e45034e6
# Parent  6dafad99008698216881e0a75012d9eff9ef05bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"

diff -r 6dafad990086 -r 4f65e343ecdf macros.xml
--- a/macros.xml	Thu Jul 16 07:26:37 2020 -0400
+++ b/macros.xml	Tue Apr 27 09:35:13 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>
diff -r 6dafad990086 -r 4f65e343ecdf stacks_refmap.xml
--- a/stacks_refmap.xml	Thu Jul 16 07:26:37 2020 -0400
+++ b/stacks_refmap.xml	Tue Apr 27 09:35:13 2021 +0000
@@ -57,7 +57,7 @@
             <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done."/></assert_contents></output>
             <output_collection name="gstacks_out" type="list" count="2">
                 <element name="catalog.calls.vcf" file="refmap/catalog.calls.vcf" ftype="vcf" lines_diff="4"/>
-                <element name="catalog.fa.gz" file="refmap/catalog.fa.gz" ftype="fasta.gz" compare="sim_size" delta_frac="0.01"/>
+                <element name="catalog.fa.gz" file="refmap/catalog.fa.gz" ftype="fasta.gz" compare="diff"/>
             </output_collection>
             <output ftype="tabular" name="out_haplotypes" value="refmap/populations.haplotypes.tsv"/>
             <output ftype="tabular" name="out_hapstats" value="refmap/populations.hapstats.tsv"/>
diff -r 6dafad990086 -r 4f65e343ecdf test-data/kmerfilter/Discarded1_0001.1.1.fq
diff -r 6dafad990086 -r 4f65e343ecdf test-data/kmerfilter/Discarded2_0001.2.2.fq
diff -r 6dafad990086 -r 4f65e343ecdf test-data/kmerfilter/Removed1_0001.1.1.fq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kmerfilter/Removed1_0001.1.1.fq	Tue Apr 27 09:35:13 2021 +0000
@@ -0,0 +1,16 @@
+@K00392:16:HJ2G2BBXX:7:1102:10825:462401 1:N:0:ATCACG
+GGACATTGGCTGCAGTACTCTGACCCTGGCCACCTCAACCTGTCTCTCTCGCACCGGAAACCTCCGATCCGCAGAAACATGAGCAACCCTACAGTTGACACACACAACAGTTTTCGACCGAAACTACACATTCCTCTGTCCCATTTCCTC
++
+--A-FF-F-<A<-FAF7AAF--F--FF-A<-JJFJFFFF-<<-7--<FFF--77<7-77-<---7-7<-7-AA--<<-7<----<-A-FJFF-7A-F--7FF-<7A-A-<7F7---7-7-77-<7<<A--<J7--<-)-7)-7---7F<-
+@K00392:16:HJ2G2BBXX:7:1102:10825:46240 1:N:0:ATCACG
+GGACATTGGCTGCAGTACTCTGACCCTGGCCACCTCAACCTGTCTCTCTCGCACCGGAAACCTCCGATCCGCAGAAACATGAGCAACCCTACAGTTGACACACACAACAGTTTTCGACCGAAACTACACATTCCTCTGTCCCATTTCCTC
++
+--A-FF-F-<A<-FAF7AAF--F--FF-A<-JJFJFFFF-<<-7--<FFF--77<7-77-<---7-7<-7-AA--<<-7<----<-A-FJFF-7A-F--7FF-<7A-A-<7F7---7-7-77-<7<<A--<J7--<-)-7)-7---7F<-
+@K00392:16:HJ2G2BBXX:8:1201:4929:9367 1:N:0:ATCACG
+GGATTGAGGATGCAGCAACGTTCTAACATCTAGTGGAAAGCCTTCCCAGAAGAGTGGAGGCTGTTATAGCAGCAAAGGGGGGACCAACTCCATATTATTGCCCATGACTTTTGAATGAGATGTTTGACGAGCAGGGGTCGACATACTTTT
++
+AAAFFJJJJJJJFJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFAJAJFFJFJJFJFJ7FJAJJJAFFJJJJJJAJAFFFFA<JJJAJJFAFJA7<AFAFFA7F7F<-77<F<--7-7-))---)AFF-<A-7FA
+@K00392:16:HJ2G2BBXX:7:1104:19268:28727 1:N:0:ATCACG
+ATGCCGCGGCCCTTGCAGAGCAAGGGGAACCACTACTTCAACTCAAGGTCTCAAAGCGAGTGACGTAACTGATTGAAACGCTATTAGCGCGCACCACCGCTAACTAGCTATCCATTTCACATCCGTTACATATGTATGTATGTACACACA
++
+AAFFFJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJFJJJFJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJFAFJJJJJJJJ
diff -r 6dafad990086 -r 4f65e343ecdf test-data/kmerfilter/Removed1_0001.1.1.fq.single
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kmerfilter/Removed1_0001.1.1.fq.single	Tue Apr 27 09:35:13 2021 +0000
@@ -0,0 +1,20 @@
+@K00392:16:HJ2G2BBXX:7:1102:10825:462401 1:N:0:ATCACG
+GGACATTGGCTGCAGTACTCTGACCCTGGCCACCTCAACCTGTCTCTCTCGCACCGGAAACCTCCGATCCGCAGAAACATGAGCAACCCTACAGTTGACACACACAACAGTTTTCGACCGAAACTACACATTCCTCTGTCCCATTTCCTC
++
+--A-FF-F-<A<-FAF7AAF--F--FF-A<-JJFJFFFF-<<-7--<FFF--77<7-77-<---7-7<-7-AA--<<-7<----<-A-FJFF-7A-F--7FF-<7A-A-<7F7---7-7-77-<7<<A--<J7--<-)-7)-7---7F<-
+@K00392:16:HJ2G2BBXX:7:1102:10825:46240 1:N:0:ATCACG
+GGACATTGGCTGCAGTACTCTGACCCTGGCCACCTCAACCTGTCTCTCTCGCACCGGAAACCTCCGATCCGCAGAAACATGAGCAACCCTACAGTTGACACACACAACAGTTTTCGACCGAAACTACACATTCCTCTGTCCCATTTCCTC
++
+--A-FF-F-<A<-FAF7AAF--F--FF-A<-JJFJFFFF-<<-7--<FFF--77<7-77-<---7-7<-7-AA--<<-7<----<-A-FJFF-7A-F--7FF-<7A-A-<7F7---7-7-77-<7<<A--<J7--<-)-7)-7---7F<-
+@K00392:16:HJ2G2BBXX:8:1201:4929:9367 1:N:0:ATCACG
+GGATTGAGGATGCAGCAACGTTCTAACATCTAGTGGAAAGCCTTCCCAGAAGAGTGGAGGCTGTTATAGCAGCAAAGGGGGGACCAACTCCATATTATTGCCCATGACTTTTGAATGAGATGTTTGACGAGCAGGGGTCGACATACTTTT
++
+AAAFFJJJJJJJFJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFAJAJFFJFJJFJFJ7FJAJJJAFFJJJJJJAJAFFFFA<JJJAJJFAFJA7<AFAFFA7F7F<-77<F<--7-7-))---)AFF-<A-7FA
+@K00392:16:HJ2G2BBXX:7:1104:19268:28727 1:N:0:ATCACG
+ATGCCGCGGCCCTTGCAGAGCAAGGGGAACCACTACTTCAACTCAAGGTCTCAAAGCGAGTGACGTAACTGATTGAAACGCTATTAGCGCGCACCACCGCTAACTAGCTATCCATTTCACATCCGTTACATATGTATGTATGTACACACA
++
+AAFFFJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJFJJJFJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJFAFJJJJJJJJ
+@K00392:16:HJ2G2BBXX:8:2125:3011:15574 1:N:0:ATCACG
+TCAGAAGAAAAACCCACAAAATAGAACCGGAGTCCTATTCCATTATTCCTAGCTGCGGTATTCAGGCGACCGGGCCTGCTTTGAACACTCTAATTTTTTCAAAGTAAACGCTTCGGACCCCGCGGGCCACTCAGTTAAGAGCATCGAGGG
++
+AAFFFJJJJJJJJFJFJFJFJJJJFJJJJJ<J-7FJFAJJJJJJJJAJJFJAJJJJJJJJFJJFAAFAJJJJJFJJJJJFAJJJJJFFJJ<J-FFAJJJF-J<7-7<<A<---AF<7JJJJ-A)77-7--)F-7----<--7A7A<--7-
diff -r 6dafad990086 -r 4f65e343ecdf test-data/kmerfilter/Removed1_0001.1.1.fq.single.gz
--- a/test-data/kmerfilter/Removed1_0001.1.1.fq.single.gz	Thu Jul 16 07:26:37 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-@K00392:16:HJ2G2BBXX:7:1102:10825:462401 1:N:0:ATCACG
-GGACATTGGCTGCAGTACTCTGACCCTGGCCACCTCAACCTGTCTCTCTCGCACCGGAAACCTCCGATCCGCAGAAACATGAGCAACCCTACAGTTGACACACACAACAGTTTTCGACCGAAACTACACATTCCTCTGTCCCATTTCCTC
-+
---A-FF-F-<A<-FAF7AAF--F--FF-A<-JJFJFFFF-<<-7--<FFF--77<7-77-<---7-7<-7-AA--<<-7<----<-A-FJFF-7A-F--7FF-<7A-A-<7F7---7-7-77-<7<<A--<J7--<-)-7)-7---7F<-
-@K00392:16:HJ2G2BBXX:7:1102:10825:46240 1:N:0:ATCACG
-GGACATTGGCTGCAGTACTCTGACCCTGGCCACCTCAACCTGTCTCTCTCGCACCGGAAACCTCCGATCCGCAGAAACATGAGCAACCCTACAGTTGACACACACAACAGTTTTCGACCGAAACTACACATTCCTCTGTCCCATTTCCTC
-+
---A-FF-F-<A<-FAF7AAF--F--FF-A<-JJFJFFFF-<<-7--<FFF--77<7-77-<---7-7<-7-AA--<<-7<----<-A-FJFF-7A-F--7FF-<7A-A-<7F7---7-7-77-<7<<A--<J7--<-)-7)-7---7F<-
-@K00392:16:HJ2G2BBXX:8:1201:4929:9367 1:N:0:ATCACG
-GGATTGAGGATGCAGCAACGTTCTAACATCTAGTGGAAAGCCTTCCCAGAAGAGTGGAGGCTGTTATAGCAGCAAAGGGGGGACCAACTCCATATTATTGCCCATGACTTTTGAATGAGATGTTTGACGAGCAGGGGTCGACATACTTTT
-+
-AAAFFJJJJJJJFJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFAJAJFFJFJJFJFJ7FJAJJJAFFJJJJJJAJAFFFFA<JJJAJJFAFJA7<AFAFFA7F7F<-77<F<--7-7-))---)AFF-<A-7FA
-@K00392:16:HJ2G2BBXX:7:1104:19268:28727 1:N:0:ATCACG
-ATGCCGCGGCCCTTGCAGAGCAAGGGGAACCACTACTTCAACTCAAGGTCTCAAAGCGAGTGACGTAACTGATTGAAACGCTATTAGCGCGCACCACCGCTAACTAGCTATCCATTTCACATCCGTTACATATGTATGTATGTACACACA
-+
-AAFFFJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJFJJJFJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJFAFJJJJJJJJ
-@K00392:16:HJ2G2BBXX:8:2125:3011:15574 1:N:0:ATCACG
-TCAGAAGAAAAACCCACAAAATAGAACCGGAGTCCTATTCCATTATTCCTAGCTGCGGTATTCAGGCGACCGGGCCTGCTTTGAACACTCTAATTTTTTCAAAGTAAACGCTTCGGACCCCGCGGGCCACTCAGTTAAGAGCATCGAGGG
-+
-AAFFFJJJJJJJJFJFJFJFJJJJFJJJJJ<J-7FJFAJJJJJJJJAJJFJAJJJJJJJJFJJFAAFAJJJJJFJJJJJFAJJJJJFFJJ<J-FFAJJJF-J<7-7<<A<---AF<7JJJJ-A)77-7--)F-7----<--7A7A<--7-
diff -r 6dafad990086 -r 4f65e343ecdf test-data/kmerfilter/Removed2_0001.2.2.fq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kmerfilter/Removed2_0001.2.2.fq	Tue Apr 27 09:35:13 2021 +0000
@@ -0,0 +1,16 @@
+@K00392:16:HJ2G2BBXX:7:1102:10825:462401 2:N:0:ATCACG
+GGACATTGGCTGATGTGTTATAGGTGTCTACGTTTATGGGCATGTCGCAGCAGTGTGTAGGAGGGAGATTCCAAGATGTGTGAAGTGTGTAGGAGGACATGGGACAGAGGAATGTGTAGTTTCGGTAGAAAACGGTTGTGTGTGTGAACT
++
+AAFAF7FJ77FA--<AF-<FJF<FFA7AJJJ77-<AJ<A-FJJ-<7A7FF-7FA<-AAAA7F7J<<JJFAAAAAF--7<--<--A7F-A--7F-<---7-FFF<-<F-AFF<--FJJFA<A-77F--7-A----7-7)7<7FFAJ7----
+@K00392:16:HJ2G2BBXX:7:1102:10825:46240 2:N:0:ATCACG
+GGACATTGGCTGATGTGTTATAGGTGTCTACGTTTATGGGCATGTCGCAGCAGTGTGTAGGAGGGAGATTCCAAGATGTGTGAAGTGTGTAGGAGGACATGGGACAGAGGAATGTGTAGTTTCGGTAGAAAACGGTTGTGTGTGTGAACT
++
+AAFAF7FJ77FA--<AF-<FJF<FFA7AJJJ77-<AJ<A-FJJ-<7A7FF-7FA<-AAAA7F7J<<JJFAAAAAF--7<--<--A7F-A--7F-<---7-FFF<-<F-AFF<--FJJFA<A-77F--7-A----7-7)7<7FFAJ7----
+@K00392:16:HJ2G2BBXX:8:1201:4929:9367 2:N:0:ATCACG
+GTAATGGAAACATGTGCAACCTGTCAAAATACACCAAAAGTATGTGGACACCTGCTCGTCAAACATCTCATTCAAAAGTCATGGGCAATAATATGGAGTTGGTCCCCCCTTTGCTGCTATAACAGCCTCCACTCTTCTGGGAAGGCTTTC
++
+AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJFJJFJJJJJJJJJJJJJJJJJ7JJJFJA<JFJFJJJJ<JJJJJJFJJJJJJJJJJAFJF-AJJFJJFJJJFJJJJ7AAAAFFAFJJAJJJJJJJFFJJF
+@K00392:16:HJ2G2BBXX:7:1104:19268:28727 2:N:0:ATCACG
+GGACACTGACTGCAGCCAGAGTTTGTCCACCCTCTCGGTCATCGAGGAGTTCTTGGCCAAGAGGCCCATACCGGCGGGCAGTGCCAGAGAGGGCCACAACCAAAACTGGCTCCGCAACCACAACTACTACAGTATGTTTTATTTGTGCTT
++
+AAAFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFJFJJJJJJJJJJJJJFJJJFJJJJJAJFJJJJAJJJJ----<F<JFJJFJFJFF
diff -r 6dafad990086 -r 4f65e343ecdf test-data/populations/populations.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/populations/populations.gtf	Tue Apr 27 09:35:13 2021 +0000
@@ -0,0 +1,4 @@
+# Stacks v2.55; GTF export; March 16, 2021
+un	Stacks	locus	1	204	.	+	.	locus_id "1"; sample_cnt "2"
+un	Stacks	locus	205	409	.	+	.	locus_id "2"; sample_cnt "2"
+un	Stacks	locus	410	613	.	+	.	locus_id "3"; sample_cnt "2"