Repository 'stacks2_cstacks'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/stacks2_cstacks

Changeset 7:42d9087b4789 (2022-05-23)
Previous changeset 6:8501601a118d (2022-05-11)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit feda4e2ea70c013fcddd1dbdeab73158fe9c86a4
modified:
macros.xml
added:
test-data/populations/populations.fst_parent-progeny.tsv
test-data/populations/populations.fst_summary_wgenotypes.tsv
test-data/populations/populations.phistats_summary_wgenotypes.tsv
b
diff -r 8501601a118d -r 42d9087b4789 macros.xml
--- a/macros.xml Wed May 11 06:44:59 2022 +0000
+++ b/macros.xml Mon May 23 17:51:46 2022 +0000
[
@@ -10,7 +10,7 @@
     </xml>
 
     <token name="@TOOL_VERSION@">2.55</token>
-    <token name="@VERSION_SUFFIX@">3</token>
+    <token name="@VERSION_SUFFIX@">4</token>
     <token name="@PROFILE@">20.05</token>
 
     <xml name="citation">
@@ -474,6 +474,10 @@
         <data format="tabular" name="out_fststats_sum" label="${tool.name} on ${on_string} Summary of Fst statistics" from_work_dir="stacks_outputs/populations.fst_summary.tsv">
             <filter>fstats_conditional['fstats']=='yes' or kernel_smoothing['options_kernel']['kernel'] in ['--k', '--smooth-fstats']</filter>
         </data>
+        <collection type="list" name="out_fstats_popcompare" label="${tool.name} on ${on_string} Fst statistics between populations">
+            <discover_datasets pattern="populations\.fst_(?P&lt;designation&gt;[\w]+-[\w]+)\.tsv" format="tabular" directory="stacks_outputs"/>
+            <filter>fstats_conditional['fstats']=='yes' or kernel_smoothing['options_kernel']['kernel'] in ['--k', '--smooth-fstats']</filter>
+        </collection>
 
         <!-- fasta_loci populations.loci.fa
              fasta_samples populations.samples.fa
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diff -r 8501601a118d -r 42d9087b4789 test-data/populations/populations.fst_parent-progeny.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/populations/populations.fst_parent-progeny.tsv Mon May 23 17:51:46 2022 +0000
b
@@ -0,0 +1,5 @@
+# Locus ID Pop 1 ID Pop 2 ID Chr BP Column Overall Pi AMOVA Fst Fisher's P Odds Ratio CI Low CI High LOD Corrected AMOVA Fst Smoothed AMOVA Fst Smoothed AMOVA Fst P-value Window SNP Count
+10 parent progeny Contig_3091 34 33 0.66667 0.00000 1.000000000 1.00000 0.01984 50.40044 0.00000 0.00000 0.00000 0.00000 0
+10 parent progeny Contig_3091 89 88 0.66667 0.00000 1.000000000 1.00000 0.01984 50.40044 0.00000 0.00000 0.00000 0.00000 0
+12 parent progeny Contig_3358 34 33 0.66667 0.00000 1.000000000 1.00000 0.01984 50.40044 0.00000 0.00000 0.00000 0.00000 0
+12 parent progeny Contig_3358 89 88 0.66667 0.00000 1.000000000 1.00000 0.01984 50.40044 0.00000 0.00000 0.00000 0.00000 0
b
diff -r 8501601a118d -r 42d9087b4789 test-data/populations/populations.fst_summary_wgenotypes.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/populations/populations.fst_summary_wgenotypes.tsv Mon May 23 17:51:46 2022 +0000
b
@@ -0,0 +1,2 @@
+ parent progeny
+parent 0
b
diff -r 8501601a118d -r 42d9087b4789 test-data/populations/populations.phistats_summary_wgenotypes.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/populations/populations.phistats_summary_wgenotypes.tsv Mon May 23 17:51:46 2022 +0000
b
@@ -0,0 +1,11 @@
+# Phi_st Means
+ parent progeny
+parent -1
+
+# Fst' Means
+ parent progeny
+parent 0
+
+# Dxy Means
+ parent progeny
+parent 0.0107921