Mercurial > repos > iuc > stacks2_populations

changeset 8:564c33e5c3e3 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit feda4e2ea70c013fcddd1dbdeab73158fe9c86a4
author iuc
date Mon, 23 May 2022 17:47:23 +0000
parents a5969aa9347e
children
files macros.xml stacks_populations.xml test-data/populations/populations.fst_parent-progeny.tsv test-data/populations/populations.fst_summary_wgenotypes.tsv test-data/populations/populations.phistats_summary_wgenotypes.tsv
diffstat 5 files changed, 39 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Wed May 11 06:42:48 2022 +0000
+++ b/macros.xml	Mon May 23 17:47:23 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
--- a/stacks_populations.xml	Wed May 11 06:42:48 2022 +0000
+++ b/stacks_populations.xml	Mon May 23 17:47:23 2022 +0000
@@ -346,7 +346,7 @@
             <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output>
         </test>
         <!-- test w gstacks output as input and + all outputs -->
-        <test expect_num_outputs="27">
+        <test expect_num_outputs="28">
             <param name="options_usage|input_type" value="stacks"/>
             <param name="options_usage|input_aln">
                 <collection type="list">
@@ -377,13 +377,18 @@
             <output ftype="txt" name="output_log"><assert_contents><has_text text="Populations is done."/></assert_contents></output>
             <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/>
             <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv"/>
-            <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs" lines_diff="2"/>
+            <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs" lines_diff="2">
+                <assert_contents>
+                    <has_text text="Calculating F statistics...done."/>
+                </assert_contents>
+            </output>
             <output ftype="tabular" name="out_sumstats_sum" value="populations/populations.sumstats_summary.tsv"/>
             <output ftype="tabular" name="out_sumstats" value="populations/populations.sumstats.tsv"/>
 
             <output ftype="tabular" name="out_phistats" value="populations/populations.phistats.tsv"/>
             <output ftype="tabular" name="out_phistats_sum" value="populations/populations.phistats_summary.tsv"/>
             <output ftype="tabular" name="out_fststats_sum" value="populations/populations.fst_summary.tsv"/>
+            <output_collection name="out_fstats_popcompare" type="list" count="0"/>
             <output ftype="tabular" name="out_fasta_strict" value="populations/populations.loci.fa" compare="sim_size" delta="50"/><!--there seems to be reordering of the lines, so differences are expected only in the date contained in the Header -->
             <output ftype="tabular" name="out_fasta" value="populations/populations.samples.fa" compare="sim_size" delta="50"/><!-- " -->
             <output ftype="tabular" name="out_fasta_raw" value="populations/populations.samples-raw.fa" compare="sim_size" delta="50"/><!-- " -->
@@ -526,7 +531,7 @@
             <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output>
         </test>
         <!-- test w gstacks output as input and non default fstats/kernel/bootstrap -->
-        <test expect_num_outputs="9">
+        <test expect_num_outputs="10">
             <param name="options_usage|input_type" value="stacks"/>
             <param name="options_usage|input_aln">
                 <collection type="list">
@@ -534,7 +539,7 @@
                     <element name="catalog.fa.gz" ftype="fasta.gz" value="refmap/catalog.fa.gz"/>
                </collection>
             </param>
-            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
+            <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks_genotypes.tsv"/>
             <conditional name="fstats_conditional">
                 <param name="fstats" value="yes"/>
                 <param name="fst_correction" value="--fst-correction"/>
@@ -565,13 +570,16 @@
             <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text=""/></assert_contents></output>
             <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text=""/></assert_contents></output>
             <output ftype="tabular" name="out_phistats" value="populations/populations.phistats.tsv"/>
-            <output ftype="tabular" name="out_phistats_sum" value="populations/populations.phistats_summary.tsv"/>
-            <output ftype="tabular" name="out_fststats_sum" value="populations/populations.fst_summary.tsv"/>
+            <output ftype="tabular" name="out_phistats_sum" value="populations/populations.phistats_summary_wgenotypes.tsv"/>
+            <output ftype="tabular" name="out_fststats_sum" value="populations/populations.fst_summary_wgenotypes.tsv"/>
+            <output_collection name="out_fstats_popcompare" type="list" count="1">
+                <element name="parent-progeny" file="populations/populations.fst_parent-progeny.tsv" ftype="tabular"/>
+            </output_collection>
         </test>
         <!-- same as previous test but without fstats parameter in order to check if the filter 
              for out_phistats* and out_fststats_sum works (also instead of -k \-\-smooth-fstats
              is used) -->
-        <test expect_num_outputs="9">
+        <test expect_num_outputs="10">
             <param name="options_usage|input_type" value="stacks"/>
             <param name="options_usage|input_aln">
                 <collection type="list">
@@ -610,6 +618,7 @@
             <output ftype="tabular" name="out_phistats" value="populations/populations.phistats.tsv"/>
             <output ftype="tabular" name="out_phistats_sum" value="populations/populations.phistats_summary.tsv"/>
             <output ftype="tabular" name="out_fststats_sum" value="populations/populations.fst_summary.tsv"/>
+            <output_collection name="out_fstats_popcompare" type="list" count="0"/>
         </test>
         <!-- test w gstacks output as input and default options -->
         <test expect_num_outputs="6">
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/populations/populations.fst_parent-progeny.tsv	Mon May 23 17:47:23 2022 +0000
@@ -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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/populations/populations.fst_summary_wgenotypes.tsv	Mon May 23 17:47:23 2022 +0000
@@ -0,0 +1,2 @@
+	parent	progeny
+parent		0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/populations/populations.phistats_summary_wgenotypes.tsv	Mon May 23 17:47:23 2022 +0000
@@ -0,0 +1,11 @@
+# Phi_st Means
+	parent	progeny
+parent		-1
+
+# Fst' Means
+	parent	progeny
+parent		0
+
+# Dxy Means
+	parent	progeny
+parent		0.0107921