Mercurial > repos > iuc > stacks2_shortreads
changeset 7:c287418eb288 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit feda4e2ea70c013fcddd1dbdeab73158fe9c86a4
| author | iuc |
|---|---|
| date | Mon, 23 May 2022 17:48:31 +0000 |
| parents | 97575d01f06b |
| children | |
| files | macros.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 | 4 files changed, 23 insertions(+), 1 deletions(-) [+] |
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--- a/macros.xml Wed May 11 06:48:08 2022 +0000 +++ b/macros.xml Mon May 23 17:48:31 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<designation>[\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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.fst_parent-progeny.tsv Mon May 23 17:48:31 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 17:48:31 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 17:48:31 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