Mercurial > repos > iuc > stacks2_ustacks
changeset 4:8a35a3bc6752 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
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--- a/macros.xml Tue Apr 27 09:30:21 2021 +0000 +++ b/macros.xml Wed Sep 01 11:25:12 2021 +0000 @@ -10,8 +10,8 @@ </xml> <token name="@STACKS_VERSION@">2.55</token> - <token name="@WRAPPER_VERSION@">0</token> - <token name="@PROFILE@">20.01</token> + <token name="@WRAPPER_VERSION@">1</token> + <token name="@PROFILE@">20.05</token> <xml name="citation"> <citations> @@ -424,11 +424,11 @@ <filter>add_log_distribs</filter> </data> <collection name="gstacks_alns_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Read alignments"> - <discover_datasets pattern="(?P<name>.*).alns.bam$" ext="bam" directory="stacks_outputs"/> - <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] != "" and popmap!=None</filter> + <discover_datasets pattern="(?P<name>.*).alns.bam$" format="bam" directory="stacks_outputs"/> + <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] and popmap!=None</filter> </collection> <data name="gstacks_aln_out" format="bam" label="${tool.name} @TOOLADD@ on ${on_string} Read alignment" from_work_dir="stacks_outputs/alignments.bam"> - <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] != "" and popmap==None</filter> + <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] and popmap==None</filter> </data> </xml> <xml name="gstacks_outputs_macro" token_tooladd="">
--- a/test-data/cstacks/catalog.alleles.tsv Tue Apr 27 09:30:21 2021 +0000 +++ b/test-data/cstacks/catalog.alleles.tsv Wed Sep 01 11:25:12 2021 +0000 @@ -1,4 +1,4 @@ -# cstacks version 2.52; catalog generated on 2020-03-16 15:39:40 +# cstacks version 2.55; catalog generated on 2021-08-24 13:29:01 0 1 AC 0 0 0 1 CA 0 0 -# cstacks completed on 2020-03-16 15:39:40 +# cstacks completed on 2021-08-24 13:29:01
--- a/test-data/cstacks/catalog.snps.tsv Tue Apr 27 09:30:21 2021 +0000 +++ b/test-data/cstacks/catalog.snps.tsv Wed Sep 01 11:25:12 2021 +0000 @@ -1,4 +1,4 @@ -# cstacks version 2.52; catalog generated on 2020-03-16 15:39:40 +# cstacks version 2.55; catalog generated on 2021-08-24 13:29:01 0 1 33 E 0 A C - - 0 1 88 E 0 A C - - -# cstacks completed on 2020-03-16 15:39:40 +# cstacks completed on 2021-08-24 13:29:01
--- a/test-data/cstacks/catalog.tags.tsv Tue Apr 27 09:30:21 2021 +0000 +++ b/test-data/cstacks/catalog.tags.tsv Wed Sep 01 11:25:12 2021 +0000 @@ -1,5 +1,5 @@ -# cstacks version 2.52; catalog generated on 2020-03-16 15:39:40 +# cstacks version 2.55; catalog generated on 2021-08-24 13:29:01 0 1 consensus 0 1_1,2_1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC 0 0 0 0 2 consensus 0 1_2,2_2 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT 0 0 0 0 3 consensus 0 1_3,2_3 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA 0 0 0 -# cstacks completed on 2020-03-16 15:39:40 +# cstacks completed on 2021-08-24 13:29:01
--- a/test-data/denovo_map/denovo_map.log Tue Apr 27 09:30:21 2021 +0000 +++ b/test-data/denovo_map/denovo_map.log Wed Sep 01 11:25:12 2021 +0000 @@ -1,5 +1,5 @@ -denovo_map.pl version 2.52 started at 2020-03-16 15:39:40 -/home/berntm/miniconda3/envs/__stacks@2.52/bin/denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired +denovo_map.pl version 2.55 started at 2021-08-24 13:29:01 +/home/berntm/miniconda3/envs/mulled-v1-4cbe4390dde1292aa8dbfc7f3537b788791787f5ad55cd86edeadacb1e3df63a/bin/denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired ustacks ========== @@ -305,4 +305,4 @@ Populations is done. denovo_map.pl is done. -denovo_map.pl completed at 2020-03-16 15:39:40 +denovo_map.pl completed at 2021-08-24 13:29:01
--- a/test-data/gentest.sh Tue Apr 27 09:30:21 2021 +0000 +++ b/test-data/gentest.sh Wed Sep 01 11:25:12 2021 +0000 @@ -1,9 +1,6 @@ #!/usr/bin/env bash -eval "$(conda shell.bash hook)" -conda activate __stacks@2.52 - - - +#eval "$(conda shell.bash hook)" +#conda activate __stacks@2.52 mkdir stacks_outputs denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired &&
--- a/test-data/gstacks/catalog.calls.vcf Tue Apr 27 09:30:21 2021 +0000 +++ b/test-data/gstacks/catalog.calls.vcf Wed Sep 01 11:25:12 2021 +0000 @@ -1,6 +1,6 @@ ##fileformat=VCFv4.2 -##fileDate=20200316 -##source="Stacks v2.52" +##fileDate=20210824 +##source="Stacks v2.55" ##INFO=<ID=AD,Number=R,Type=Integer,Description="Total Depth for Each Allele"> ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
--- a/test-data/gstacks/gstacks.log Tue Apr 27 09:30:21 2021 +0000 +++ b/test-data/gstacks/gstacks.log Wed Sep 01 11:25:12 2021 +0000 @@ -1,4 +1,4 @@ -gstacks v2.52, executed 2020-03-16 15:39:40 (zlib-1.2.11) +gstacks v2.55, executed 2021-08-24 13:29:01 (zlib-1.2.11) gstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv Locus/sample distributions will be written to 'stacks_outputs/gstacks.log.distribs'.
--- a/test-data/gstacks/gstacks.log.distribs Tue Apr 27 09:30:21 2021 +0000 +++ b/test-data/gstacks/gstacks.log.distribs Wed Sep 01 11:25:12 2021 +0000 @@ -19,25 +19,25 @@ Num. threads: 1 Parallel time: 0.0 Average thread time spent: - 0.0 reading (3.0%) - 0.0 processing (95.7%) - 0.0 pre-alignments block (74.4%) - 0.0 reformatting fw-reads (0.2%) - 0.0 assembling (27.3%) - 0.0 initializing alignments (8.7%) - 0.0 aligning (36.6%) + 0.0 reading (2.8%) + 0.0 processing (95.9%) + 0.0 pre-alignments block (76.1%) + 0.0 reformatting fw-reads (0.1%) + 0.0 assembling (17.5%) + 0.0 initializing alignments (4.0%) + 0.0 aligning (52.9%) 0.0 merging read pairs (1.6%) - 0.0 post-alignments block (19.8%) + 0.0 post-alignments block (18.7%) 0.0 filtering reads (0.0%) - 0.0 counting nucleotides (3.2%) - 0.0 genotyping (1.5%) - 0.0 haplotyping (0.9%) + 0.0 counting nucleotides (2.8%) + 0.0 genotyping (1.2%) + 0.0 haplotyping (1.0%) 0.0 computing consensus (0.1%) 0.0 building_fa (0.1%) - 0.0 building_vcf (14.0%) + 0.0 building_vcf (13.4%) 0.0 writing_fa (0.0%) 0.0 writing_vcf (0.9%) - 0.0 clocking (0.1%) -Total time spent writing vcf: 0.0 (0.8%) + 0.0 clocking (0.2%) +Total time spent writing vcf: 0.0 (0.9%) VCFwrite block size: mean=1.0(n=3); max=1 END clockings
--- a/test-data/populations/populations.log Tue Apr 27 09:30:21 2021 +0000 +++ b/test-data/populations/populations.log Wed Sep 01 11:25:12 2021 +0000 @@ -1,4 +1,4 @@ -populations v2.52, executed 2020-03-16 15:39:40 (zlib-1.2.11) +populations v2.55, executed 2021-08-24 13:29:01 (zlib-1.2.11) populations -P stacks_outputs -M denovo_map/popmap_cstacks.tsv Locus/sample distributions will be written to 'stacks_outputs/populations.log.distribs'. populations parameters selected:
--- a/test-data/sstacks/PopA_01.matches.tsv Tue Apr 27 09:30:21 2021 +0000 +++ b/test-data/sstacks/PopA_01.matches.tsv Wed Sep 01 11:25:12 2021 +0000 @@ -1,6 +1,6 @@ -# sstacks version 2.52; generated on 2020-03-16 15:39:40 +# sstacks version 2.55; generated on 2021-08-24 13:29:01 1 1 1 AC 9 94M 1 1 1 CA 9 94M 2 1 2 consensus 28 94M 3 1 3 consensus 20 94M -# sstacks completed on 2020-03-16 15:39:40 +# sstacks completed on 2021-08-24 13:29:01
--- a/test-data/sstacks/PopA_02.matches.tsv Tue Apr 27 09:30:21 2021 +0000 +++ b/test-data/sstacks/PopA_02.matches.tsv Wed Sep 01 11:25:12 2021 +0000 @@ -1,6 +1,6 @@ -# sstacks version 2.52; generated on 2020-03-16 15:39:40 +# sstacks version 2.55; generated on 2021-08-24 13:29:01 1 2 1 AC 6 94M 1 2 1 CA 6 94M 2 2 2 consensus 28 94M 3 2 3 consensus 20 94M -# sstacks completed on 2020-03-16 15:39:40 +# sstacks completed on 2021-08-24 13:29:01
--- a/test-data/tsv2bam/tsv2bam.log Tue Apr 27 09:30:21 2021 +0000 +++ b/test-data/tsv2bam/tsv2bam.log Wed Sep 01 11:25:12 2021 +0000 @@ -1,4 +1,4 @@ -tsv2bam v2.52, executed 2020-03-16 15:39:40 (zlib-1.2.11) +tsv2bam v2.55, executed 2021-08-24 13:29:01 (zlib-1.2.11) tsv2bam -P stacks_outputs -M denovo_map/popmap_cstacks.tsv -R demultiplexed/ Configuration for this run: Stacks directory: 'stacks_outputs/'
--- a/test-data/ustacks/PopA_01.alleles.tsv Tue Apr 27 09:30:21 2021 +0000 +++ b/test-data/ustacks/PopA_01.alleles.tsv Wed Sep 01 11:25:12 2021 +0000 @@ -1,4 +1,4 @@ -# ustacks version 2.52; generated on 2020-03-16 15:39:40 +# ustacks version 2.55; generated on 2021-08-24 13:29:01 1 1 AC 50.00 9 1 1 CA 50.00 9 -# ustacks completed on 2020-03-16 15:39:40 +# ustacks completed on 2021-08-24 13:29:01
--- a/test-data/ustacks/PopA_01.snps.tsv Tue Apr 27 09:30:21 2021 +0000 +++ b/test-data/ustacks/PopA_01.snps.tsv Wed Sep 01 11:25:12 2021 +0000 @@ -1,4 +1,4 @@ -# ustacks version 2.52; generated on 2020-03-16 15:39:40 +# ustacks version 2.55; generated on 2021-08-24 13:29:01 1 1 0 O 24.95 A - 1 1 1 O 24.95 A - 1 1 2 O 24.95 T - @@ -281,4 +281,4 @@ 1 3 91 O 27.73 A - 1 3 92 O 27.73 G - 1 3 93 O 27.73 A - -# ustacks completed on 2020-03-16 15:39:40 +# ustacks completed on 2021-08-24 13:29:01
--- a/test-data/ustacks/PopA_01.tags.tsv Tue Apr 27 09:30:21 2021 +0000 +++ b/test-data/ustacks/PopA_01.tags.tsv Wed Sep 01 11:25:12 2021 +0000 @@ -1,4 +1,4 @@ -# ustacks version 2.52; generated on 2020-03-16 15:39:40 +# ustacks version 2.55; generated on 2021-08-24 13:29:01 1 1 consensus AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC 0 0 0 1 1 model OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOO 1 1 primary 0 lane1_fakedata7_0 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC @@ -71,4 +71,4 @@ 1 3 primary 0 lane1_fakedata2_19 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA 1 3 secondary lane1_fakedata2_5 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTAAAACACTCTGACTGCCACGCCAGCTACCTCTAGA 1 3 secondary lane1_fakedata2_17 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCCAGA -# ustacks completed on 2020-03-16 15:39:40 +# ustacks completed on 2021-08-24 13:29:01
--- a/test-data/ustacks/PopA_02.alleles.tsv Tue Apr 27 09:30:21 2021 +0000 +++ b/test-data/ustacks/PopA_02.alleles.tsv Wed Sep 01 11:25:12 2021 +0000 @@ -1,4 +1,4 @@ -# ustacks version 2.52; generated on 2020-03-16 15:39:40 +# ustacks version 2.55; generated on 2021-08-24 13:29:01 2 1 AC 50.00 6 2 1 CA 50.00 6 -# ustacks completed on 2020-03-16 15:39:40 +# ustacks completed on 2021-08-24 13:29:01
--- a/test-data/ustacks/PopA_02.snps.tsv Tue Apr 27 09:30:21 2021 +0000 +++ b/test-data/ustacks/PopA_02.snps.tsv Wed Sep 01 11:25:12 2021 +0000 @@ -1,4 +1,4 @@ -# ustacks version 2.52; generated on 2020-03-16 15:39:40 +# ustacks version 2.55; generated on 2021-08-24 13:29:01 2 1 0 O 16.64 A - 2 1 1 O 16.64 A - 2 1 2 O 16.64 T - @@ -281,4 +281,4 @@ 2 3 91 O 27.73 A - 2 3 92 O 27.73 G - 2 3 93 O 27.73 A - -# ustacks completed on 2020-03-16 15:39:40 +# ustacks completed on 2021-08-24 13:29:01
--- a/test-data/ustacks/PopA_02.tags.tsv Tue Apr 27 09:30:21 2021 +0000 +++ b/test-data/ustacks/PopA_02.tags.tsv Wed Sep 01 11:25:12 2021 +0000 @@ -1,4 +1,4 @@ -# ustacks version 2.52; generated on 2020-03-16 15:39:40 +# ustacks version 2.55; generated on 2021-08-24 13:29:01 2 1 consensus AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC 0 0 0 2 1 model OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOO 2 1 primary 0 lane1_fakedata7_7 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC @@ -65,4 +65,4 @@ 2 3 primary 0 lane1_fakedata2_18 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA 2 3 primary 0 lane1_fakedata2_19 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA 2 3 secondary lane1_fakedata2_1 1:N:0:/1 AATTCTCTACACCACTGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA -# ustacks completed on 2020-03-16 15:39:40 +# ustacks completed on 2021-08-24 13:29:01