| Previous changeset 2:6dafad990086 (2020-07-16) Next changeset 4:5e10f396979e (2021-09-01) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009" |
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modified:
macros.xml stacks_refmap.xml |
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added:
test-data/kmerfilter/Discarded1_0001.1.1.fq test-data/kmerfilter/Discarded2_0001.2.2.fq test-data/kmerfilter/Removed1_0001.1.1.fq test-data/kmerfilter/Removed1_0001.1.1.fq.single test-data/kmerfilter/Removed2_0001.2.2.fq test-data/populations/populations.gtf |
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removed:
test-data/kmerfilter/Removed1_0001.1.1.fq.single.gz |
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| 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> |
| b |
| 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 |
| b |
| @@ -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"/> |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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- |
| b |
| 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 |
| b |
| @@ -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- |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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" |