Mercurial > repos > iuc > stacks2_cstacks
diff macros.xml @ 3:c207119ba5f6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
author | iuc |
---|---|
date | Tue, 27 Apr 2021 09:37:11 +0000 |
parents | fcce77c09289 |
children | 0345dbaaa79b |
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--- a/macros.xml Thu Jul 16 07:23:04 2020 -0400 +++ b/macros.xml Tue Apr 27 09:37:11 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>