Mercurial > repos > iuc > stacks2_sstacks
diff macros.xml @ 2:0b8c84a7fdb5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
| author | iuc |
|---|---|
| date | Wed, 15 Jul 2020 17:20:51 -0400 |
| parents | e58e2ecb6285 |
| children | cd034465d4a4 |
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--- a/macros.xml Mon Sep 30 14:14:39 2019 -0400 +++ b/macros.xml Wed Jul 15 17:20:51 2020 -0400 @@ -3,12 +3,14 @@ <xml name="requirements"> <requirements> <requirement type="package" version="@STACKS_VERSION@">stacks</requirement> + <requirement type="package" version="3.7">python</requirement> + <requirement type="package" version="4.6.0">findutils</requirement> <yield/> </requirements> </xml> - <token name="@STACKS_VERSION@">2.4</token> - <token name="@WRAPPER_VERSION@">1</token> + <token name="@STACKS_VERSION@">2.53</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> @@ -107,16 +109,11 @@ <!-- log file handling --> <token name="@TEE_APPEND_LOG@"><![CDATA[ #if $output_log - 2>> '$output_log' && - #end if - ]]></token> - <token name="@CAT_LOG_TO_STDERR@"><![CDATA[ - #if $output_log - cat '$output_log' 2>&1 + 2> '$output_log' #end if ]]></token> <xml name="in_log"> - <param name="add_log" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Add log output as dataset" /> + <param name="add_log" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Add log output as dataset"/> </xml> <xml name="out_log"> <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file"> @@ -126,19 +123,19 @@ <!-- inputs from previous pipeline steps --> <xml name="input_stacks_macro"> - <param name="input_stacks" format="tabular,txt" type="data_collection" collection_type="list" label="Loci and polymorphism" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or ustacks" /> + <param name="input_stacks" format="tabular,txt" type="data_collection" collection_type="list" label="Loci and polymorphism" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or ustacks"/> </xml> <xml name="input_cat_macro"> - <param name="input_cat" format="tabular,txt" type="data_collection" collection_type="list" label="Catalog of loci" help="output from a previous Stacks pipeline steps e.g. denovo_map, refmap or cstacks" /> + <param name="input_cat" format="tabular,txt" type="data_collection" collection_type="list" label="Catalog of loci" help="output from a previous Stacks pipeline steps e.g. denovo_map, refmap or cstacks"/> </xml> <xml name="input_matches_macro"> - <param name="input_matches" format="tabular,txt" type="data_collection" collection_type="list" label="Matches to the catalog" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or sstacks" /> + <param name="input_matches" format="tabular,txt" type="data_collection" collection_type="list" label="Matches to the catalog" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or sstacks"/> </xml> <xml name="bam_input_macro"> - <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="Aligned data" help="either the matches to the catalog (bam), i.e. tsv2bam, or reads aligned to a reference" /> + <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="Aligned data" help="either the matches to the catalog (bam), i.e. tsv2bam, or reads aligned to a reference"/> </xml> <xml name="input_aln_macro"> - <param name="input_aln" format="vcf,fasta.gz" type="data_collection" collection_type="list" label="Assembled contigs and variant sites" help="output from previous Stacks pipeline steps (e.g. gstacks, denovo_map, or refmap)" argument="-P" /> + <param name="input_aln" format="vcf,fasta.gz" type="data_collection" collection_type="list" label="Assembled contigs and variant sites" help="output from previous Stacks pipeline steps (e.g. gstacks, denovo_map, or refmap)" argument="-P"/> </xml> <!-- code for creating links to the data sets from previous pipeline steps @@ -195,15 +192,15 @@ <option value="paired">Paired-end files</option> </param> <when value="single"> - <param name="fqinputs" argument="-f" type="data" format="fastqsanger,fastqsanger.gz" multiple="@MULTIPLE@" label="Singles-end reads" /> + <param name="fqinputs" argument="-f" type="data" format="fastqsanger,fastqsanger.gz" multiple="@MULTIPLE@" label="Singles-end reads"/> <param name="barcode_encoding" type="select" label="Barcode location"> - <expand macro="barcode_encoding_single" type="Barcode" /> + <expand macro="barcode_encoding_single" type="Barcode"/> </param> </when> <when value="paired"> <param name="fqinputs" type="data_collection" collection_type="@LISTTYPE@" label="Paired-end reads" format="fastqsanger,fastqsanger.gz"/> <param name="barcode_encoding" type="select" label="Barcode location"> - <expand macro="barcode_encoding_pair" type="Barcode" /> + <expand macro="barcode_encoding_pair" type="Barcode"/> </param> </when> </conditional> @@ -212,7 +209,7 @@ <xml name="fastq_input_bc_file" token_multiple="false" token_listtype="paired"> <expand macro="fastq_input_bc" multiple="@MULTIPLE@" listtype="@LISTTYPE@"> - <param name="barcode" argument="-b" type="data" format="tabular,txt" label="Barcode file" /> + <param name="barcode" argument="-b" type="data" format="tabular,txt" label="Barcode file"/> </expand> </xml> @@ -392,27 +389,27 @@ <!-- TODO tags, snps, and alleles could go to sub collections; same for other tools --> <xml name="ustacks_outputs_macro" token_tooladd=""> <collection name="tabs" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Loci and polymorphism"> - <discover_datasets pattern="(?P<name>(?!catalog).+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" /> - <discover_datasets pattern="(?P<name>(?!catalog).+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" /> - <discover_datasets pattern="(?P<name>(?!catalog).+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>(?!catalog).+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs"/> + <discover_datasets pattern="(?P<name>(?!catalog).+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs"/> + <discover_datasets pattern="(?P<name>(?!catalog).+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs"/> </collection> </xml> <!-- cstacks outputs collection containing catalog.tags.tsv, catalog.snps.tsv, catalog.alleles.tsv --> <xml name="cstacks_outputs_macro" token_tooladd=""> <collection name="catalog" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Catalog of loci"> - <discover_datasets pattern="(?P<name>catalog\.(tags|snps|alleles))\.tsv$" ext="tabular" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>catalog\.(tags|snps|alleles))\.tsv$" ext="tabular" directory="stacks_outputs"/> </collection> </xml> <!-- sstacks outputs collection containing SAMPLE.matches.tsv --> <xml name="sstacks_outputs_macro" token_tooladd=""> <collection name="matches" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Matches to the catalog"> - <discover_datasets pattern="(?P<name>.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs"/> </collection> </xml> <!-- tsv2bam outputs collection containing SAMPLE.matches.bam --> <xml name="tsv2bam_outputs_macro" token_tooladd=""> <collection name="bams" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Matches to the catalog (bam)"> - <discover_datasets pattern="(?P<name>.+\.matches)\.bam$" ext="bam" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+\.matches)\.bam$" ext="bam" directory="stacks_outputs"/> </collection> </xml> <!-- gstacks outputs collection containing catalog.calls.vcf and catalog.fa.gz @@ -423,7 +420,7 @@ <filter>add_log_distribs</filter> </data> <collection name="gstacks_alns_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Read alignments"> - <discover_datasets pattern="(?P<name>.*).alns.bam$" ext="bam" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.*).alns.bam$" ext="bam" directory="stacks_outputs"/> <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] != "" and popmap!=None</filter> </collection> <data name="gstacks_aln_out" format="bam" label="${tool.name} @TOOLADD@ on ${on_string} Read alignment" from_work_dir="stacks_outputs/alignments.bam"> @@ -432,24 +429,27 @@ </xml> <xml name="gstacks_outputs_macro" token_tooladd=""> <collection name="gstacks_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Assembled contigs and variant sites"> - <discover_datasets pattern="(?P<name>catalog\.calls\.vcf)$" ext="vcf" directory="stacks_outputs" /> - <discover_datasets pattern="(?P<name>catalog\.fa\.gz)$" ext="fasta.gz" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>catalog\.calls\.vcf)$" ext="vcf" directory="stacks_outputs"/> + <discover_datasets pattern="(?P<name>catalog\.fa\.gz)$" ext="fasta.gz" directory="stacks_outputs"/> </collection> </xml> <!-- default output of populations --> <xml name="populations_output_light" token_tooladd=""> - <data format="tabular" name="out_haplotypes" label="${tool.name} @TOOLADD@ on ${on_string} Raw Genotypes/Haplotypes" from_work_dir="stacks_outputs/populations.haplotypes.tsv" /> - <data format="tabular" name="out_hapstats" label="${tool.name} @TOOLADD@ on ${on_string} Population-level haplotype summary statistics" from_work_dir="stacks_outputs/populations.hapstats.tsv" /> - <data format="txt" name="out_populations_log_distribs" label="${tool.name} @TOOLADD@ on ${on_string} Populations log distributions" from_work_dir="stacks_outputs/populations.log.distribs" /> - <data format="tabular" name="out_sumstats_sum" label="${tool.name} @TOOLADD@ on ${on_string} Summary of Population-level summary statistics" from_work_dir="stacks_outputs/populations.sumstats_summary.tsv" /> - <data format="tabular" name="out_sumstats" label="${tool.name} @TOOLADD@ on ${on_string} Population-level summary statistics" from_work_dir="stacks_outputs/populations.sumstats.tsv" /> - <data format="tabular" name="out_sql" label="${tool.name} @TOOLADD@ on ${on_string} Genotyping markers" from_work_dir="stacks_outputs/populations.markers.tsv" /> + <data format="tabular" name="out_haplotypes" label="${tool.name} @TOOLADD@ on ${on_string} Raw Genotypes/Haplotypes" from_work_dir="stacks_outputs/populations.haplotypes.tsv"/> + <data format="tabular" name="out_hapstats" label="${tool.name} @TOOLADD@ on ${on_string} Population-level haplotype summary statistics" from_work_dir="stacks_outputs/populations.hapstats.tsv"/> + <data format="txt" name="out_populations_log_distribs" label="${tool.name} @TOOLADD@ on ${on_string} Populations log distributions" from_work_dir="stacks_outputs/populations.log.distribs"/> + <data format="tabular" name="out_sumstats_sum" label="${tool.name} @TOOLADD@ on ${on_string} Summary of Population-level summary statistics" from_work_dir="stacks_outputs/populations.sumstats_summary.tsv"/> + <data format="tabular" name="out_sumstats" label="${tool.name} @TOOLADD@ on ${on_string} Population-level summary statistics" from_work_dir="stacks_outputs/populations.sumstats.tsv"/> </xml> <xml name="populations_output_full"> <expand macro="populations_output_light"/> + <data format="txt" name="out_sql" label="${tool.name} @TOOLADD@ on ${on_string} Genotyping markers" from_work_dir="stacks_outputs/populations.sql.tsv"> + <filter>genetic_map_options['map_type'] and genetic_map_options['map_format']</filter> + </data> + <!-- log_fst_comp populations.fst_summary.tsv populations.phistats_summary.tsv populations.phistats.tsv--> <data format="tabular" name="out_phistats" label="${tool.name} on ${on_string} Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats.tsv"> <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter> @@ -533,6 +533,26 @@ </data> </xml> + <!-- fastq output for kmer/clone-filter --> + <xml name="fastq_output_filter"> + <data name="clean" format_source="fqinputs" label="${tool.name} on ${on_string}"> + <filter>input_type['input_type_select'] == 'single'</filter> + <yield/> + </data> + <collection name="clean_pair" type="paired" format_source="fqinputs" label="${tool.name} on ${on_string}"> + <filter>input_type['input_type_select'] == 'paired'</filter> + <yield/> + </collection> + <data name="discarded" format_source="fqinputs" label="${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"> + <filter>capture and input_type['input_type_select'] == 'paired'</filter> + <yield/> + </collection> + </xml> + <xml name="snp_options_alpha"> <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > <option value="0.1">0.1</option> @@ -554,7 +574,7 @@ </when> <when value="bounded"> <param argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="Lower bound for epsilon, the error rate" help="between 0 and 1.0"/> - <param argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="Upper bound for epsilon, the error rate" help="between 0 and 1.0" /> + <param argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="Upper bound for epsilon, the error rate" help="between 0 and 1.0"/> <expand macro="snp_options_alpha"/> </when> <when value="fixed"> @@ -574,8 +594,8 @@ "Error: No value was provided for \-\-var-alpha and there is no default for this model)" --> <xml name="variant_calling_options_vg" token_varalpha_default=""> - <param argument="--var-alpha" name="var_alpha" type="float" value="@VARALPHA_DEFAULT@" min="0" label="Alpha threshold for discovering SNPs" help="Default is 0.01 if the marukilow model is used (which is the case in refmap and denovomap), otherwise no default value is available." /> - <param argument="--gt-alpha" name="gt_alpha" type="float" value="0.05" min="0" label="Alpha threshold for calling genotypes" /> + <param argument="--var-alpha" name="var_alpha" type="float" value="@VARALPHA_DEFAULT@" min="0" label="Alpha threshold for discovering SNPs" help="Default is 0.01 if the marukilow model is used (which is the case in refmap and denovomap), otherwise no default value is available."/> + <param argument="--gt-alpha" name="gt_alpha" type="float" value="0.05" min="0" label="Alpha threshold for calling genotypes"/> </xml> <xml name="barcode_encoding_single" token_type="">