Mercurial > repos > iuc > stacks2_tsv2bam
diff macros.xml @ 0:1b270fc77c81 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
| author | iuc |
|---|---|
| date | Mon, 01 Jul 2019 10:59:53 -0400 |
| parents | |
| children | 8c2617661c49 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jul 01 10:59:53 2019 -0400 @@ -0,0 +1,596 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@STACKS_VERSION@">stacks</requirement> + <yield/> + </requirements> + </xml> + + <token name="@STACKS_VERSION@">2.4</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> + + <xml name="citation"> + <citations> + <citation type="doi">10.1111/mec.12354</citation> + <citation type="doi">10.1111/mec.12330</citation> + <citation type="doi">10.1534/g3.111.000240</citation> + <citation type="doi">10.1534/genetics.111.127324</citation> + <citation type="doi">10.1111/j.1755-0998.2010.02967.x</citation> + <citation type="doi">10.1073/pnas.1006538107</citation> + </citations> + </xml> + + <xml name="version_cmd"> + <version_command><![CDATA[ + process_radtags -h |& grep process_radtags | head -n 1 | cut -d" " -f 2 + ]]> + </version_command> + </xml> + + <token name="@STACKS_INFOS@"> +<![CDATA[ +-------- + +**Created by:** + +Stacks was developed by Julian Catchen with contributions from Angel Amores, Paul Hohenlohe, and Bill Cresko + +**Project links:** + +`Stacks website <http://catchenlab.life.illinois.edu/stacks/>`_ + +`Stacks manual <http://catchenlab.life.illinois.edu/stacks/manual/>`_ + +`Stacks google group <http://groups.google.com/group/stacks-users>`_ +]]></token> + + <!-- enzyme list for procrad and denovo --> + <xml name="enzymes"> + <option value="">Unspecified</option> + <option value="aciI">aciI</option> + <option value="ageI">ageI</option> + <option value="aluI">aluI</option> + <option value="apaLI">apaLI</option> + <option value="apeKI">apeKI</option> + <option value="apoI">apoI</option> + <option value="aseI">aseI</option> + <option value="bamHI">bamHI</option> + <option value="bbvCI">bbvCI</option> + <option value="bfaI">bfaI</option> + <option value="bfuCI">bfuCI</option> + <option value="bgIII">bgIII</option> + <option value="bsaHI">bsaHI</option> + <option value="bspDI">bspDI</option> + <option value="bstYI">bstYI</option> + <option value="cac8I">cac8I</option> + <option value="claI">claI</option> + <option value="csp6I">csp6I</option> + <option value="ddeI">ddeI</option> + <option value="dpnII">dpnII</option> + <option value="eaeI">eaeI</option> + <option value="ecoRI">ecoRI</option> + <option value="ecoRV">ecoRV</option> + <option value="ecoT22I">ecoT22I</option> + <option value="haeIII">haeIII</option> + <option value="hindIII">hindIII</option> + <option value="hinP1I">hinP1I</option> + <option value="hpaII">hpaII</option> + <option value="kpnI">kpnI</option> + <option value="mluCI">mluCI</option> + <option value="mseI">mseI</option> + <option value="mslI">mslI</option> + <option value="mspI">mspI</option> + <option value="ncoI">ncoI</option> + <option value="ndeI">ndeI</option> + <option value="nheI">nheI</option> + <option value="nlaIII">nlaIII</option> + <option value="notI">notI</option> + <option value="nsiI">nsiI</option> + <option value="nspI">nspI</option> + <option value="pstI">pstI</option> + <option value="rsaI">rsaI</option> + <option value="sacI">sacI</option> + <option value="sau3AI">sau3AI</option> + <option value="sbfI">sbfI</option> + <option value="sexAI">sexAI</option> + <option value="sgrAI">sgrAI</option> + <option value="speI">speI</option> + <option value="sphI">sphI</option> + <option value="taqI">taqI</option> + <option value="xbaI">xbaI</option> + <option value="xhoI">xhoI</option> + </xml> + + <!-- 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 + #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" /> + </xml> + <xml name="out_log"> + <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file"> + <filter>add_log</filter> + </data> + </xml> + + <!-- 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" /> + </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" /> + </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" /> + </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" /> + </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" /> + </xml> + + <!-- code for creating links to the data sets from previous pipeline steps + - stacks (i.e ustacks outputs POP.tags.tsv, POP.alleles.tsv, POP.snps.tsv) + also stores sample names in list (samples) + - cat (cstacks catalog.tags.tsv, catalog.alleles.tsv, catalog.snps.tsv) + - matches (sstacks POP.matches.tsv) --> + <token name="@LINK_STACKS_INPUT@"><![CDATA[ + #set $samples = [] + #for $input_file in $input_stacks + #set $filename = str($input_file.element_identifier) + #if not filename.endswith('.tsv') + #set $filename = $filename + ".tsv" + #end if + #if re.search('^(?!catalog).+\.(tags|alleles|snps)\.tsv$', $filename) + ln -s '${input_file}' 'stacks_inputs/$filename' && + #if $filename.endswith('.tags.tsv') + $samples.append($filename[:-9]) + #end if + #end if + #end for + ]]> + </token> + <token name="@LINK_CAT_INPUT@"><![CDATA[ + #for $input_file in $input_cat + #set $filename = str($input_file.element_identifier) + #if not filename.endswith('.tsv') + #set $filename = $filename + ".tsv" + #end if + #if re.search('^catalog\.(tags|alleles|snps)\.tsv$', $filename) + ln -s '${input_file}' 'stacks_inputs/$filename' && + #end if + #end for + ]]></token> + <token name="@LINK_MATCHES_INPUT@"><![CDATA[ + #for $input_file in $input_matches + #set $filename = str($input_file.element_identifier) + #if not filename.endswith('.tsv') + #set $filename = $filename + ".tsv" + #end if + #if re.search('matches.tsv$', $filename) + ln -s '${input_file}' 'stacks_inputs/$filename' && + #end if + #end for + ]]></token> + + <!-- fastq input for process_radtags/shortreads (non-batch) and clone/kmerfilter (batch) + for batch processing chose multiple=false and paired + otherwise multiple=true and listtype=list:paired --> + <xml name="fastq_input_bc" token_multiple="false" token_listtype="paired"> + <conditional name="input_type"> + <param name="input_type_select" type="select" label="Single-end or paired-end reads"> + <option value="single" selected="True">Single-end files</option> + <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="barcode_encoding" type="select" label="Barcode location"> + <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" /> + </param> + </when> + </conditional> + <yield/> + </xml> + + <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" /> + </expand> + </xml> + + <!-- fastq input (used in denovomap, tsv2bam, ustacks) + - fastq_optional: makes fastq input optional (true/false) + - se_option: wording for "single end" option (for tsv2bam this is the + reverse reads for the others its the forward reads) + - help: help text --> + <xml name="fastq_input" token_fastq_optional="false" token_se_option="single end or forward reads" token_help=""> + <conditional name="input_type"> + <param name="input_type_select" type="select" label="Short read data from individuals" help="@HELP@"> + <option value="single" selected="true">@SE_OPTION@</option> + <option value="paired">(paired) dataset list</option> + </param> + <when value="single"> + <param name="fqinputs" argument="-f" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" type="data" label="Reads" multiple="true" optional="@FASTQ_OPTIONAL@"/> + </when> + <when value="paired"> + <param name="fqinputs" argument="-f" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="List for forward reads or read pairs" optional="@FASTQ_OPTIONAL@"/> + </when> + </conditional> + </xml> + + <!-- helper functions for linking fastq data sets --> + <token name="@FASTQ_INPUT_FUNCTIONS@"><![CDATA[ + #from os.path import splitext + #import re + + #def clean_ext($identifier) + #while $identifier.endswith(('.1', '.2', '.fa', '.fq', '.fasta', '.fastq', '.gz', '.gzip', '.sam', '.bam')) + #set $identifier = splitext($identifier)[0] + #end while +$identifier#slurp + #end def + + #def fastq_input_foo( $sample, $read_direction="", $infix="" ) + #set $name = $clean_ext($sample.element_identifier) + #if $sample.is_collection: + #set $cur_sample=$sample[$read_direction] + #else: + #set $cur_sample=$sample + #end if + + #if $cur_sample.is_of_type('fastqsanger') + #set $ext = "fastq" + #set $inputype = "fastq" + #else if $cur_sample.is_of_type('fastqsanger.gz') + #set $ext = "fastq.gz" + #set $inputype = "gzfastq" + #else if $cur_sample.is_of_type('fasta') + #set $ext = "fasta" + #set $inputype = "fasta" + #else if $cur_sample.is_of_type('fasta.gz') + #set $ext = "fasta.gz" + #set $inputype = "gzfasta" + #else + #set $inputype = "UNKNOWN" + #end if + #set $data_path = "stacks_inputs/"+$name+$infix+"."+$ext + #set $link_cmd = "ln -s '%s' '%s' &&" % ($cur_sample, $data_path) + #return ($link_cmd, $data_path, $name, $inputype) + #end def + + ## fastq_input_batch determine link command, access path(s), and input type + ## for batch tools + ## + ## inputs + ## - sample data set / pair + ## - type "single" / "paired" + ## return (link_command, fwd_path, rev_path, inputype) + ## - link_command bash command(s) to link the data sets + ## - fwd_path file name of the link to the forward data set + ## - rev_path file name of the link to the forward data set (if type=paired) + ## - inputype input type as used in stacks ([gz]fast(a|q)) + #def fastq_input_batch($sample, $type) + #if $type == "single" + #set ($link_cmd, $path, $name, $inputype) = $fastq_input_foo($sample, "", "") + #return ($link_cmd, $path, "", $inputype) + #else: + #set ($fwd_link_cmd, $fwd_path, $name, $inputype) = $fastq_input_foo($sample, "forward", ".1") + #set ($rev_link_cmd, $rev_path, $name, $inputype) = $fastq_input_foo($sample, "reverse", ".2") + #return ( $fwd_link_cmd+$rev_link_cmd, $fwd_path, $rev_path, $inputype) + #end if + #end def + + ## fastq_input_nonbatch determine link command, access path(s), and input type + ## for non-batch tools (procrad, shortreads, denovomap the former need R[12]_ + ## and the latter needs .[12]) + ## + ## inputs + ## - samples list of data set / pair + ## - type "single" / "paired" + ## - infix_pattern pattern for the infix of the files (needs to contain %d which is replaced by 1/2) + ## return (link_command, inputype) + ## - link_command bash command(s) to link the data sets + ## - inputype input type as used in stacks ([gz]fast(a|q)) + #def fastq_input_nonbatch( $samples, $type, $infix_pattern ) + #set $link_command = "" + #for $sample in $samples + #if $type == "single" + #set ($lc, $path, $name, $inputype) = $fastq_input_foo($sample, "", "") + #set link_command += lc + #else: + #set ($lc, $path, $name, $inputype) = $fastq_input_foo($sample, "forward", $infix_pattern % (1)) + #set link_command += lc + #set ($lc, $path, $name, $inputype) = $fastq_input_foo($sample, "reverse", $infix_pattern % (2)) + #set link_command += lc + #end if + #end for + #return ($link_command, $inputype) + #end def + ]]></token> + + <!-- macro and token for BAM input, for each bam file w identifier NAME + - creates a link NAME.bam <- bam_inputs/NAME.INFIX.bam + - appends -B bam_inputs/NAME.INFIX.bam to variable bamlist + + INFIX is set to"" per default, can be set with optional variable $infix + only needed for gstacks in denovo mode which needs .matches.bam --> + <token name="@BAM_INPUT@"><![CDATA[ + #set $bamlist = "" + #for $bam in $input_bam: + #if $bam.is_of_type('bam') + #set $filename = $clean_ext($bam.element_identifier)+".bam" + ln -s '$bam' bam_inputs/$filename && + #set bamlist += " -B 'bam_inputs/"+$filename+"'" + #end if + #end for + ]]></token> + + <token name="@EXTRACT_VCF@"><![CDATA[ + ## the catalog.calls output is a gzip-ed vcf extract it + ## to make it usable in Galaxy (with the downside that we + ## need to gzip it again for downstream calls like populations) + && gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf + ]]></token> + + + + <!-- tokens and macros for gapped alignment options + the _onoff macro gives an empty conditional (which is not so nice + but allows to be used also in the full macro) --> + <token name="@GAP_OPTIONS@"><![CDATA[ + #if $gapped.use_gapped == "yes" + --max_gaps $gapped.max_gaps + --min_aln_len $gapped.min_aln_len + #else + --disable-gapped + #end if + ]]></token> + <token name="@GAP_OPTIONS_ONOFF@"><![CDATA[ + #if $gapped.use_gapped != "yes" + --disable-gapped + #end if + ]]></token> + <xml name="gap_options"> + <expand macro="gap_options_onoff"> + <param argument="--max_gaps" type="float" value="2.0" label="Number of gaps allowed between stacks before merging"/> + <param argument="--min_aln_len" type="float" value="0.8" min="0.0" max="1.0" label="Minimum length of aligned sequence in a gapped alignment"/> + </expand> + </xml> + <xml name="gap_options_onoff"> + <conditional name="gapped"> + <param name="use_gapped" argument="--disable-gapped" type="select" label="Perform gapped alignments between stacks"> + <option value="no">No</option> + <option value="yes" selected="true">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <yield/> + </when> + </conditional> + </xml> + + + <!-- ustacks outputs collection containing SAMPLE.tags.tsv, SAMPLE.snps.tsv, SAMPLE.alleles.tsv (SAMPLE!=catalog) --> + <!-- TODO tags, snps, and alleles could go to sub collections; same for other tools --> + <xml name="ustacks_outputs_macro" token_tooladd=""> + <collection name="tabs" type="list" label="${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" /> + </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" /> + </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" /> + </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" /> + </collection> + </xml> + <!-- gstacks outputs collection containing catalog.calls.vcf and catalog.fa.gz + + optional output alignments.bam (if no popmap is given) and POP.alns.bam otherwise--> + <xml name="gstacks_outputs_full_macro" token_tooladd=""> + <expand macro="gstacks_outputs_macro"/> + <data format="txt" name="distribs" label="${tool.name} on ${on_string} log.distribs" from_work_dir="stacks_outputs/gstacks.log.distribs"> + <filter>add_log_distribs</filter> + </data> + <collection name="gstacks_alns_out" type="list" label="${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> + </collection> + <data name="gstacks_aln_out" format="bam" label="${tool.name} @TOOLADD@ on ${on_string} Read alignment" from_work_dir="stacks_outputs/alignments.bam"> + <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] != "" and popmap==None</filter> + </data> + </xml> + <xml name="gstacks_outputs_macro" token_tooladd=""> + <collection name="gstacks_out" type="list" label="${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)$" ext="fasta.gz" directory="stacks_outputs" /> + </collection> + </xml> + + <!-- default output of populations --> + <xml name="populations_output_light" token_tooladd=""> + <data format="tabular" name="out_haplotypes" label="${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 ${on_string} Genotyping markers" from_work_dir="stacks_outputs/populations.markers.tsv" /> + </xml> + + <xml name="populations_output_full"> + <expand macro="populations_output_light"/> + + <!-- log_fst_comp populations.fst_summary.tsv populations.phistats_summary.tsv populations.phistats.tsv--> + <data format="tabular" name="out_phistats" label="${tool.name} on ${on_string} Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats.tsv"> + <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter> + </data> + <data format="tabular" name="out_phistats_sum" label="${tool.name} on ${on_string} Summary of Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats_summary.tsv"> + <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter> + </data> + <data format="tabular" name="out_fststats_sum" label="${tool.name} on ${on_string} Summary of Fst statistics" from_work_dir="stacks_outputs/populations.fst_summary.tsv"> + <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter> + </data> + + <!-- fasta_loci populations.loci.fa + fasta_samples populations.samples.fa + fasta_samples_raw populations.samples-raw.fa--> + <data format="tabular" name="out_fasta_strict" label="${tool.name} on ${on_string} per-locus consensus sequences" from_work_dir="stacks_outputs/populations.loci.fa"> + <filter>populations_output['fasta_loci']</filter> + </data> + <data format="tabular" name="out_fasta" label="${tool.name} on ${on_string} per-locus, per-haplotpye sequences" from_work_dir="stacks_outputs/populations.samples.fa"> + <filter>populations_output['fasta_samples']</filter> + </data> + <data format="tabular" name="out_fasta_raw" label="${tool.name} on ${on_string} per-locus, per-haplotpye sequences (regardless of biological plausibility)" from_work_dir="stacks_outputs/populations.samples-raw.fa"> + <filter>populations_output['fasta_samples_raw']</filter> + </data> + + <!-- phylip populations.fixed.phylip populations.fixed.phylip.log + phylip_var populations.var.phylip populations.var.phylip.log--> + <data format="tabular" name="out_phylip_all_pop_fix" label="${tool.name} on ${on_string} Phylip nucleotides that are fixed-within, and variant among populations" from_work_dir="stacks_outputs/populations.fixed.phylip"> + <filter>populations_output['phylip']</filter> + </data> + <data format="tabular" name="out_phylip_all_loci_fix" label="${tool.name} on ${on_string} Phylip (loci) nucleotides that are fixed-within, and variant among populations" from_work_dir="stacks_outputs/populations.fixed.phylip.log"> + <filter>populations_output['phylip']</filter> + </data> + <data format="tabular" name="out_phylip_all_pop_var" label="${tool.name} on ${on_string} Phylip all sequence as well as variable sites" from_work_dir="stacks_outputs/populations.var.phylip"> + <filter>populations_output['phylip_var']</filter> + </data> + <data format="tabular" name="out_phylip_all_loci_var" label="${tool.name} on ${on_string} Phylip (loci) all sequence as well as variable sites" from_work_dir="stacks_outputs/populations.var.phylip.log"> + <filter>populations_output['phylip_var']</filter> + </data> + + <!-- genepop populations.haps.genepop populations.snps.genepop --> + <data format="tabular" name="out_genepop_snps" label="${tool.name} on ${on_string} SNPs in GenePop format" from_work_dir="stacks_outputs/populations.snps.genepop"> + <filter>populations_output['genepop']</filter> + </data> + <data format="tabular" name="out_genepop_haps" label="${tool.name} on ${on_string} Haplotypes in GenePop format" from_work_dir="stacks_outputs/populations.haps.genepop"> + <filter>populations_output['genepop']</filter> + </data> + + <!-- vcf populations.haps.vcf populations.snps.vcf --> + <data format="vcf" name="out_vcf_haplotypes_snps" label="${tool.name} on ${on_string} SNPs in VCF format" from_work_dir="stacks_outputs/populations.snps.vcf"> + <filter>populations_output['vcf']</filter> + </data> + <data format="vcf" name="out_vcf_haplotypes_haps" label="${tool.name} on ${on_string} Haplotypes in VCF format" from_work_dir="stacks_outputs/populations.haps.vcf"> + <filter>populations_output['vcf']</filter> + </data> + + <!--plink populations.plink.map populations.plink.ped--> + <data format="tabular" name="out_plink_markers" label="${tool.name} on ${on_string} PLINK (makers)" from_work_dir="stacks_outputs/populations.plink.map"> + <filter>populations_output['plink']</filter> + </data> + <data format="tabular" name="out_plink_genotypes" label="${tool.name} on ${on_string} PLINK format (genotypes)" from_work_dir="stacks_outputs/populations.plink.ped"> + <filter>populations_output['plink']</filter> + </data> + + <!--structure populations.hzar--> + <data format="tabular" name="out_hzar" label="${tool.name} on ${on_string} hzar format" from_work_dir="stacks_outputs/populations.hzar.csv"> + <filter>populations_output['hzar']</filter> + </data> + <!--structure populations.structure--> + <data format="tabular" name="out_structure" label="${tool.name} on ${on_string} Structure format" from_work_dir="stacks_outputs/populations.structure"> + <filter>populations_output['structure']</filter> + </data> + + <!-- radpainter populations.haps.radpainter --> + <data format="tabular" name="out_radpainter" label="${tool.name} on ${on_string} Radpainter format" from_work_dir="stacks_outputs/populations.haps.radpainter"> + <filter>populations_output['radpainter']</filter> + </data> + + <!-- treemix populations.treemix --> + <data format="tabular" name="out_treemix" label="${tool.name} on ${on_string} Treemix format" from_work_dir="stacks_outputs/populations.treemix"> + <filter>populations_output['treemix']</filter> + </data> + </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> + <option value="0.05" selected="True">0.05</option> + <option value="0.01">0.01</option> + <option value="0.001">0.001</option> + </param> + </xml> + + <xml name="snp_options"> + <conditional name="select_model"> + <param argument="--model_type" type="select" label="Choose the model"> + <option value="snp" selected="true">SNP</option> + <option value="bounded">Bounded SNP</option> + <option value="fixed">Fixed</option> + </param> + <when value="snp"> + <expand macro="snp_options_alpha"/> + </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" /> + <expand macro="snp_options_alpha"/> + </when> + <when value="fixed"> + <yield/> + </when> + </conditional> + </xml> + <xml name="snp_options_full"> + <expand macro="snp_options"> + <param argument="--bc_err_freq" type="float" value="0.1" min="0.0" max="1.0" label="Barcode error frequency" help="between 0 and 1.0"/> + </expand> + </xml> + + <!-- variant calling option for use in gstacks and denovomap + default for var_alpha is 0.01 if model == marukilow (which is the case in denovomap and refmap) + otherwise no default is is available and gstacks will output and error + "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" /> + </xml> + + <xml name="barcode_encoding_single" token_type=""> + <option value="--inline_null" selected="True">@TYPE@ is inline with sequence, occurs only on single-end read (--inline_null)</option> + <option value="--index_null">@TYPE@ is provded in FASTQ header (Illumina i5 or i7 read) (--index_null)</option> + <yield/> + </xml> + + <xml name="barcode_encoding_pair" token_type=""> + <expand macro="barcode_encoding_single" type="@TYPE@"> + <option value="--null_index">@TYPE@ is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided) (--null_index)</option> + <option value="--inline_inline">@TYPE@ is inline with sequence, occurs on single and paired-end read (--inline_inline)</option> + <option value="--index_index">@TYPE@ is provded in FASTQ header (Illumina i5 and i7 reads) (--index_index)</option> + <option value="--inline_index">@TYPE@ is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read) (--inline_index)</option> + <option value="--index_inline">@TYPE@ occurs in FASTQ header (Illumina i5 or i7 read) and is inline with sequence on single-end read (if single read data) or paired-end read (if paired data) (--index_inline)</option> + </expand> + </xml> +</macros>