Mercurial > repos > matthias > stacks2_ustacks
diff macros.xml @ 5:ccbb048a4178 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
| author | matthias |
|---|---|
| date | Wed, 27 Feb 2019 09:47:34 -0500 |
| parents | adbf47759371 |
| children | 742c94cfb8cf |
line wrap: on
line diff
--- a/macros.xml Fri Jan 04 03:28:15 2019 -0500 +++ b/macros.xml Wed Feb 27 09:47:34 2019 -0500 @@ -7,14 +7,10 @@ </requirements> </xml> - <token name="@STACKS_VERSION@">2.2</token> - <token name="@WRAPPER_VERSION@">2</token> - - <xml name="stdio"> - <stdio> - <exit_code range="1:" level="fatal" description="Error in Stacks execution" /> - </stdio> - </xml> + <token name="@STACKS_VERSION@">2.3c</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> @@ -51,8 +47,8 @@ `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> @@ -61,7 +57,7 @@ <option value="apeKI">apeKI</option> <option value="apoI">apoI</option> <option value="aseI">aseI</option> - <option value="bamHI">bamHI</option> + <option value="bamHI">bamHI</option> <option value="bbvCI">bbvCI</option> <option value="bfaI">bfaI</option> <option value="bfuCI">bfuCI</option> @@ -93,7 +89,7 @@ <option value="nlaIII">nlaIII</option> <option value="notI">notI</option> <option value="nsiI">nsiI</option> - <option value="nspI">nspI</option> + <option value="nspI">nspI</option> <option value="pstI">pstI</option> <option value="rsaI">rsaI</option> <option value="sacI">sacI</option> @@ -116,11 +112,11 @@ ]]></token> <token name="@CAT_LOG_TO_STDERR@"><![CDATA[ #if $output_log - cat $output_log 2>&1 + cat $output_log 2>&1 #end if ]]></token> <xml name="in_log"> - <param name="add_log" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Add log output as data set" /> + <param name="add_log" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Add log output as dataset" /> </xml> <xml name="out_log"> <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file"> @@ -129,112 +125,245 @@ </xml> <!-- inputs from previous pipeline steps --> - <xml name="input_cat_macro"> - <param name="input_cat" format="tabular,txt" type="data_collection" collection_type="list" label="Catalog files" help="output from a previous Stacks pipeline steps e.g. denovo_map, refmap or cstacks" /> + <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_tags_macro"> - <param name="input_tags" format="tabular,txt" type="data_collection" collection_type="list" label="Samples stacks" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or ustacks" /> + <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="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. gstacks, denovo_map, or refmap)" argument="-P" /> + <param name="input_aln" format="tabular,txt" 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 --> - <xml name="fastq_input_macro" token_fastq_optional="false"> + <!-- 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_selector" type="select" label="Short read data from individuals" help="Single end data or forward reads. If a paired list is provided only the forward reads are used in ustacks"> - <option value="manual" selected="true">single end or forward reads</option> - <option value="list">(paired) data set list</option> + <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="manual"> - <param name="samples" argument="-f" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" type="data" label="Reads" multiple="true" optional="@FASTQ_OPTIONAL@"/> + <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> - <when value="list"> - <param name="samples" 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@"/> + </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) --> + <xml name="fastq_input" token_fastq_optional="false" 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">single end or forward reads</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> - <!-- requires a variable $read_direction=None|"forward"|"reverse" to be set - appends noting/.1/.2 to the link name for accessing the fastq data - sets variables $name and $data_path--> - <token name="@FASTQ_INPUT@"><![CDATA[ - ## TODO should use sample.identidfier if possible (see corresp. preproc macro) - #set $name = $clean_ext($sample.name) - #set $data_path = "stacks_inputs/" + $name - #if $sample.is_collection: - #set $cur_sample=$sample[$read_direction] - #else: - #set $cur_sample=$sample - #end if - #if $read_direction == "forward": - #set $data_path = $data_path + ".1" - #elif $read_direction == "reverse": - #set $data_path = $data_path + ".2" - #end if - #if $cur_sample.is_of_type('fastqsanger') - #set $data_path = $data_path + ".fq" - #set inputype = "fastq" - #else if $cur_sample.is_of_type('fastqsanger.gz') - #set $data_path = $data_path + ".fq.gz" - #set inputype = "gzfastq" - #else if $cur_sample.is_of_type('fasta') - #set $data_path = $data_path + ".fa" - #set inputype = "fasta" - #else - #set $data_path = $data_path + ".fa.gz" - #set inputype = "gzfasta" - #end if - ln -s '$cur_sample' '${data_path}' && + + <!-- helper functions for linking fastq data sets --> + <token name="@FASTQ_INPUT_FUNCTIONS@"><![CDATA[ + #from os.path import splitext + #import re + + #def clean_ext($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--> - <xml name="bam_input_macro"> - <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="BAM files" /> - </xml> + <!-- 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: - #set $filename = $clean_ext($bam.element_identifier)+".bam" - #if re.search('.*\.bam$', $filename) + #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/"+$filename+"'" #end if #end for ]]></token> - <token name="@CLEAN_EXT@"> - <![CDATA[ - #from os.path import splitext - #import re - #def clean_ext($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 - ]]> - </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 + + + <!-- 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> + #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> + #if $gapped.use_gapped != "yes" + --disable-gapped + #end if + ]]></token> <xml name="gap_options"> <expand macro="gap_options_onoff"> <param argument="--max_gaps" type="float" value="2.0" label="Number of gaps allowed between stacks before merging"/> @@ -254,10 +383,11 @@ </conditional> </xml> + <!-- ustacks outputs collection containing SAMPLE.tags.tsv, SAMPLE.snps.tsv, SAMPLE.alleles.tsv (SAMPLE!=catalog) --> <!-- TODO tags, snps, and alleles could go to sub collections; same for other tools --> <xml name="ustacks_outputs_macro" token_tooladd=""> - <collection name="tabs" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Loci per sample"> + <collection name="tabs" type="list" label="${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" /> @@ -277,11 +407,25 @@ </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 ${on_string} Loci"> + <collection name="bams" type="list" label="${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 --> + <!-- 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" /> @@ -302,7 +446,7 @@ <xml name="populations_output_full"> <expand macro="populations_output_light"/> - <!-- log_fst_comp populations.fst_summary.tsv populations.phistats_summary.tsv populations.phistats.tsv--> + <!-- log_fst_comp populations.fst_summary.tsv populations.phistats_summary.tsv populations.phistats.tsv--> <data format="tabular" name="out_phistats" label="${tool.name} on ${on_string} Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats.tsv"> <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter> </data> @@ -313,9 +457,9 @@ <filter>advanced_options['log_fst_comp'] and fstats_conditional['fstats']=='yes'</filter> </data> - <!-- fasta_loci populations.loci.fa - fasta_samples populations.samples.fa - fasta_samples_raw populations.samples-raw.fa--> + <!-- fasta_loci populations.loci.fa + fasta_samples populations.samples.fa + fasta_samples_raw populations.samples-raw.fa--> <data format="tabular" name="out_fasta_strict" label="${tool.name} on ${on_string} per-locus consensus sequences" from_work_dir="stacks_outputs/populations.loci.fa"> <filter>populations_output['fasta_loci']</filter> </data> @@ -326,8 +470,8 @@ <filter>populations_output['fasta_samples_raw']</filter> </data> - <!-- phylip populations.fixed.phylip populations.fixed.phylip.log - phylip_var populations.var.phylip populations.var.phylip.log--> + <!-- phylip populations.fixed.phylip populations.fixed.phylip.log + phylip_var populations.var.phylip populations.var.phylip.log--> <data format="tabular" name="out_phylip_all_pop_fix" label="${tool.name} on ${on_string} Phylip nucleotides that are fixed-within, and variant among populations" from_work_dir="stacks_outputs/populations.fixed.phylip"> <filter>populations_output['phylip']</filter> </data> @@ -341,7 +485,7 @@ <filter>populations_output['phylip_var']</filter> </data> - <!-- genepop populations.haps.genepop populations.snps.genepop --> + <!-- genepop populations.haps.genepop populations.snps.genepop --> <data format="tabular" name="out_genepop_snps" label="${tool.name} on ${on_string} SNPs in GenePop format" from_work_dir="stacks_outputs/populations.snps.genepop"> <filter>populations_output['genepop']</filter> </data> @@ -349,7 +493,7 @@ <filter>populations_output['genepop']</filter> </data> - <!-- vcf populations.haps.vcf populations.snps.vcf --> + <!-- vcf populations.haps.vcf populations.snps.vcf --> <data format="vcf" name="out_vcf_haplotypes_snps" label="${tool.name} on ${on_string} SNPs in VCF format" from_work_dir="stacks_outputs/populations.snps.vcf"> <filter>populations_output['vcf']</filter> </data> @@ -357,7 +501,7 @@ <filter>populations_output['vcf']</filter> </data> - <!--plink populations.plink.map populations.plink.ped--> + <!--plink populations.plink.map populations.plink.ped--> <data format="tabular" name="out_plink_markers" label="${tool.name} on ${on_string} PLINK (makers)" from_work_dir="stacks_outputs/populations.plink.map"> <filter>populations_output['plink']</filter> </data> @@ -365,16 +509,20 @@ <filter>populations_output['plink']</filter> </data> - <!--structure populations.structure--> + <!--structure populations.structure--> <data format="tabular" name="out_structure" label="${tool.name} on ${on_string} Structure format" from_work_dir="stacks_outputs/populations.structure"> <filter>populations_output['structure']</filter> </data> - <!-- radpainter populations.haps.radpainter --> + <!-- radpainter populations.haps.radpainter --> <data format="tabular" name="out_radpainter" label="${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"> @@ -397,8 +545,8 @@ <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" /> + <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"> @@ -414,11 +562,8 @@ <!-- variant calling option for use in gstacks and denovomap --> <xml name="variant_calling_options_vg"> - <param argument="--var-alpha" name="var_alpha" type="float" value="0.05" min="0" label="alpha threshold for discovering SNPs" /> - <expand macro="variant_calling_options_g"/> - </xml> - <xml name="variant_calling_options_g"> - <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="0.01" min="0" label="Alpha threshold for discovering SNPs" /> + <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=""> @@ -428,12 +573,12 @@ </xml> <xml name="barcode_encoding_pair" token_type=""> - <expand macro="barcode_encoding_single" type="@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> + </expand> </xml> </macros>