comparison bcftools_call.xml @ 1:8959eda17fca draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643

0:a531317a3527

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
  <description>SNP/indel variant calling from VCF/BCF</description>
  <macros>
    <token name="@EXECUTABLE@">call</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <expand macro="version_command" />
  <command detect_errors="aggressive"><![CDATA[
bcftools @EXECUTABLE@

## Consensus/variant calling section
#if $sec_consensus_variant_calling.select_caller == "consensus":
    --consensus-caller
#else:
    --multiallelic-caller
#end if

#if $sec_consensus_variant_calling.constraints.constrain_select == "alleles":
  --constrain alleles
#elif $sec_consensus_variant_calling.constraints.constrain_select == "trio":
  --constrain trio
  --novel-rate ${sec_consensus_variant_calling.constraints.novel_snp},${sec_consensus_variant_calling.constraints.novel_ins},${sec_consensus_variant_calling.constraints.novel_del}
  --pval-threshold "${sec_consensus_variant_calling.constraints.pval_threshold}"
#end if

#if $sec_consensus_variant_calling.prior:
  --prior "${sec_consensus_variant_calling.prior}"
#end if
${sec_consensus_variant_calling.chromosome_X}
${sec_consensus_variant_calling.chromosome_Y}


## File format section
#if str($sec_default.select_output_type) != "__none__":
  --output-type "${sec_default.select_output_type}"
#end if
@SEC_DEF_REGIONS@
@SEC_DEF_SAMPLES@
@SEC_DEF_TARGETS@


## Input/output section
${sec_input_output.keep_alts}
#set values_sec_input_output_format_fields = '","'.join([str($value) for $value in $sec_input_output.format_fields_repeat])
#if $values_sec_input_output_format_fields:
  --format-fields "${values_sec_input_output_format_fields}"
#end if

#if str($sec_input_output.gvcf) != "":
  --gvcf "${sec_input_output.gvcf}"
#end if

${sec_input_output.insert_missed}
${sec_input_output.keep_masked_ref}

#if str($sec_input_output.skip_variants) != "__none__":
  --skip-variants "${sec_input_output.skip_variants}"
#end if

${sec_input_output.variants_only}

## Primary Input/Outputs

$input_file
>
$output_file
]]>
</command>
  <inputs>
    <param name="input_file" label="VCF/BCF Data" type="data" format="vcf,bcf,vcf_bgz,bcf_bgz" />
    <section name="sec_consensus_variant_calling" expanded="true" title="Consensus/variant calling Options">
      <param name="select_caller" label="Calling Method" type="select">
        <option value="consensus">the original calling method (-c, --consensus-caller)</option>
        <option value="multiallelic">alternative model for multiallelic and rare-variant calling (-m, --multiallelic-caller)</option>
      </param>
      <conditional name="constraints" label="Constraints">
        <param name="constrain_select" label="Constraints" type="select" argument="-C">
          <option value="__none__" selected="True">No constraints</option>
          <option value="alleles">call genotypes given alleles (alleles)</option>
          <option value="trio">call genotypes given the father-mother-child constraint (trio)</option>
        </param>
        <when value="__none__" />
        <when value="alleles" />
        <when value="trio">
          <param name="novel_snp" label="Novel Rate: SNPs" type="float" default="1e-8" optional="True" help="mutation rate of SNPs" argument="--novel-rate"/>
          <param name="novel_ins" label="Novel Rate: Insertions" type="float" default="1e-9" optional="True" help="mutation rate of insertions according to their length" argument="--novel-rate" />
          <param name="novel_del" label="Novel Rate: Deletions" type="float" default="1e-9" optional="True" help="mutation rate of deletions according to their length" argument="--novel-rate" />
          <param name="pval_threshold" label="Pval Threshold" type="float" default="0.5" optional="True" help="variant if P(ref|D)&lt;FLOAT with -c" argument="--pval-treshold"/>
        </when>
      </conditional>
      <param name="prior" label="Prior" type="float" default="1.1e-3" optional="True" help="mutation rate (use bigger for greater sensitivity)" argument="--prior" />
      <param name="chromosome_X" label="Chromosome X" type="boolean" truevalue="--chromosome-X" falsevalue="" help="haploid output for male samples (requires PED file with -s)" argument="--chromosome-X"/>
      <param name="chromosome_Y" label="Chromosome Y" type="boolean" truevalue="--chromosome-Y" falsevalue="" help="haploid output for males and skips females (requires PED file with -s)" argument="--chromosome-Y"/>
    </section>
    <section name="sec_default" expanded="true" title="Default Options">
      <expand macro="macro_select_output_type" />
      <expand macro="macro_regions" />
      <expand macro="macro_samples" />
      <expand macro="macro_targets" />
    </section>
    <section name="sec_input_output" expanded="true" title="Input/output Options">
      <param name="keep_alts" label="Keep Alts" type="boolean" truevalue="--keep-alts" falsevalue="" help="keep all possible alternate alleles at variant sites" argument="--keep-alts"/>
      <repeat name="format_fields_repeat" title="Format Fields">
        <param name="format_fields" type="text" label="Format Fields" help="output format fields: e.g. GQ, GP (lowercase allowed)" argument="--format-fields" />
      </repeat>
      <param name="gvcf" label="Gvcf" type="integer" optional="True" help="output gVCF blocks of homozygous REF calls. The parameter is the minimum per-sample depth required to include a site in the non-variant block." argument="--gvcf"/>
      <param name="insert_missed" label="Insert Missed" type="boolean" truevalue="--insert-missed" falsevalue="" help="output also sites missed by mpileup but present in -T" argument="--insert-missed"/>
      <param name="keep_masked_ref" label="Keep Masked Ref" type="boolean" truevalue="--keep-masked-ref" falsevalue="" help="keep sites with masked reference allele (REF=N)" argument="--keep-masked-ref"/>
      <param name="skip_variants" label="Skip Variants" type="select" help="Skip indels/SNP sites" argument="--skip-variants">
        <option value="__none__" selected="True">Don't skip any</option>
        <option value="indels">Skip indels</option>
        <option value="snps">Skip snps</option>
      </param>
      <param name="variants_only" label="Variants Only" type="boolean" truevalue="--variants-only" falsevalue="" help="output variant sites only" argument="--variants-only"/>
    </section>
  </inputs>
  <outputs>
    <data name="output_file" format="vcf">
      <change_format>
        <when input="sec_file_format|select_output_type" value="b" format="bcf_bgz" />
        <when input="sec_file_format|select_output_type" value="u" format="bcf" />
        <when input="sec_file_format|select_output_type" value="z" format="vcf_bgz" />
        <when input="sec_file_format|select_output_type" value="v" format="vcf" />
      </change_format>
    </data>
  </outputs>
  <tests>
      <test>
          <param name="input_file" value="mpileup.vcf" />
          <param name="sec_consensus_variant_calling|select_caller" value="multiallelic" />
          <param name="sec_input_output|variants_only" value="--variants-only" />
          <param name="sec_file_format|select_output_type" value="v" />
          <output name="output_file" file="mpileup.1.out" lines_diff="2" ftype="vcf" />
      </test>
      <test>
          <param name="input_file" value="mpileup.vcf" />
          <param name="sec_consensus_variant_calling|select_caller" value="multiallelic" />
          <param name="sec_input_output|variants_only" value="--variants-only" />
          <param name="sec_input_output|gvcf" value="0" />
          <param name="sec_file_format|select_output_type" value="v" />
          <output name="output_file" file="mpileup.2.out" lines_diff="2" ftype="vcf" />
      </test>
  </tests>
  <help>
      <![CDATA[
      **bcftools call**

      SNP/indel variant calling from VCF/BCF. To be used in conjunction with
      samtools mpileup. This command replaces the former "bcftools view"
      caller. Some of the original functionality has been temporarily lost in
      the process of transition to htslib, but will be added back on popular
      demand. The original calling model can be invoked with the -c
      option.
      ]]>
  </help>
  <expand macro="citations" />
</tool>

1:8959eda17fca

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
    <description>SNP/indel variant calling from VCF/BCF</description>
    <macros>
        <token name="@EXECUTABLE@">call</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="aggressive"><![CDATA[
@PREPARE_ENV@
@PREPARE_INPUT_FILE@
#set $section = $sec_consensus_variant_calling.variant_calling
#set $targets_path = None
#if $section.method == 'multiallelic':
 #if $section.genotypes.constrain == 'alleles':  
  #set $section = $sec_consensus_variant_calling.variant_calling.genotypes
  @PREPARE_TARGETS_FILE@
 #end if
#end if

bcftools @EXECUTABLE@

#set $section = $sec_consensus_variant_calling.variant_calling
#if $section.method == 'multiallelic':
 -m
 #if str($section.gvcf) != '':
  --gvcf $section.gvcf
 #end if
 #if $section.genotypes.constrain == 'alleles':  
  --constrain alleles $section.genotypes.insert_missed
  #set $section = $sec_consensus_variant_calling.variant_calling.genotypes
  @TARGETS_FILE@
 #else
   #if $section.genotypes.constrain == 'trio':
    --constrain trio
    #if $section.genotypes.novel_rate:
     --novel-rate '$section.genotypes.novel_rate'
    #end if
   #end if
   #set $section = $sec_consensus_variant_calling.variant_calling.genotypes
   @TARGETS@
 #end if
#else 
 -c
#end if

#set $section = $sec_restrict
@REGIONS@
@SAMPLES@

#set $section = $sec_consensus_variant_calling
#if $section.pval_threshold:
  --pval-threshold  "$section.pval_threshold"
#end if
#if $section.prior:
  --prior "$section.prior"
#end if

## File format section
#set $section = $sec_file_format
#if $section.ploidy:
  --ploidy "${section.ploidy}"
#end if
#if $section.ploidy_file:
  --ploidy-file "${section.ploidy_file}"
#end if

## Input/output section
#set $section = $sec_input_output
${section.keep_alts}
## #if section.format_fields:
##   --format-fields "${section.format_fields}"
## #end if
${section.keep_masked_ref}
#if $section.skip_variants:
  --skip-variants "${section.skip_variants}"
#end if
${section.variants_only}

@OUTPUT_TYPE@
@THREADS@

## Primary Input/Outputs
@INPUT_FILE@
> "$output_file"
]]>
    </command>
    <inputs>
        <expand macro="macro_input" />
        <section name="sec_restrict" expanded="false" title="Restrict to">
            <expand macro="macro_regions" />
            <expand macro="macro_samples" />
        </section>
        <section name="sec_consensus_variant_calling" expanded="true" title="Consensus/variant calling Options">
            <conditional name="variant_calling">
                <param name="method" type="select" label="calling method">
                    <option value="multiallelic">Multiallelic and rare-variant Caller</option>
                    <option value="consensus">Consensus Caller</option>
                </param>
                <when value="multiallelic">
                    <conditional name="genotypes">
                        <param name="constrain" type="select" label="Constrain" help="one of: alleles, trio (see manual)">
                            <option value="none">Do not constrain</option>
                            <option value="alleles">alleles - call genotypes given alleles</option>
                            <option value="trio">trio - call genotypes given the father-mother-child constraint</option>
                        </param>
                        <when value="none">
                            <expand macro="macro_targets" />
                        </when>
                        <when value="alleles">
                            <expand macro="macro_targets_file"/>
                            <param name="insert_missed" type="boolean" truevalue="--insert-missed" falsevalue="" label="Insert Missed" help="output also sites missed by mpileup but present in -T" />
                        </when>
                        <when value="trio">
                            <expand macro="macro_targets" />
                            <param name="novel_rate" type="float" label="Novel Rate" default="1e-8,1e-9,1e-9" optional="true" help="likelihood of novel mutation for constrained trio calling, see man page for details" />
                        </when>
                    </conditional>
                    <param name="gvcf" type="integer" label="gvcf" optional="True" help="group non-variant sites into gVCF blocks by minimum per-sample DP" />
                </when>
                <when value="consensus">
                    <conditional name="genotypes">
                        <param name="constrain" type="select" label="Constrain" help="one of: alleles, trio (see manual)">
                            <option value="none">Do not constrain</option>
                            <option value="trio">trio - call genotypes given the father-mother-child constraint</option>
                        </param>
                        <when value="none">
                        </when>
                        <when value="trio">
                            <param name="novel_rate" type="float" label="Novel Rate" default="1e-8,1e-9,1e-9" optional="true" help="likelihood of novel mutation for constrained trio calling, see man page for details" />
                        </when>
                    </conditional>
                    <expand macro="macro_targets" />
                </when>
            </conditional>
            <param name="pval_threshold" type="float" label="Pval Threshold" default="0.5" optional="True" help="variant if P(ref|D)&lt;FLOAT with -c" />
            <param name="prior" type="float" label="Prior" default="1.1e-3" optional="True" help="mutation rate (use bigger for greater sensitivity)" />
        </section>
        <section name="sec_file_format" expanded="false" title="File format Options">
            <param name="ploidy" type="select" label="Select Predefined Ploidy" optional="true">
                <option value="GRCh37">GRCh37 - Human Genome reference assembly GRCh37 / hg19</option>
                <option value="GRCh38">GRCh37 - Human Genome reference assembly GRCh38 / hg38</option>
                <option value="X">X - Treat male samples as haploid and female as diploid regardless of the chromosome name</option>
                <option value="Y">Y - Treat male samples as haploid and female as no-copy, regardless of the chromosome name"</option>
                <option value="1">1 - Treat all samples as haploid</option>
            </param>
            <param name="ploidy_file" type="data" format="tabular" label="Ploidy File" optional="True" help="space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
            <expand macro="macro_regions" />
            <expand macro="macro_samples" />
        </section>
        <section name="sec_input_output" expanded="false" title="Input/output Options">
            <param name="keep_alts" type="boolean" truevalue="--keep-alts" falsevalue="" label="Keep Alts" help="keep all possible alternate alleles at variant sites" />
            <param name="format_fields" type="text" value="" optional="true" label="Format Fields" 
               help="output format fields: GQ,GP" >
                <validator type="regex" message="FORMAT terms separated by commas">^([A-Za-z]+(,[A-Za-z]+)*)?$</validator>
            </param>
            <param name="keep_masked_ref" type="boolean" truevalue="--keep-masked-ref" falsevalue="" label="Keep Masked Ref" help="keep sites with masked reference allele (REF=N)" />
            <param name="skip_variants" type="select" label="Skip Variants" optional="True" help="skip indels/snps">
                <option value="indels">indels</option>
                <option value="snps">snps</option>
            </param>
            <param name="variants_only" type="boolean" truevalue="--variants-only" falsevalue="" label="Variants Only" help="output variant sites only" />
        </section>
        <expand macro="macro_select_output_type" />
    </inputs>
    <outputs>
        <expand macro="macro_vcf_output"/>
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="vcf" value="mpileup.vcf" />
            <param name="method" value="multiallelic" />
            <param name="variants_only" value="true" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="DP4=2,4,8,11;MQ=49" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_file" ftype="vcf" value="mpileup.vcf" />
            <param name="method" value="multiallelic" />
            <param name="gvcf" value="0" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="MinDP" />
                    <has_text text="DP4=2,4,8,11;MQ=49" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_file" ftype="vcf" value="mpileup.X.vcf" />
            <param name="method" value="multiallelic" />
            <param name="ploidy_file" value="mpileup.ploidy" />
            <param name="samples_file" value="mpileup.samples" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="DP4=2,4,8,11;MQ=49" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_file" ftype="vcf" value="mpileup.X.vcf" />
            <param name="method" value="consensus" />
            <param name="output_type" value="v" />
            <param name="ploidy_file" value="mpileup.ploidy" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="DP4=2,4,8,11" />
                    <has_text text="PV4=1,1,1,1" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
==================================
 bcftools @EXECUTABLE@
==================================

SNP/indel variant calling from VCF/BCF. To be used in conjunction with samtools mpileup. 

  - This command replaces the former "bcftools view" caller. 
  - Some of the original functionality has been temporarily lost in the process of transition to htslib, but will be added back on popular demand. 
  - The original calling model can be invoked with the -c option.

@REGIONS_HELP@
@TARGETS_HELP@

@BCFTOOLS_MANPAGE@#@EXECUTABLE@

@BCFTOOLS_WIKI@
]]>
    </help>
    <expand macro="citations" />
</tool>