comparison macros.xml @ 7:a1213a0b7b66 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69

6:501bfb078342

<macros>
  <token name="@VERSION@">1.4.0</token>
  <xml name="stdio">
    <stdio>
      <exit_code range="1:" />
      <exit_code range=":-1" />
      <regex match="Error:" />
      <regex match="Exception:" />
    </stdio>
  </xml>
  <xml name="requirements">
    <requirements>
      <requirement type="package" version="1.4">bcftools</requirement>
      <requirement type="package" version="1.4">htslib</requirement>
      <yield />
    </requirements>
  </xml>
  <xml name="samtools_requirement">
      <requirement type="package" version="1.3.1">samtools</requirement>
  </xml>
  <xml name="version_command">
    <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
  </xml>

<![CDATA[
export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`;
]]>
  </token>
  <xml name="macro_input">
    <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf,bcf_bgzip" label="VCF/BCF Data" />
  </xml>
  <token name="@PREPARE_INPUT_FILE@">
<![CDATA[
## May need to symlink input if there is an associated
#set $input_vcf = 'input.vcf.gz'
#if $input_file.is_of_type('vcf')
  bgzip -c '$input_file' > $input_vcf &&
  bcftools index $input_vcf &&
#elif $input_file.is_of_type('vcf_bgzip')
  ln -s '$input_file' $input_vcf &&
#elif $input_file.is_of_type('bcf')
  #set $input_vcf = 'input.bcf'
  ln -s '$input_file' $input_vcf &&
  #if $input_file.metadata.bcf_index:
    ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
  #else
    bcftools index $input_vcf &&
  #end if
#elif $input_file.is_of_type('bcf_bgzip')
  ln -s '$input_file' $input_vcf &&
#end if
]]>
  </token>
  <token name="@INPUT_FILE@">
$input_vcf
  </token>

  <xml name="macro_inputs">
    <param name="input_files" type="data" format="vcf,bcf" label="Other VCF/BCF Datasets" multiple="True" />
  </xml>
  <token name="@PREPARE_INPUT_FILES@">
<![CDATA[
## May need to symlink input if there is an associated
#set $input_vcfs = []

#for (i, input_file) in enumerate($input_files):
  #set $input_vcf = 'input' + str($i) + '.vcf.gz'
  #if $input_file.is_of_type('vcf')
    bgzip -c '$input_file' > $input_vcf &&
    bcftools index $input_vcf &&
  #elif $input_file.is_of_type('vcf_bgz')
    ln -s '$input_file' $input_vcf
  #elif $input_file.is_of_type('bcf')
    #set $input_vcf = 'input' + str($i) + '.bcf.gz'
    ln -s '$input_file' $input_vcf &&
    #if $input_file.metadata.bcf_index:
      ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
    #else
      bcftools index $input_vcf &&
    #end if
  #elif $input_file.is_of_type('bcfvcf_bgz')
    ln -s '$input_file' $input_vcf &&
  #end if
  echo '$input_vcf' >> $vcfs_list_file &&
  $input_vcfs.append($input_vcf)
#end for
]]>

  <token name="@INPUT_LIST_FILE@">
$vcfs_list_file
  </token>

  <xml name="macro_fasta_ref">
    <param name="fasta_ref" argument="--fasta-ref" type="data" format="data" label="Reference sequence in FASTA format" optional="True" />
  </xml>
  <token name="@PREPARE_FASTA_REF@">
<![CDATA[
#set $input_fa_ref = None
#if 'fasta_ref' in $section and $section.fasta_ref:

     </conditional>
  </xml>


  <xml name="macro_AF_file">
    <param name="AF_file" argument="--AF-file" type="data" format="tabular" label="Allele frequencies file" optional="True" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" />
  </xml>
  <!-- This may need to bgzip and tabix the file -->
  <token name="@PREPARE_AF_FILE@">
<![CDATA[
#if 'AF_file' in $section and $section.AF_file:

  --AF-file '${section.AF_file}'
#end if
  </token>

  <xml name="macro_estimate_AF">
      <param name="estimate_AF" argument="--estimate-AF" type="data" format="data" label="Estimate allele frequency" optional="True" help="calculate AC,AN counts on the fly, using either all samples (&quot;-&quot;) or samples listed in &lt;file&gt;" />
  </xml>
  <token name="@ESTIMATE_AF@">
#if 'estimate_AF' in $section and $section.estimate_AF:
  --estimate-AF "${section.estimate_AF}"
#end if
  </token>

  <xml name="macro_exons_file">
    <param name="exons_file" type="data" format="tabular" label="exons file" optional="True" help="tab-delimited file with exons for indel frameshifts (chr,from,to; 1-based, inclusive, bgzip compressed)" />
  </xml>
  <token name="@PREPARE_EXONS_FILE@">
<![CDATA[
#set $exons_path = None
#if 'exons_file' in $section and $section.exons_file:

  --exons $exons_path
#end if
  </token>

  <xml name="macro_ploidy_file">
    <param name="ploidy_file" type="data" format="tabular" label="Ploidy file" optional="True" help="tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
  </xml>
  <token name="@PLOIDY_FILE@">
#if 'ploidy_file' in $section and $section.ploidy_file:
  --ploidy "${section.ploidy_file}"
#end if

  </xml>
  <xml name="macro_collapse_opt_id">
      <option value="id">id - only records with identical ID column are compatible. </option>
  </xml>
  <xml name="macro_collapse">
    <param name="collapse" type="select" label="Collapse" optional="True" help="Controls how to treat records with duplicate positions and defines compatible records across multiple input files">
      <option value="snps">snps - allow different alleles, as long as they all are SNPs</option>
      <option value="indels">indels - allow different alleles, as long as they all are indels</option>
      <option value="both">both - indels and snps </option>
      <option value="some">some - at least some of the ALTs must match</option>
      <option value="any">any - any combination of alleles</option>

  --collapse ${section.collapse}
#end if
  </token>

  <xml name="macro_apply_filters">
    <param name="apply_filters" type="text" value="" label="Apply Filters" optional="true"
           help="(-f --apply-filters) Skip sites where FILTER column does not contain any of the strings listed (e.g. &quot;PASS,.&quot;)">
      <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator>
    </param>
  </xml>
  <token name="@APPLY_FILTERS@">
#if $section.apply_filters:

            <option value="regions">regions</option>
            <option value="regions_file">regions-file</option>
        </param>
        <when value="__none__"/>
        <when value="regions">
            <param name="regions" type="text" value="" label="restrict to comma-separated list of regions" optional="true"
                   help="Each region is specifed as: chr or chr:pos or chr:from-to">
                 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
            </param>
        </when>
        <when value="regions_file">
            <param name="regions_file" type="data" format="vcf,bed,tabular" label="Regions File" optional="True" help="restrict to regions listed in a file" />
        </when>
    </conditional>
  </xml>
  <token name="@PREPARE_REGIONS_FILE@">
<![CDATA[

            <option value="targets">targets</option>
            <option value="targets_file">targets-file</option>
        </param>
        <when value="__none__"/>
        <when value="targets">
            <param name="targets" type="text" value="" label="Restrict to comma-separated list of targets" optional="true"
                   help="Each target is specifed as: chr or chr:pos or chr:from-to">
                 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
            </param>
            <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the targets" />
        </when>

#end if
]]>
  </token>

  <xml name="macro_samples">
      <param name="samples" type="text" value="" label="Samples" optional="true"
             help="(-s) comma separated list of samples to annotate (or exclude)">
          <validator type="regex" message="">^(\w+(,\w+)*)?$</validator>
      </param>
      <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
             help="inverts the query/filtering applied by Samples (adds &quot;^&quot; prefix to exclude)" />
      <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True"
             help="(-S) file of samples to include" />
      <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples File"
             help="inverts the query/filtering applied by Samples File" />
  </xml>
  <token name="@SAMPLES@">
#set $samples_defined = False
#if str($section.samples) != '':
  #set $samples_defined = True

  --samples-file "${section.invert_samples_file}${section.samples_file}"
#end if
  </token>

  <xml name="macro_sample">
      <param name="sample" type="text" label="Sample" optional="True" help="apply variants of the given sample" />
  </xml>
  <token name="@SAMPLE@">
#if $section.sample:
  --sample '${section.sample}'
#end if
  </token>


  <xml name="macro_include">
    <param name="include" type="text" label="Include" optional="True" help="(-i) select sites for which the expression is true">
        <validator type="regex" message="Single quote not allowed">^[^']*$</validator>
        <sanitizer sanitize="False"/>
    </param>
  </xml>
  <token name="@INCLUDE@">

  --include '${section.include}'
#end if
  </token>

  <xml name="macro_exclude">
    <param name="exclude" type="text" label="Exclude" optional="True" help="(-e) exclude sites for which the expression is true">
        <validator type="regex" message="Single quote not allowed">^[^']*$</validator>
        <sanitizer sanitize="False"/>
    </param>
  </xml>
  <token name="@EXCLUDE@">

  --exclude '${section.exclude}'
#end if
  </token>

  <xml name="macro_columns">
    <param name="columns" type="text" value="" label="Columns" optional="true"
            help="list of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">
        <validator type="regex" message="COLUMN names  separated by commas">^([^,]+(,[^,]+)*)?$</validator>
    </param>
  </xml>
  <token name="@COLUMNS@">
#if $section.columns != '':

7:a1213a0b7b66

<macros>
  <token name="@TOOL_VERSION@">1.9</token>
  <xml name="stdio">
    <stdio>
      <exit_code range="1:" />
      <exit_code range=":-1" />
      <regex match="Error:" />
      <regex match="Exception:" />
    </stdio>
  </xml>
  <xml name="requirements">
    <requirements>
      <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>
      <requirement type="package" version="1.9">htslib</requirement>
      <yield />
    </requirements>
  </xml>
  <xml name="samtools_requirement">
      <requirement type="package" version="1.9">samtools</requirement>
  </xml>
  <xml name="version_command">
    <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
  </xml>

<![CDATA[
export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`;
]]>
  </token>
  <xml name="macro_input">
    <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf" label="VCF/BCF Data" />
  </xml>
  <token name="@PREPARE_INPUT_FILE@">
<![CDATA[
## May need to symlink input if there is an associated
#set $input_vcf = 'input.vcf.gz'
#if $input_file.is_of_type('vcf')
  bgzip -c '$input_file' > $input_vcf &&
  bcftools index $input_vcf &&
#elif $input_file.is_of_type('vcf_bgzip')
  ln -s '$input_file' $input_vcf &&
  #if $input_file.metadata.tabix_index:
    ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
  #else
    bcftools index $input_vcf &&
  #end if
#elif $input_file.is_of_type('bcf')
  #set $input_vcf = 'input.bcf'
  ln -s '$input_file' $input_vcf &&
  #if $input_file.metadata.bcf_index:
    ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
  #else
    bcftools index $input_vcf &&
  #end if
#end if
]]>
  </token>
  <token name="@INPUT_FILE@">
$input_vcf
  </token>

  <xml name="macro_inputs">
    <param name="input_files" type="data" format="vcf,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />
  </xml>
  <token name="@PREPARE_INPUT_FILES@">
<![CDATA[
## May need to symlink input if there is an associated
#set $input_vcfs = []

#for (i, input_file) in enumerate($input_files):
  #set $input_vcf = 'input' + str($i) + '.vcf.gz'
  #if $input_file.is_of_type('vcf')
    bgzip -c '$input_file' > $input_vcf &&
    bcftools index $input_vcf &&
  #elif $input_file.is_of_type('vcf_bgzip')
    ln -s '$input_file' $input_vcf &&
    #if $input_file.metadata.tabix_index:
      ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
    #else
      bcftools index $input_vcf &&
    #end if
  #elif $input_file.is_of_type('bcf')
    #set $input_vcf = 'input' + str($i) + '.bcf.gz'
    ln -s '$input_file' $input_vcf &&
    #if $input_file.metadata.bcf_index:
      ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
    #else
      bcftools index $input_vcf &&
    #end if
  #end if
  echo '$input_vcf' >> $vcfs_list_file &&
  $input_vcfs.append($input_vcf)
#end for
]]>

  <token name="@INPUT_LIST_FILE@">
$vcfs_list_file
  </token>

  <xml name="macro_fasta_ref">
    <param name="fasta_ref" argument="--fasta-ref" type="data" format="data" optional="true" label="Reference sequence in FASTA format" />
  </xml>
  <token name="@PREPARE_FASTA_REF@">
<![CDATA[
#set $input_fa_ref = None
#if 'fasta_ref' in $section and $section.fasta_ref:

     </conditional>
  </xml>


  <xml name="macro_AF_file">
    <param name="AF_file" argument="--AF-file" type="data" format="tabular" optional="true" label="Allele frequencies file" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" />
  </xml>
  <!-- This may need to bgzip and tabix the file -->
  <token name="@PREPARE_AF_FILE@">
<![CDATA[
#if 'AF_file' in $section and $section.AF_file:

  --AF-file '${section.AF_file}'
#end if
  </token>

  <xml name="macro_estimate_AF">
      <param name="estimate_AF" argument="--estimate-AF" type="data" format="data" optional="true" label="Estimate allele frequency" help="Calculate AC,AN counts on the fly, using either all samples (&quot;-&quot;) or samples listed in &lt;file&gt;" />
  </xml>
  <token name="@ESTIMATE_AF@">
#if 'estimate_AF' in $section and $section.estimate_AF:
  --estimate-AF "${section.estimate_AF}"
#end if
  </token>

  <xml name="macro_exons_file">
    <param name="exons_file" type="data" format="tabular" optional="true" label="Exons file" help="Tab-delimited file with exons for indel frameshifts (chr,from,to; 1-based, inclusive, bgzip compressed)" />
  </xml>
  <token name="@PREPARE_EXONS_FILE@">
<![CDATA[
#set $exons_path = None
#if 'exons_file' in $section and $section.exons_file:

  --exons $exons_path
#end if
  </token>

  <xml name="macro_ploidy_file">
    <param name="ploidy_file" type="data" format="tabular" optional="true" label="Ploidy file" help="Tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
  </xml>
  <token name="@PLOIDY_FILE@">
#if 'ploidy_file' in $section and $section.ploidy_file:
  --ploidy "${section.ploidy_file}"
#end if

  </xml>
  <xml name="macro_collapse_opt_id">
      <option value="id">id - only records with identical ID column are compatible. </option>
  </xml>
  <xml name="macro_collapse">
    <param name="collapse" type="select" optional="true" label="Collapse" help="Controls how to treat records with duplicate positions and defines compatible records across multiple input files">
      <option value="snps">snps - allow different alleles, as long as they all are SNPs</option>
      <option value="indels">indels - allow different alleles, as long as they all are indels</option>
      <option value="both">both - indels and snps </option>
      <option value="some">some - at least some of the ALTs must match</option>
      <option value="any">any - any combination of alleles</option>

  --collapse ${section.collapse}
#end if
  </token>

  <xml name="macro_apply_filters">
    <param argument="--apply_filters" type="text" value="" optional="true" label="Apply filters"
           help="Skip sites where FILTER column does not contain any of the strings listed (e.g. &quot;PASS,.&quot;)">
      <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator>
    </param>
  </xml>
  <token name="@APPLY_FILTERS@">
#if $section.apply_filters:

            <option value="regions">regions</option>
            <option value="regions_file">regions-file</option>
        </param>
        <when value="__none__"/>
        <when value="regions">
            <param name="regions" type="text" value="" optional="true" label="Restrict to comma-separated list of regions"
                   help="Each region is specifed as: chr or chr:pos or chr:from-to">
                 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
            </param>
        </when>
        <when value="regions_file">
            <param name="regions_file" type="data" format="vcf,bed,tabular" optional="true" label="Regions file" help="Restrict to regions listed in a file" />
        </when>
    </conditional>
  </xml>
  <token name="@PREPARE_REGIONS_FILE@">
<![CDATA[

            <option value="targets">targets</option>
            <option value="targets_file">targets-file</option>
        </param>
        <when value="__none__"/>
        <when value="targets">
            <param name="targets" type="text" value="" optional="true" label="Restrict to comma-separated list of targets"
                   help="Each target is specifed as: chr or chr:pos or chr:from-to">
                 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
            </param>
            <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the targets" />
        </when>

#end if
]]>
  </token>

  <xml name="macro_samples">
      <param argument="--samples" type="text" value="" optional="true" label="Samples"
             help="Comma separated list of samples to annotate (or exclude)">
          <validator type="regex" message="">^(\w+(,\w+)*)?$</validator>
      </param>
      <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
             help="Inverts the query/filtering applied by Samples (adds &quot;^&quot; prefix to exclude)" />
      <param argument="--samples_file" type="data" format="tabular" optional="true" label="Samples file"
             help="File of samples to include" />
      <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples file"
             help="inverts the query/filtering applied by Samples file" />
  </xml>
  <token name="@SAMPLES@">
#set $samples_defined = False
#if str($section.samples) != '':
  #set $samples_defined = True

  --samples-file "${section.invert_samples_file}${section.samples_file}"
#end if
  </token>

  <xml name="macro_sample">
      <param name="sample" type="text" optional="true" label="Sample" help="Apply variants of the given sample" />
  </xml>
  <token name="@SAMPLE@">
#if $section.sample:
  --sample '${section.sample}'
#end if
  </token>


  <xml name="macro_include">
    <param argument="--include" type="text" optional="true" label="Include" help="Select sites for which the expression is true">
        <validator type="regex" message="Single quote not allowed">^[^']*$</validator>
        <sanitizer sanitize="False"/>
    </param>
  </xml>
  <token name="@INCLUDE@">

  --include '${section.include}'
#end if
  </token>

  <xml name="macro_exclude">
    <param argument="--exclude" type="text" optional="true" label="Exclude" help="Exclude sites for which the expression is true">
        <validator type="regex" message="Single quote not allowed">^[^']*$</validator>
        <sanitizer sanitize="False"/>
    </param>
  </xml>
  <token name="@EXCLUDE@">

  --exclude '${section.exclude}'
#end if
  </token>

  <xml name="macro_columns">
    <param name="columns" type="text" value="" optional="true" label="Columns"
            help="List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">
        <validator type="regex" message="COLUMN names  separated by commas">^([^,]+(,[^,]+)*)?$</validator>
    </param>
  </xml>
  <token name="@COLUMNS@">
#if $section.columns != '':