comparison macros.xml @ 3:35f66846632e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e

2:d30460440cbc

  <xml name="requirements">
    <requirements>
      <requirement type="package" version="1.3">bcftools</requirement>
      <!-- conda dependency -->
      <requirement type="package" version="1.3">htslib</requirement>
      <requirement type="package" version="0.2.6">tabix</requirement>
      <requirement type="package" version="1.2">samtools</requirement>
    </requirements>
  </xml>
  <xml name="version_command">
    <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
  </xml>
  
  <xml name="citations">
    <citations>
      <citation type="doi">10.1093/bioinformatics/btp352</citation>
      <yield />
    </citations>

  </xml>
  <token name="@PREPARE_INPUT_FILE@">
<![CDATA[
## May need to symlink input if there is an associated
#set $input_vcf = 'input.vcf.gz'
#if $input_file.datatype.file_ext == 'vcf'
  bgzip -c "$input_file" > $input_vcf &&
  bcftools index $input_vcf &&
#elif $input_file.datatype.file_ext == 'vcf_bgzip'
  ln -s "$input_file" $input_vcf
#elif $input_file.datatype.file_ext == '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 $input_file.datatype.file_ext == 'bcf_bgzip'
  ln -s "$input_file" $input_vcf
#end if
]]>
  </token>
  <token name="@INPUT_FILE@">

## May need to symlink input if there is an associated
#set $input_vcfs = []
#set $vcfs_list_file = 'vcfs_list'
#for (i,input_file) in enumerate($input_files):
  #set $input_vcf = 'input' + str($i) + '.vcf.gz'
  #if $input_file.datatype.file_ext == 'vcf'
    bgzip -c "$input_file" > $input_vcf &&
    bcftools index $input_vcf &&
  #elif $input_file.datatype.file_ext == 'vcf_bgz'
    ln -s "$input_file" $input_vcf
  #elif $input_file.datatype.file_ext == 'bcf'
    #set $input_vcf = 'input' + str($i) + '.bcf.gz'
    ## bgzip -c "$input_file" > $input_vcf &&
    ln -s "$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 $input_file.datatype.file_ext == 'bcfvcf_bgz'
    ln -s "$input_file" $input_vcf &&
  #end if
  echo '$input_vcf' >> $vcfs_list_file &&
  $input_vcfs.append($input_vcf)
#end for

  --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@">

            <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="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the target file selection" />
  </xml>
  <token name="@PREPARE_TARGETS_FILE@">
<![CDATA[
#set $targets_path = None
#if 'targets' in $section 
  #if $section.targets.targets_src == 'targets_file':
    #set $targets_path = 'targets_file.tab.gz'
    bgzip -c "$section.targets.targets_file" > $targets_path &&
    tabix -s 1 -b 2 -e 2 $targets_path &&
  #end if

            <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 with &quot;^&quot; prefix)">
          <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" />
      <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) != '':

  --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@">

  <token name="@OUTPUT_HELP@">
      <![CDATA[
Output Type
-----------

Output compressed BCF (b), or uncompressed VCF (v). 
Use the BCF option when piping between bcftools subcommands to speed up
performance by removing unecessary compression/decompression
and VCF<->BCF conversion.

This Galaxy tool recommends using the compressed BCF format

3:35f66846632e

  <xml name="requirements">
    <requirements>
      <requirement type="package" version="1.3">bcftools</requirement>
      <!-- conda dependency -->
      <requirement type="package" version="1.3">htslib</requirement>
      <!-- htslib provides tabix and bgzip
      <requirement type="package" version="0.2.6">tabix</requirement>
      -->
      <requirement type="package" version="1.2">samtools</requirement>
    </requirements>
  </xml>
  <xml name="version_command">
    <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
  </xml>

  <xml name="citations">
    <citations>
      <citation type="doi">10.1093/bioinformatics/btp352</citation>
      <yield />
    </citations>

  </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@">

## May need to symlink input if there is an associated
#set $input_vcfs = []
#set $vcfs_list_file = 'vcfs_list'
#for (i,input_file) in enumerate($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'
    ## bgzip -c "$input_file" > $input_vcf &&
    ln -s "$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

  --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@">

            <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="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the target file selection" />
  </xml>
  <token name="@PREPARE_TARGETS_FILE@">
<![CDATA[
#set $targets_path = None
#if 'targets' in $section
  #if $section.targets.targets_src == 'targets_file':
    #set $targets_path = 'targets_file.tab.gz'
    bgzip -c "$section.targets.targets_file" > $targets_path &&
    tabix -s 1 -b 2 -e 2 $targets_path &&
  #end if

            <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 with &quot;^&quot; prefix)">
          <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" />
      <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) != '':

  --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@">

  <token name="@OUTPUT_HELP@">
      <![CDATA[
Output Type
-----------

Output compressed BCF (b), or uncompressed VCF (v).
Use the BCF option when piping between bcftools subcommands to speed up
performance by removing unecessary compression/decompression
and VCF<->BCF conversion.

This Galaxy tool recommends using the compressed BCF format