comparison bwa_macros.xml @ 2:b4dfb5470bf3 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 13b3ab10ff1a2e4be39b44f885df6bbe7c23099a

1:8955a9521def

<macros>
  <import>read_group_macros.xml</import>
  <token name="@set_rg_string@">
      #set $rg_string = "@RG\\tID:" + str($rg_id)
      #set $rg_string += $format_read_group("\\tSM:", $rg_sm)
      #set $rg_string += $format_read_group("\\tPL:", $rg_pl)
      #set $rg_string += $format_read_group("\\tLB:", $rg_lb)

      #set $rg_string += $format_read_group("\\tPG:", $rg_pg)
      #set $rg_string += $format_read_group("\\tPI:", $rg_pi)
      #set $rg_string += $format_read_group("\\tPU:", $rg_pu)
  </token>

  <xml name="requirements">
    <requirements>
      <requirement type="package" version="0.7.12">bwa</requirement>
      <requirement type="package" version="1.2">samtools</requirement>
    </requirements>
  </xml>

  <xml name="stdio">
      <stdio>

          <exit_code range=":-1" />
          <regex match="Error:" />
          <regex match="Exception:" />
      </stdio>
  </xml>

  <macro name="dbKeyActionsBwa">
    <expand macro="dbKeyActions">
      <option type="from_data_table" name="bwa_indexes" column="1" offset="0">
        <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>

  1. https://biostar.usegalaxy.org/
  2. https://www.biostars.org/
  3. https://github.com/lh3/bwa
  4. http://bio-bwa.sourceforge.net/
  
  </token>
    
  <token name="@dataset_collections@">
------

**Dataset collections - processing large numbers of datasets at once**

2:b4dfb5470bf3

<macros>
  <import>read_group_macros.xml</import>

  <token name="@VERSION@">0.7.15</token>

  <token name="@set_rg_string@">
      #set $rg_string = "@RG\\tID:" + str($rg_id)
      #set $rg_string += $format_read_group("\\tSM:", $rg_sm)
      #set $rg_string += $format_read_group("\\tPL:", $rg_pl)
      #set $rg_string += $format_read_group("\\tLB:", $rg_lb)

      #set $rg_string += $format_read_group("\\tPG:", $rg_pg)
      #set $rg_string += $format_read_group("\\tPI:", $rg_pi)
      #set $rg_string += $format_read_group("\\tPU:", $rg_pu)
  </token>

  <token name="@set_reference_fasta_filename@"><![CDATA[
    #if str( $reference_source.reference_source_selector ) == "history":
        #set $reference_fasta_filename = "localref.fa"
        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
        bwa index
        #if str($reference_source.index_a) != 'auto'
            -a ${reference_source.index_a}
        #end if
        "${reference_fasta_filename}" &&
    #else:
        #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
    #end if
  ]]></token>

  <xml name="requirements">
    <requirements>
      <requirement type="package" version="@VERSION@">bwa</requirement>
      <requirement type="package" version="1.3.1">samtools</requirement>
    </requirements>
  </xml>

  <xml name="stdio">
      <stdio>

          <exit_code range=":-1" />
          <regex match="Error:" />
          <regex match="Exception:" />
      </stdio>
  </xml>

  <macro name="reference_source_conditional">
    <conditional name="reference_source">
      <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
        <option value="cached">Use a built-in genome index</option>
        <option value="history">Use a genome from history and build index</option>
      </param>
      <when value="cached">
        <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
          <options from_data_table="bwa_mem_indexes">
            <filter type="sort_by" column="2" />
            <validator type="no_options" message="No indexes are available" />
          </options>
          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
        </param>
      </when>
      <when value="history">
        <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" />
        <param name="index_a" type="select" label="Algorithm for constructing the BWT index" help="(-a)">
          <option value="auto">Auto. Let BWA decide the best algorithm to use</option>
          <option value="is">IS linear-time algorithm for constructing suffix array. It requires 5.37N memory where N is the size of the database. IS is moderately fast, but does not work with database larger than 2GB</option>
          <option value="bwtsw">BWT-SW algorithm. This method works also with big genomes</option>
        </param>
      </when>
    </conditional>
  </macro>

  <macro name="dbKeyActionsBwa">
    <expand macro="dbKeyActions">
      <option type="from_data_table" name="bwa_indexes" column="1" offset="0">
        <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>

  1. https://biostar.usegalaxy.org/
  2. https://www.biostars.org/
  3. https://github.com/lh3/bwa
  4. http://bio-bwa.sourceforge.net/

  </token>

  <token name="@dataset_collections@">
------

**Dataset collections - processing large numbers of datasets at once**