comparison bwa_macros.xml @ 6:09a7281d24c5 draft

planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty

5:fbf460831036

      #set $rg_string += $format_read_group("\tKS:", $rg_ks)
      #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="@RG@">
-----

.. class:: warningmark

6:09a7281d24c5

      #set $rg_string += $format_read_group("\tKS:", $rg_ks)
      #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="stdio">
      <stdio>
          <exit_code range="1:" />
          <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"/>
        <filter type="param_value" ref="reference_source.ref_file" column="0"/>
      </option>
    </expand>
  </macro>

  <macro name="dbKeyActionsBwaMem">
    <expand macro="dbKeyActions">
      <option type="from_data_table" name="bwa_mem_indexes" column="1" offset="0">
        <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
        <filter type="param_value" ref="reference_source.ref_file" column="0"/>
      </option>
    </expand>
  </macro>

  <macro name="dbKeyActions">
      <actions>
          <conditional name="reference_source.reference_source_selector">
              <when value="cached">
                  <action type="metadata" name="dbkey">
                      <yield />
                  </action>
              </when>
              <when value="history">
                  <action type="metadata" name="dbkey">
                    <option type="from_param" name="reference_source.ref_file" param_attribute="dbkey" />
                  </action>
              </when>
          </conditional>
      </actions>
  </macro>

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

.. class:: warningmark