comparison bamtools-filter.xml @ 8:709d8669e8d6 draft

planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

7:255d1b5c962e

          <!-- would be fanstastic to have AND and OR constructs in when statements -->
          <when value="alignmentFlag">
            <param name="bam_property_value" type="integer" value="3" label="Filter on this alignment flag" help="Default (3) is for a paired read mapped in a proper pair"/>
          </when>
          <when value="cigar">
            <param name="bam_property_value" type="text" size="10" value="101M" label="Filter on this CIGAR string" help="Default (101M) is for 101 continuously matched bases"/>
          </when>
          <when value="insertSize">
            <param name="bam_property_value" type="text" size="10" value=">=250" label="Filter on inster size" help="You can use &gt;, &lt;, =, and ! (not) in your expression. E.g., to select pairs with inster size above 250 nt use &quot;>=250&quot;">
              <sanitizer invalid_char="">
                <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
              </sanitizer>
            </param>
          </when>

      </repeat>
    </repeat>
    <conditional name="rule_configuration">
      <param name="rules_selector" type="boolean" truevalue="true" falsevalue="false" label="Would you like to set rules?" help="Allows complex logical constructs. See Example 4 below." />
      <when value="true">
        <param name="rules" type="text" size="20" label="Enter rules here" help="This option can only be used with at least two conditions. Read help below (Example 4) to understand how it works." >
          <sanitizer invalid_char="">
            <valid initial="string.printable"/>
          </sanitizer>
        </param>
      </when>

8:709d8669e8d6

          <!-- would be fanstastic to have AND and OR constructs in when statements -->
          <when value="alignmentFlag">
            <param name="bam_property_value" type="integer" value="3" label="Filter on this alignment flag" help="Default (3) is for a paired read mapped in a proper pair"/>
          </when>
          <when value="cigar">
            <param name="bam_property_value" type="text" value="101M" label="Filter on this CIGAR string" help="Default (101M) is for 101 continuously matched bases"/>
          </when>
          <when value="insertSize">
            <param name="bam_property_value" type="text" value=">=250" label="Filter on inster size" help="You can use &gt;, &lt;, =, and ! (not) in your expression. E.g., to select pairs with inster size above 250 nt use &quot;>=250&quot;">
              <sanitizer invalid_char="">
                <valid initial="string.letters,string.digits"><add value="&gt;"/><add value="&lt;"/><add value="!="/></valid>
              </sanitizer>
            </param>
          </when>

      </repeat>
    </repeat>
    <conditional name="rule_configuration">
      <param name="rules_selector" type="boolean" truevalue="true" falsevalue="false" label="Would you like to set rules?" help="Allows complex logical constructs. See Example 4 below." />
      <when value="true">
        <param name="rules" type="text" label="Enter rules here" help="This option can only be used with at least two conditions. Read help below (Example 4) to understand how it works." >
          <sanitizer invalid_char="">
            <valid initial="string.printable"/>
          </sanitizer>
        </param>
      </when>