annotate pal_finder_macros.xml @ 7:5e133b7b79a6 draft

Uploaded version 0.02.04.6 (uses conda dependency resolution).

<macros>
  <!--
       Set the path for the pal_finder data files
  -->
  <token name="@CONDA_PAL_FINDER_SCRIPT_DIR@">if [ -z "\$PALFINDER_SCRIPT_DIR" ]; then export PALFINDER_SCRIPT_DIR=\$(dirname \$(readlink -e \$(which pal_finder))); fi</token>
  <token name="@CONDA_PAL_FINDER_DATA_DIR@">if [ -z "\$PALFINDER_DATA_DIR" ]; then export PALFINDER_DATA_DIR=\$(dirname \$(readlink -e \$(which pal_finder))); fi</token>
  <xml name="output_illumina_microsat_summary">
    <output name="output_microsat_summary">
      <assert_contents>
	<has_line line="allExtended:&#009;0" />
	<has_line line="allSpan:&#009;0" />
	<has_line line="broken:&#009;2" />
	<has_line line="compound:&#009;2" />
	<has_line line="readsWithMicrosat:&#009;13" />
	<has_line line="totalBases:&#009;2320" />
	<has_line line="totalReads:&#009;20&#009;(2 x 10)" />
	<has_line line="Microsat Type&#009;monomer length&#009;total loci&#009;loci w/ primers&#009;reads with loci&#009;total bases&#009;extended&#009;extended w/ primers&#009;spanning&#009;spanning w/ primers" />
	<has_line_matching expression="(AC|TG)\t2\t7\t4\t7\t116\t0?\t0?\t0?\t0?" />
	<has_line_matching expression="(AT|CG)\t2\t8\t0\t6\t106\t0?\t0?\t0?\t0?" />
	<has_line_matching expression="(AG|TC)\t2\t2\t1\t2\t26\t0?\t0?\t0?\t0?" />
      </assert_contents>
    </output>
  </xml>
  <xml name="output_454_microsat_summary">
    <output name="output_microsat_summary">
      <assert_contents>
	<has_line line="broken:&#009;1" />
	<has_line line="compound:&#009;0" />
	<has_line line="readsWithMicrosat:&#009;1" />
	<has_line line="readsWithPrimers:&#009;0" />
	<has_line line="totalBases:&#009;8639" />
	<has_line line="totalReads:&#009;38" />
	<has_line line="Microsat Type&#009;monomer length&#009;reads with loci&#009;total loci&#009;loci amplified&#009;total loci bases&#009;loci bases amplified" />
	<has_line_matching expression="(AC|TG|AT|CG|AG|TC)\t.*" />
      </assert_contents>
    </output>
  </xml>
</macros>