diff pal_finder_macros.xml @ 7:5e133b7b79a6 draft

Uploaded version 0.02.04.6 (uses conda dependency resolution).

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pal_finder_macros.xml	Mon Mar 19 06:33:32 2018 -0400
@@ -0,0 +1,38 @@
+<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>