Mercurial > repos > pjbriggs > pal_finder

annotate pal_finder_macros.xml @ 7:5e133b7b79a6 draft

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Uploaded version 0.02.04.6 (uses conda dependency resolution).
author pjbriggs
date Mon, 19 Mar 2018 06:33:32 -0400
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children 4e625d3672ba
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1 <macros>
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2 <!--
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3 Set the path for the pal_finder data files
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4 -->
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5 <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>
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6 <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>
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7 <xml name="output_illumina_microsat_summary">
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8 <output name="output_microsat_summary">
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9 <assert_contents>
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10 <has_line line="allExtended:&#009;0" />
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11 <has_line line="allSpan:&#009;0" />
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12 <has_line line="broken:&#009;2" />
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13 <has_line line="compound:&#009;2" />
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14 <has_line line="readsWithMicrosat:&#009;13" />
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15 <has_line line="totalBases:&#009;2320" />
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16 <has_line line="totalReads:&#009;20&#009;(2 x 10)" />
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17 <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" />
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18 <has_line_matching expression="(AC|TG)\t2\t7\t4\t7\t116\t0?\t0?\t0?\t0?" />
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19 <has_line_matching expression="(AT|CG)\t2\t8\t0\t6\t106\t0?\t0?\t0?\t0?" />
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20 <has_line_matching expression="(AG|TC)\t2\t2\t1\t2\t26\t0?\t0?\t0?\t0?" />
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21 </assert_contents>
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22 </output>
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23 </xml>
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24 <xml name="output_454_microsat_summary">
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25 <output name="output_microsat_summary">
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26 <assert_contents>
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27 <has_line line="broken:&#009;1" />
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28 <has_line line="compound:&#009;0" />
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29 <has_line line="readsWithMicrosat:&#009;1" />
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30 <has_line line="readsWithPrimers:&#009;0" />
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31 <has_line line="totalBases:&#009;8639" />
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32 <has_line line="totalReads:&#009;38" />
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33 <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" />
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34 <has_line_matching expression="(AC|TG|AT|CG|AG|TC)\t.*" />
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35 </assert_contents>
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36 </output>
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37 </xml>
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38 </macros>