Mercurial > repos > pjbriggs > pal_finder

comparison pal_finder_macros.xml @ 7:5e133b7b79a6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded version 0.02.04.6 (uses conda dependency resolution).
author pjbriggs
date Mon, 19 Mar 2018 06:33:32 -0400
parents
children 4e625d3672ba
comparison
equal deleted inserted replaced
6:a73c48890bde 7:5e133b7b79a6
1 <macros>
2 <!--
3 Set the path for the pal_finder data files
4 -->
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>
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>
7 <xml name="output_illumina_microsat_summary">
8 <output name="output_microsat_summary">
9 <assert_contents>
10 <has_line line="allExtended:&#009;0" />
11 <has_line line="allSpan:&#009;0" />
12 <has_line line="broken:&#009;2" />
13 <has_line line="compound:&#009;2" />
14 <has_line line="readsWithMicrosat:&#009;13" />
15 <has_line line="totalBases:&#009;2320" />
16 <has_line line="totalReads:&#009;20&#009;(2 x 10)" />
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" />
18 <has_line_matching expression="(AC|TG)\t2\t7\t4\t7\t116\t0?\t0?\t0?\t0?" />
19 <has_line_matching expression="(AT|CG)\t2\t8\t0\t6\t106\t0?\t0?\t0?\t0?" />
20 <has_line_matching expression="(AG|TC)\t2\t2\t1\t2\t26\t0?\t0?\t0?\t0?" />
21 </assert_contents>
22 </output>
23 </xml>
24 <xml name="output_454_microsat_summary">
25 <output name="output_microsat_summary">
26 <assert_contents>
27 <has_line line="broken:&#009;1" />
28 <has_line line="compound:&#009;0" />
29 <has_line line="readsWithMicrosat:&#009;1" />
30 <has_line line="readsWithPrimers:&#009;0" />
31 <has_line line="totalBases:&#009;8639" />
32 <has_line line="totalReads:&#009;38" />
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" />
34 <has_line_matching expression="(AC|TG|AT|CG|AG|TC)\t.*" />
35 </assert_contents>
36 </output>
37 </xml>
38 </macros>