Mercurial > repos > pjbriggs > pal_finder

annotate pal_finder_macros.xml @ 9:52dbe2089d14 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Version 0.02.04.8 (update fastq subsetting).
author pjbriggs
date Wed, 04 Jul 2018 06:05:52 -0400
parents 4e625d3672ba
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
1 <macros>
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
2 <!--
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
3 Set the path for the pal_finder data files
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
4 -->
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
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>
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
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>
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
7 <xml name="output_illumina_microsat_summary">
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
8 <output name="output_microsat_summary">
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
9 <assert_contents>
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
10 <has_line line="allExtended:&#009;0" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
11 <has_line line="allSpan:&#009;0" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
12 <has_line line="broken:&#009;2" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
13 <has_line line="compound:&#009;2" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
14 <has_line line="readsWithMicrosat:&#009;13" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
15 <has_line line="totalBases:&#009;2320" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
16 <has_line line="totalReads:&#009;20&#009;(2 x 10)" />
8
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
17 <has_line line="readsWithBadRanges:&#009;0" />
7
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
18 <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" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
19 <has_line_matching expression="(AC|TG)\t2\t7\t4\t7\t116\t0?\t0?\t0?\t0?" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
20 <has_line_matching expression="(AT|CG)\t2\t8\t0\t6\t106\t0?\t0?\t0?\t0?" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
21 <has_line_matching expression="(AG|TC)\t2\t2\t1\t2\t26\t0?\t0?\t0?\t0?" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
22 </assert_contents>
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
23 </output>
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
24 </xml>
8
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
25 <xml name="output_illumina_microsat_subset_summary">
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
26 <output name="output_microsat_summary">
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
27 <assert_contents>
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
28 <has_line line="allExtended:&#009;0" />
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
29 <has_line line="allSpan:&#009;0" />
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
30 <has_line line="broken:&#009;0" />
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
31 <has_line line="compound:&#009;2" />
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
32 <has_line line="readsWithMicrosat:&#009;7" />
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
33 <has_line line="totalBases:&#009;1160" />
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
34 <has_line line="totalReads:&#009;10&#009;(2 x 5)" />
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
35 <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" />
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
36 <has_line_matching expression="(AC|TG)\t2\t6\t3\t6\t104\t0?\t0?\t0?\t0?" />
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
37 <has_line_matching expression="(AT|CG)\t2\t3\t0\t3\t38\t0?\t0?\t0?\t0?" />
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
38 <has_line_matching expression="(AG|TC)\t2\t0\t0\t0\t0\t0?\t0?\t0?\t0?" />
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
39 </assert_contents>
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
40 </output>
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
41 </xml>
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
42 <xml name="output_illumina_microsat_summary_bad_ranges">
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
43 <output name="output_microsat_summary">
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
44 <assert_contents>
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
45 <has_line line="allExtended:&#009;2" />
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
46 <has_line line="allSpan:&#009;0" />
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
47 <has_line line="broken:&#009;0" />
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
48 <has_line line="compound:&#009;4" />
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
49 <has_line line="readsWithMicrosat:&#009;12" />
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
50 <has_line line="totalBases:&#009;2231" />
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
51 <has_line line="totalReads:&#009;12&#009;(2 x 6)" />
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
52 <has_line line="readsWithBadRanges:&#009;2" />
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
53 <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" />
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
54 <!--
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
55 I'd like to do a basic check on the remainder of the file but
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
56 there are too many lines for the 'assert_contents' method (and
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
57 the tag doesn't provide the functionality to do a simple line
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
58 count
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
59 -->
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
60 </assert_contents>
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
61 </output>
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
pjbriggs
parents: 7
diff changeset
62 </xml>
7
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
63 <xml name="output_454_microsat_summary">
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
64 <output name="output_microsat_summary">
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
65 <assert_contents>
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
66 <has_line line="broken:&#009;1" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
67 <has_line line="compound:&#009;0" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
68 <has_line line="readsWithMicrosat:&#009;1" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
69 <has_line line="readsWithPrimers:&#009;0" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
70 <has_line line="totalBases:&#009;8639" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
71 <has_line line="totalReads:&#009;38" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
72 <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" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
73 <has_line_matching expression="(AC|TG|AT|CG|AG|TC)\t.*" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
74 </assert_contents>
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
75 </output>
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
76 </xml>
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents:
diff changeset
77 </macros>