pal_finder: pal_finder_macros.xml annotate

annotate pal_finder_macros.xml @ 17:831c838927c7 draft

Test updated fastq_subset.py utility.

author	pjbriggs
date	Mon, 02 Jul 2018 10:57:46 -0400
parents	a3af1ff4cad1
children

rev	line source
12 d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	1 <macros>
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	2 <!--
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	3 Set the path for the pal_finder data files
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	4 -->
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. 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>
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. 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>
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	7 <xml name="output_illumina_microsat_summary">
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	8 <output name="output_microsat_summary">
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	9 <assert_contents>
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	10 <has_line line="allExtended: 0" />
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	11 <has_line line="allSpan: 0" />
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	12 <has_line line="broken: 2" />
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	13 <has_line line="compound: 2" />
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	14 <has_line line="readsWithMicrosat: 13" />
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	15 <has_line line="totalBases: 2320" />
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	16 <has_line line="totalReads: 20 (2 x 10)" />
15 a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	17 <has_line line="readsWithBadRanges: 0" />
12 d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	18 <has_line line="Microsat Type monomer length total loci loci w/ primers reads with loci total bases extended extended w/ primers spanning spanning w/ primers" />
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	19 <has_line_matching expression="(AC\|TG)\t2\t7\t4\t7\t116\t0?\t0?\t0?\t0?" />
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	20 <has_line_matching expression="(AT\|CG)\t2\t8\t0\t6\t106\t0?\t0?\t0?\t0?" />
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	21 <has_line_matching expression="(AG\|TC)\t2\t2\t1\t2\t26\t0?\t0?\t0?\t0?" />
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	22 </assert_contents>
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	23 </output>
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	24 </xml>
15 a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	25 <xml name="output_illumina_microsat_subset_summary">
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	26 <output name="output_microsat_summary">
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	27 <assert_contents>
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	28 <has_line line="allExtended: 0" />
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	29 <has_line line="allSpan: 0" />
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	30 <has_line line="broken: 0" />
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	31 <has_line line="compound: 2" />
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	32 <has_line line="readsWithMicrosat: 7" />
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	33 <has_line line="totalBases: 1160" />
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	34 <has_line line="totalReads: 10 (2 x 5)" />
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	35 <has_line line="Microsat Type monomer length total loci loci w/ primers reads with loci total bases extended extended w/ primers spanning spanning w/ primers" />
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	36 <has_line_matching expression="(AC\|TG)\t2\t6\t3\t6\t104\t0?\t0?\t0?\t0?" />
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	37 <has_line_matching expression="(AT\|CG)\t2\t3\t0\t3\t38\t0?\t0?\t0?\t0?" />
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	38 <has_line_matching expression="(AG\|TC)\t2\t0\t0\t0\t0\t0?\t0?\t0?\t0?" />
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	39 </assert_contents>
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	40 </output>
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	41 </xml>
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	42 <xml name="output_illumina_microsat_summary_bad_ranges">
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	43 <output name="output_microsat_summary">
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	44 <assert_contents>
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	45 <has_line line="allExtended: 2" />
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	46 <has_line line="allSpan: 0" />
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	47 <has_line line="broken: 0" />
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	48 <has_line line="compound: 4" />
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	49 <has_line line="readsWithMicrosat: 12" />
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	50 <has_line line="totalBases: 2231" />
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	51 <has_line line="totalReads: 12 (2 x 6)" />
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	52 <has_line line="readsWithBadRanges: 2" />
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	53 <has_line line="Microsat Type monomer length total loci loci w/ primers reads with loci total bases extended extended w/ primers spanning spanning w/ primers" />
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	54 <!--
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	55 I'd like to do a basic check on the remainder of the file but
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	56 there are too many lines for the 'assert_contents' method (and
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	57 the tag doesn't provide the functionality to do a simple line
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	58 count
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	59 -->
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	60 </assert_contents>
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	61 </output>
a3af1ff4cad1 pal_finder 0.02.04.7 for testing. pjbriggs parents: 13 diff changeset	62 </xml>
12 d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	63 <xml name="output_454_microsat_summary">
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	64 <output name="output_microsat_summary">
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	65 <assert_contents>
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	66 <has_line line="broken: 1" />
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	67 <has_line line="compound: 0" />
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	68 <has_line line="readsWithMicrosat: 1" />
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	69 <has_line line="readsWithPrimers: 0" />
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	70 <has_line line="totalBases: 8639" />
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	71 <has_line line="totalReads: 38" />
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	72 <has_line line="Microsat Type monomer length reads with loci total loci loci amplified total loci bases loci bases amplified" />
13 88c972081f15 Uploaded pjbriggs parents: 12 diff changeset	73 <has_line_matching expression="(AC\|TG\|AT\|CG\|AG\|TC)\t.*" />
12 d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	74 </assert_contents>
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	75 </output>
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	76 </xml>
d26fb5260c67 0.02.04.6: update to use conda to resolve dependencies. pjbriggs parents: diff changeset	77 </macros>

Mercurial > repos > pjbriggs > pal_finder

annotate pal_finder_macros.xml @ 17:831c838927c7 draft