# HG changeset patch
# User greg
# Date 1675806222 0
# Node ID 5626dc2d0ef274816142459de1e1dbd549c89502

Uploaded

diff -r 000000000000 -r 5626dc2d0ef2 .shed.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml	Tue Feb 07 21:43:42 2023 +0000
@@ -0,0 +1,9 @@
+name: call_insertions
+owner: greg
+description: Extracts aligned regions of 2 genomes and produces reference alignment and genome alignment BED files
+long_description: Extracts aligned regions of 2 genomes and produces reference alignment and genome alignment BED files
+categories: 
+- Nanopore
+remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/pima/call_insertions
+homepage_url: https://github.com/gregvonkuster/galaxy_tools
+type: unrestricted
diff -r 000000000000 -r 5626dc2d0ef2 call_insertions.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/call_insertions.xml	Tue Feb 07 21:43:42 2023 +0000
@@ -0,0 +1,39 @@
+<tool id="call_insertions" name="PIMA: call insertions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+grep AvgIdentity '$dnadiff_report' | head -1 | awk '{print $2}' > reference_identity &&
+grep AlignedBases '$dnadiff_report' | head -1 | awk '{sub(/\(.*/, "", $2); print $2 * 100}' > reference_aligned_bases &&
+cat '$dnadiff_1coords' | awk '{OFS = "\t"; if ($2 < $1){t = $2; $2 = $1; $1 = t} print $12,$1,$2}' | sort -k 1,1 -k 2,2n > '$reference_aligned' &&
+cat '$dnadiff_1coords' | awk '{OFS = "\t"; if ($4 < $3){t = $4; $4 = $3; $3 = t} print $13,$3,$4}' | sort -k 1,1 -k 2,2n > '$genome_aligned'
+]]></command>
+    <inputs>
+        <param argument="--dnadiff_report" type="data" format="txt" label="DNAdiff report file"/>
+        <param argument="--dnadiff_1coords" type="data" format="tabular" label="DNAdiff 1coords file"/>
+        <param argument="--reference_identity_min" type="float" value="98.0" min="0" label="Minimum reference identity"/>
+        <param argument="--reference_alignment_min" type="float" value="97.0" min="0" label="Minimum reference alignment"/>
+    </inputs>
+    <outputs>
+        <data name="reference_aligned" format="bed" label="${tool.name} on ${on_string} (reference alignment)"/>
+        <data name="genome_aligned" format="bed" label="${tool.name} on ${on_string} (genome alignment)"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="dnadiff_report" value="dnadiff_report.txt" ftype="txt"/>
+            <param name="dnadiff_1coords" value="dnadiff_1coords.tsv" ftype="tsv"/>
+            <output name="reference_aligned" value="reference_aligned.bed" ftype="bed"/>
+            <output name="genome_aligned" value="genome_aligned.bed" ftype="bed"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Accepts DNAdiff report and DNAdiff 1coords files and extracts the aligned regions of the two genomes, producing reference alignment
+and genome alignment BED files.
+    </help>
+    <expand macro="citations"/>
+</tool>
+
diff -r 000000000000 -r 5626dc2d0ef2 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Feb 07 21:43:42 2023 +0000
@@ -0,0 +1,18 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.0.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">21.01</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="9.1">coreutils</requirement>
+            <requirement type="package" version="5.1.0">gawk</requirement>
+            <requirement type="package" version="3.4">grep</requirement>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1101/011650</citation>
+        </citations>
+    </xml>
+</macros>
+
diff -r 000000000000 -r 5626dc2d0ef2 test-data/dnadiff_1coords.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dnadiff_1coords.tsv	Tue Feb 07 21:43:42 2023 +0000
@@ -0,0 +1,78 @@
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diff -r 000000000000 -r 5626dc2d0ef2 test-data/dnadiff_report.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dnadiff_report.txt	Tue Feb 07 21:43:42 2023 +0000
@@ -0,0 +1,87 @@
+/home/galaxies/lrn/galaxy/database/files/000/dataset_17.dat /home/galaxies/lrn/galaxy/database/files/002/dataset_2176.dat
+NUCMER
+
+                               [REF]                [QRY]
+[Sequences]
+TotalSeqs                      34305                    6
+AlignedSeqs             697(2.0318%)          3(50.0000%)
+UnalignedSeqs        33608(97.9682%)          3(50.0000%)
+
+[Bases]
+TotalBases                2077959494             11421968
+AlignedBases        3025775(0.1456%)      228614(2.0015%)
+UnalignedBases  2074933719(99.8544%)   11193354(97.9985%)
+
+[Alignments]
+1-to-1                            78                   78
+TotalLength                   187128               187163
+AvgLength                  2399.0769            2399.5256
+AvgIdentity                  94.7915              94.7915
+
+M-to-M                          3246                 3246
+TotalLength                  4521754              4532531
+AvgLength                  1393.0234            1396.3435
+AvgIdentity                  90.0308              90.0308
+
+[Feature Estimates]
+Breakpoints                     6288                 6480
+Relocations                       10                    2
+Translocations                     1                   67
+Inversions                         2                    0
+
+Insertions                      5794                  200
+InsertionSum                41691366             11221715
+InsertionAvg               7195.6103           56108.5750
+
+TandemIns                          0                    0
+TandemInsSum                       0                    0
+TandemInsAvg                  0.0000               0.0000
+
+[SNPs]
+TotalSNPs                       6547                 6547
+TG                      351(5.3612%)         323(4.9336%)
+TC                     967(14.7701%)        933(14.2508%)
+TA                      453(6.9192%)         435(6.6443%)
+GC                      232(3.5436%)         202(3.0854%)
+GA                     989(15.1062%)        986(15.0603%)
+GT                      323(4.9336%)         351(5.3612%)
+AG                     986(15.0603%)        989(15.1062%)
+AC                      352(5.3765%)         324(4.9488%)
+AT                      435(6.6443%)         453(6.9192%)
+CG                      202(3.0854%)         232(3.5436%)
+CA                      324(4.9488%)         352(5.3765%)
+CT                     933(14.2508%)        967(14.7701%)
+
+TotalGSNPs                       366                  366
+TC                      75(20.4918%)         59(16.1202%)
+TA                       15(4.0984%)          15(4.0984%)
+TG                       12(3.2787%)          13(3.5519%)
+AC                       13(3.5519%)          12(3.2787%)
+AG                      71(19.3989%)         73(19.9454%)
+AT                       15(4.0984%)          15(4.0984%)
+CT                      59(16.1202%)         75(20.4918%)
+CG                        4(1.0929%)           4(1.0929%)
+CA                       12(3.2787%)          13(3.5519%)
+GT                       13(3.5519%)          12(3.2787%)
+GC                        4(1.0929%)           4(1.0929%)
+GA                      73(19.9454%)         71(19.3989%)
+
+TotalIndels                      874                  874
+T.                     133(15.2174%)        156(17.8490%)
+G.                       60(6.8650%)         89(10.1831%)
+A.                     119(13.6156%)        138(15.7895%)
+C.                       80(9.1533%)         99(11.3272%)
+.A                     138(15.7895%)        119(13.6156%)
+.C                      99(11.3272%)          80(9.1533%)
+.G                      89(10.1831%)          60(6.8650%)
+.T                     156(17.8490%)        133(15.2174%)
+
+TotalGIndels                      34                   34
+T.                        1(2.9412%)          8(23.5294%)
+A.                        0(0.0000%)         15(44.1176%)
+C.                        0(0.0000%)          7(20.5882%)
+G.                        0(0.0000%)           3(8.8235%)
+.G                        3(8.8235%)           0(0.0000%)
+.A                      15(44.1176%)           0(0.0000%)
+.C                       7(20.5882%)           0(0.0000%)
+.T                       8(23.5294%)           1(2.9412%)
diff -r 000000000000 -r 5626dc2d0ef2 test-data/genome_aligned.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome_aligned.bed	Tue Feb 07 21:43:42 2023 +0000
@@ -0,0 +1,78 @@
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+contig_5	3855596	3856098
+contig_5	3858601	3859243
+contig_5	3865209	3866799
+contig_5	3926102	3929131
+contig_5	3941847	3942219
+contig_5	3953855	3955161
+contig_5	3958356	3959023
+contig_6	4	26710
+contig_6	26977	67983
+contig_6	50104	74120
+contig_6	68493	82843
+contig_6	74493	85882
diff -r 000000000000 -r 5626dc2d0ef2 test-data/reference_aligned.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reference_aligned.bed	Tue Feb 07 21:43:42 2023 +0000
@@ -0,0 +1,78 @@
+AB615353.1	6529	47531
+AJ868288.1	7527	9486
+CP001987.1	46914	47176
+CP003018.1	1538	1625
+CP003689.1	29589	29664
+CP007625.1	73265	74226
+CP010015.1	37608	61612
+CP010270.1	25405	28333
+CP010578.1	58641	58986
+CP011023.1	42307	42624
+CP012367.1	44648	47740
+CP013205.1	79448	79745
+CP013206.1	43071	45170
+CP013207.1	44872	46449
+CP013207.1	52229	54770
+CP014284.1	170608	171566
+CP014843.1	75233	75447
+CP014843.1	75233	75468
+CP017081.1	79230	79892
+CP018876.1	94468	95006
+CP018878.1	1	655
+CP018878.1	59999	60905
+CP021891.1	1634	2342
+CP021891.1	13176	13625
+CP021891.1	15668	17815
+CP022237.1	53109	53309
+CP022237.1	119514	119700
+CP022237.1	128735	128912
+CP022237.1	129269	129601
+CP024037.1	9202	9538
+CP024037.1	9729	9992
+E01503.1	179	681
+KJ411637.1	3384	4579
+KJ411638.1	6618	7255
+KX711616.1	72804	73046
+KX711616.1	88903	89871
+KX711616.1	93465	93843
+KY200664.1	6	2075
+LDKD02000015.1	16112	16600
+LKWO01000049.1	6582	6774
+LKWV01000069.1	5717	5881
+LLBO01000173.1	7162	7846
+LT622642.1	2144	2240
+LT622643.1	19438	19946
+LT622643.1	21266	29760
+MF996510.1	17455	17657
+NC_004604.2	46557	46664
+NC_004604.2	47101	47366
+NC_015149.1	47529	74217
+NC_015149.1	74221	85603
+NC_021809.1	35623	49969
+NZ_AP018310.1	67280	68584
+NZ_CM009107.1	20753	20870
+NZ_CP010270.1	28596	30249
+NZ_CP011009.1	164112	167234
+NZ_CP012367.1	41890	43503
+NZ_CP014843.1	75896	76197
+NZ_CP014851.1	64568	65235
+NZ_CP015325.1	44909	46797
+NZ_CP015325.1	48334	48870
+NZ_CP015439.1	256054	256172
+NZ_CP015439.1	256868	257244
+NZ_CP021506.1	6488	8071
+NZ_CP021506.1	12360	12999
+NZ_CP021671.1	7341	8793
+NZ_CP021671.1	63574	66590
+NZ_CP021678.1	93636	93972
+NZ_CP022237.1	128178	128474
+NZ_CP022984.1	99541	100822
+NZ_CP024037.1	5972	9092
+NZ_CP024037.1	9993	10074
+NZ_CP026740.1	70776	70947
+NZ_LFXM01000079.1	23966	24665
+NZ_LKWF01000022.1	8665	8876
+NZ_LKXT01000071.1	5962	7186
+NZ_LKYB01000177.1	11540	11625
+NZ_LKZD01000079.1	5481	6177
+NZ_LKZN01000051.1	42	389