FastGA Aligner

tools/fastga/fastga.xml

@@ -0,0 +1,89 @@
+<tool id="fastga" name="FastGA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>align long sequences</description>
+    <macros>
+        <import>fastga_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        ## FastGA directly string matches the file extensions
+        ## symlinks are used to bypass that restriction
+        ln -s "$input1" "input1.${input1.ext}" &&
+        ln -s "$input2" "input2.${input2.ext}" &&
+        FastGA 
+        #if str( $output_format ) == "paf":
+            '-paf'
+    	#elif str( $output_format ) == "psl":
+    	    '-psl'
+    	#end if
+        "input1.${input1.ext}" "input2.${input2.ext}" > output
+    ]]></command>
+    <inputs>
+        <param type="data" name="input1" format="gix,1gdb,fa,fna,fasta,fa.gz,fna.gz,fasta.gz,1seq"/>
+        <param type="data" name="input2" format="gix,1gdb,fa,fna,fasta,fa.gz,fna.gz,fasta.gz,1seq"/>
+        <param name="output_format" type="select" display="radio" label="Specify the output format">
+            <option value="paf" selected="true">paf (-paf)</option>
+            <option value="psl">psl (-psl)</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output1" format="paf" from_work_dir="output">
+            <change_format>
+                <when input="output_format" value="paf" format="paf"/>
+                <when input="output_format" value="psl" format="psl"/>
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input1" value="chrM_hg38.fa.gz"/>
+            <param name="input2" value="chrM_mm39.fa.gz"/>
+            <param name="output_format" value="paf"/>
+            <output name="output1" file="chrM_HGvMM.paf" ftype="paf" />
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input1" value="chrM_hg38.fa.gz"/>
+            <param name="input2" value="chrM_mm39.fa.gz"/>
+            <param name="output_format" value="psl"/>
+            <output name="output1" file="chrM_HGvMM.psl" ftype="psl" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Usage: FastGA [-vkMS] [-L:<log:path>] [-T<int(8)>] [-P<dir($TMPDIR)>] [<format(-paf)>]
+              [-f<int(10)>] [-c<int(85)> [-s<int(1000)>] [-l<int(100)>] [-i<float(.7)]
+              <source1:path>[<precursor>] [<source2:path>[<precursor>]]
+
+         <format> = -paf[mxsS]* | -psl | -1:<align:path>[.1aln]
+
+         <precursor> = .gix | .1gdb | <fa_extn> | <1_extn>
+
+             <fa_extn> = (.fa|.fna|.fasta)[.gz]
+             <1_extn>  = any valid 1-code sequence file type
+
+      -v: Verbose mode, output statistics as proceed.
+      -k: Keep any generated .1gdb's and .gix's.
+      -M: Use soft mask information if available.
+      -S: Use symmetric seeding (not recommended).
+      -L: Output log to specified file.
+      -T: Number of threads to use.
+      -P: Directory to use for temporary files.
+
+      -paf: Stream PAF output
+        -pafx: Stream PAF output with CIGAR string with X's
+        -pafm: Stream PAF output with CIGAR string with ='s
+        -pafs: Stream PAF output with CS string in short form
+        -pafS: Stream PAF output with CS string in long form
+      -psl: Stream PSL output
+      -1: Generate 1-code output to specified file
+
+      -f: adaptive seed count cutoff
+      -c: minimum seed chain coverage in both genomes
+      -s: threshold for starting a new seed chain
+      -l: minimum alignment length
+      -i: minimum alignment identity
+      -S: seed adaptamers from both genomes
+
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>

tools/fastga/fastga_macros.xml

@@ -0,0 +1,23 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.3.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">25.0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">fastga</requirement>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+@misc{githubFASTGA,
+  author = {Gene Myers and Chenxi Zhou},
+  year = {2025},
+  title = {FASTGA},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/thegenemyers/FASTGA},
+}</citation>
+        </citations>
+    </xml>
+</macros>

tools/fastga/test-data/chrM_HGvMM.paf

@@ -0,0 +1,2 @@
+chrM	16569	596	3105	+	chrM	16299	18	2547	2209	5038	255	dv:f:.1195	df:i:620
+chrM	16569	3112	16020	+	chrM	16299	2553	15420	11087	25775	255	dv:f:.1410	df:i:3601

tools/fastga/test-data/chrM_HGvMM.psl

@@ -0,0 +1,2 @@
+1999	408	0	0	78	102	91	122	+	chrM	16569	596	3105	chrM	16299	18	2547	170	8,1,20,2,1,3,33,3,3,2,2,2,34,3,2,3,4,4,2,8,3,1,3,9,94,5,49,2,3,6,8,1,4,4,10,14,2,6,1,8,4,3,3,12,7,4,3,7,75,129,32,7,3,20,60,19,5,13,100,7,3,8,1,4,5,72,31,2,3,1,27,4,6,3,4,8,1,4,21,18,3,4,11,1,29,3,7,4,46,5,2,18,7,36,2,47,3,36,4,3,27,23,5,2,5,14,4,2,25,4,5,3,59,13,5,2,5,3,8,27,3,26,7,12,1,3,7,3,10,7,2,23,6,27,1,3,15,1,18,3,1,137,1,36,4,76,3,2,4,4,14,1,9,3,3,5,7,28,4,9,11,5,17,6,4,8,52,2,17,132,	596,605,606,627,630,632,635,669,672,676,679,681,683,717,720,724,728,733,737,741,749,752,753,756,767,865,870,920,922,925,932,941,942,947,951,964,979,981,988,989,999,1003,1006,1010,1022,1030,1034,1037,1045,1120,1249,1282,1290,1293,1313,1373,1393,1398,1412,1518,1525,1528,1537,1538,1542,1547,1619,1650,1653,1657,1659,1687,1691,1699,1703,1707,1715,1716,1720,1741,1759,1762,1766,1778,1779,1808,1812,1819,1824,1872,1877,1879,1897,1905,1941,1944,1992,1995,2031,2036,2039,2067,2090,2096,2099,2104,2118,2123,2127,2152,2156,2162,2166,2226,2240,2245,2248,2253,2257,2265,2292,2296,2322,2330,2349,2351,2354,2361,2364,2374,2382,2384,2407,2414,2442,2444,2447,2463,2464,2483,2486,2487,2625,2626,2662,2667,2743,2747,2751,2755,2759,2774,2775,2784,2788,2791,2797,2805,2834,2838,2847,2859,2865,2882,2888,2893,2901,2954,2956,2973,	18,26,28,48,50,51,56,89,93,96,98,101,104,139,143,145,148,152,157,159,168,172,174,179,188,282,289,338,341,345,351,359,361,365,370,380,394,397,403,405,413,419,424,427,440,447,452,456,463,539,672,704,711,715,736,797,816,822,835,935,943,948,956,958,964,970,1043,1076,1078,1081,1082,1109,1114,1120,1123,1128,1137,1139,1144,1166,1185,1189,1194,1205,1207,1237,1240,1248,1252,1298,1304,1307,1326,1333,1370,1372,1419,1423,1460,1464,1468,1495,1519,1524,1526,1532,1547,1551,1553,1583,1591,1596,1599,1658,1671,1677,1679,1685,1688,1698,1726,1729,1757,1764,1776,1777,1781,1790,1796,1807,1814,1817,1845,1851,1878,1879,1883,1898,1900,1918,1922,1924,2061,2063,2100,2104,2181,2184,2186,2191,2198,2212,2214,2224,2227,2231,2236,2243,2271,2276,2286,2297,2302,2320,2327,2331,2342,2394,2397,2415,
+9712	2739	0	0	364	457	357	416	+	chrM	16569	3112	16020	chrM	16299	2553	15420	722	32,2,2,8,6,2,4,4,4,8,7,3,14,11,2,75,21,3,36,1,5,11,2,48,1,50,9,10,5,3,26,1,4,3,2,23,2,108,2,67,3,18,2,6,110,1,131,4,8,9,15,6,5,3,113,1,29,15,8,46,12,17,2,11,6,26,15,51,48,1,30,3,4,2,8,54,5,24,6,50,2,11,3,4,2,4,6,4,12,13,5,76,4,49,3,4,1,1,5,8,2,11,6,3,9,5,5,9,4,21,1,58,4,18,4,14,1,1,5,14,6,1,11,8,2,3,3,1,9,3,1,10,6,2,1,2,63,1,36,1,13,3,21,2,38,3,6,1,8,2,4,7,31,11,24,13,14,4,26,14,8,1,19,2,48,56,38,20,4,44,5,15,5,28,17,104,4,25,2,8,1,100,3,29,3,38,4,64,2,9,3,392,3,230,6,149,5,33,7,28,1,19,4,63,2,40,4,47,1,4,13,15,1,50,3,3,2,89,28,3,4,11,5,1,55,7,31,1,3,3,17,1,23,1,4,2,2,3,106,5,3,3,57,2,2,1,18,4,2,4,61,9,55,7,10,3,29,4,89,5,16,5,5,4,14,24,2,4,3,12,22,5,21,2,19,5,15,8,6,19,1,9,7,2,7,57,8,25,7,7,29,2,30,5,8,4,6,7,46,2,28,1,49,2,9,1,19,3,2,8,2,1,188,2,4,1,3,3,2,433,1,7,2,30,3,173,2,102,1,91,4,68,7,3,1,29,14,25,2,25,3,3,1,93,2,60,3,6,7,1,3,3,6,1,3,2,57,5,2,45,12,5,3,16,2,7,1,6,72,3,9,3,3,3,19,4,8,13,2,3,3,40,2,63,6,32,2,4,12,3,2,24,10,10,4,10,11,6,6,2,38,1,52,7,42,5,57,4,7,3,104,3,1,2,9,23,5,9,2,3,4,46,7,5,3,71,7,33,1,7,1,151,1,32,5,67,2,9,1,25,6,48,2,32,8,4,3,20,1,22,4,64,3,27,5,17,6,22,4,17,3,14,6,25,6,4,70,17,2,67,2,17,4,5,5,15,20,3,3,6,5,3,5,32,4,6,5,8,4,1,6,6,14,6,10,4,11,2,20,4,39,3,31,1,14,4,25,4,157,1,11,3,31,9,8,1,5,169,2,3,4,7,9,3,220,4,26,3,1,8,24,6,66,7,2,1,2,20,3,26,5,7,1,9,4,11,22,2,20,3,1,1,55,2,9,2,2,10,2,3,7,3,39,3,37,4,4,7,3,6,2,5,5,15,3,16,13,5,2,4,11,2,3,26,4,7,8,6,4,9,9,5,17,2,11,13,20,1,2,12,48,2,6,4,3,3,5,1,21,12,2,12,3,3,14,2,13,5,5,7,17,4,18,9,10,6,9,100,6,9,3,20,6,11,2,27,3,12,4,10,3,12,2,5,3,7,3,5,1,49,3,4,8,2,10,1,10,7,281,1,4,1,18,4,8,2,3,2,105,3,4,1,55,4,36,5,67,3,35,1,4,2,5,7,67,2,99,2,42,3,28,1,3,7,26,2,25,3,34,2,11,2,17,12,22,2,4,3,10,36,1,3,4,3,3,14,4,19,2,9,6,4,	3112,3144,3147,3150,3158,3164,3167,3172,3176,3180,3189,3196,3200,3214,3226,3229,3306,3327,3331,3369,3370,3375,3387,3389,3438,3439,3490,3499,3510,3516,3519,3546,3547,3552,3556,3558,3581,3584,3693,3695,3763,3766,3787,3789,3795,3906,3907,4039,4043,4051,4061,4077,4085,4090,4093,4207,4208,4238,4254,4262,4309,4321,4339,4341,4353,4359,4386,4401,4452,4501,4502,4532,4536,4541,4543,4552,4606,4612,4637,4643,4693,4696,4707,4711,4715,4718,4723,4730,4734,4747,4760,4765,4841,4846,4895,4899,4904,4906,4907,4912,4920,4922,4934,4942,4945,4954,4960,4967,4976,4981,5003,5004,5063,5067,5086,5090,5105,5106,5108,5113,5127,5133,5134,5145,5153,5155,5159,5165,5168,5177,5180,5181,5194,5200,5203,5205,5207,5271,5272,5309,5310,5324,5327,5348,5351,5389,5393,5400,5401,5409,5411,5416,5424,5456,5467,5494,5510,5526,5530,5557,5571,5580,5586,5606,5608,5656,5714,5752,5772,5777,5821,5826,5841,5846,5875,5903,6008,6012,6037,6041,6050,6051,6152,6155,6185,6188,6226,6231,6295,6298,6307,6311,6704,6707,6938,6944,7094,7099,7133,7140,7169,7170,7190,7194,7258,7260,7300,7305,7353,7354,7359,7372,7388,7389,7440,7444,7447,7449,7538,7566,7569,7574,7585,7591,7592,7648,7655,7687,7688,7692,7695,7713,7714,7738,7739,7744,7746,7749,7752,7859,7865,7868,7871,7929,7931,7934,7935,7954,7958,7961,7965,8027,8036,8091,8099,8110,8113,8143,8147,8237,8242,8263,8275,8284,8294,8310,8335,8338,8343,8346,8360,8383,8388,8410,8412,8432,8437,8453,8461,8468,8488,8489,8498,8506,8509,8516,8574,8582,8609,8616,8623,8652,8655,8685,8691,8700,8704,8711,8718,8765,8767,8796,8797,8846,8849,8859,8860,8879,8883,8886,8895,8897,8898,9086,9088,9093,9094,9098,9102,9105,9539,9540,9548,9550,9581,9584,9757,9760,9863,9864,9956,9960,10029,10036,10040,10041,10070,10088,10114,10116,10141,10145,10149,10150,10243,10246,10306,10310,10317,10325,10327,10330,10334,10340,10341,10345,10347,10404,10410,10412,10457,10469,10475,10478,10495,10497,10504,10505,10513,10586,10589,10601,10605,10608,10611,10632,10636,10644,10658,10660,10664,10667,10708,10710,10773,10780,10813,10816,10820,10833,10837,10839,10864,10874,10884,10889,10900,10911,10919,10925,10927,10966,10967,11021,11028,11070,11076,11134,11138,11145,11149,11253,11257,11259,11262,11271,11298,11304,11313,11316,11319,11323,11369,11377,11383,11386,11459,11466,11500,11501,11509,11510,11662,11663,11696,11701,11769,11771,11781,11782,11808,11814,11862,11865,11897,11906,11911,11914,11935,11936,11958,11963,12028,12031,12058,12065,12082,12089,12112,12116,12133,12137,12152,12158,12184,12191,12195,12266,12284,12286,12354,12356,12374,12378,12383,12389,12405,12426,12430,12433,12441,12446,12449,12454,12487,12491,12499,12504,12512,12517,12518,12525,12531,12547,12553,12564,12568,12579,12582,12602,12608,12648,12651,12683,12684,12698,12703,12728,12733,12891,12892,12904,12907,12939,12948,12957,12958,12964,13135,13137,13140,13145,13152,13161,13165,13386,13390,13417,13421,13422,13430,13455,13461,13530,13537,13539,13540,13543,13564,13567,13594,13599,13607,13608,13617,13621,13635,13657,13660,13680,13684,13686,13687,13742,13745,13754,13756,13758,13769,13773,13777,13785,13788,13828,13831,13868,13873,13877,13886,13891,13897,13899,13905,13910,13926,13929,13946,13961,13966,13968,13972,13984,13986,13990,14016,14022,14029,14037,140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