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Changeset 2:e379c0202766 (2024-11-20)

Previous changeset 1:2a156ec81e7a (2024-11-18)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5

modified:
test-data/trimmed_example.009.AA.mega
trimal.xml

diff -r 2a156ec81e7a -r e379c0202766 test-data/custom_trimmed_example.009.AA.nexus
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/custom_trimmed_example.009.AA.nexus Wed Nov 20 22:30:36 2024 +0000

[

@@ -0,0 +1,37 @@
+#NEXUS
+BEGIN DATA;
+ DIMENSIONS NTAX=9 NCHAR=63;
+FORMAT DATATYPE=PROTEIN INTERLEAVE=yes GAP=-;
+[Name: Csa004271    Len: 63]
+[Name: Xtr21234     Len: 63]
+[Name: LcaH         Len: 63]
+[Name: Hsa167996    Len: 63]
+[Name: Mmu024661    Len: 63]
+[Name: Dre37936     Len: 63]
+[Name: LcaM         Len: 63]
+[Name: Tru14292     Len: 63]
+[Name: Ola20972     Len: 63]
+
+MATRIX
+Csa004271     ---------- ----YMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL
+Xtr21234      SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL
+LcaH          SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL
+Hsa167996     SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL
+Mmu024661     SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL
+Dre37936      SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL
+LcaM          SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL
+Tru14292      SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL
+Ola20972      SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL
+
+Csa004271     EQVKDNLELF DKH
+Xtr21234      EQVKDNLELF DKH
+LcaH          EQVKDNLELF DKH
+Hsa167996     EQVKDNLELF DKH
+Mmu024661     EQVKDNLELF DKH
+Dre37936      EQVKDNLELF DKH
+LcaM          EQVKDNLELF DKH
+Tru14292      EQVKDNLELF DKH
+Ola20972      EQVKDNLELF DKH
+
+;
+END;

diff -r 2a156ec81e7a -r e379c0202766 test-data/custom_trimmed_window_example.005.AA.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/custom_trimmed_window_example.005.AA.fasta Wed Nov 20 22:30:36 2024 +0000

@@ -0,0 +1,12 @@
+>Sp8
+FPWNGLQIHMMGIII---------------------------------------------
+>Sp17
+FPWNGLQIHMMGIIIIIIIIIIIIIIIIII------------------------------
+>Sp10
+FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII---------------
+>Sp26
+FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+>Sp33
+FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+>Sp6
+FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

diff -r 2a156ec81e7a -r e379c0202766 test-data/custom_trimmed_window_example.009.AA.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/custom_trimmed_window_example.009.AA.html Wed Nov 20 22:30:36 2024 +0000

b'@@ -0,0 +1,54 @@\n+<!DOCTYPE html>\n+<html><head>\n+ <meta http-equiv="Content-Type" content="text/html;charset=ISO-8859-1" />\n+ <title>trimAl v1.5.0 Summary</title>\n+ <style type="text/css" media="all">\n+ #b { background-color: #3366ff; }\n+ #r { background-color: #cc0000; }\n+ #g { background-color: #33cc00; }\n+ #p { background-color: #ff6666; }\n+ #m { background-color: #cc33cc; }\n+ #o { background-color: #ff9900; }\n+ #c { background-color: #46C7C7; }\n+ #y { background-color: #FFFF00; }\n+ .sel { background-color: #B9B9B9; }\n+ .nsel { background-color: #E9E9E9; }\n+ .c1 { background-color: #FFFBF2; }\n+ .c2 { background-color: #FFF8CC; }\n+ .c3 { background-color: #FAF0BE; }\n+ .c4 { background-color: #F0EAD6; }\n+ .c5 { background-color: #F3E5AB; }\n+ .c6 { background-color: #F4C430; }\n+ .c7 { background-color: #C2B280; color: white; }\n+ .c8 { background-color: #DAA520; color: white; }\n+ .c9 { background-color: #B8860B; color: white; }\n+ .c10 { background-color: #918151; color: white; }\n+ .c11 { background-color: #967117; color: white; }\n+ .c12 { background-color: #6E5411; color: white; }\n+ </style>\n+ </head>\n+\n+ <body>\n+ <pre>\n+ Selected Sequences: 6 /Selected Residues: 60\n+ Deleted Sequences: 0 /Deleted Residues: 30\n+\n+ Gaps Scores: =0= <.001 <.050 <.100 <.150 <.200 <.250 <.350 <.500 <.750 <1.00 =1= \n+ Similarity Scores: =0= <1e-6 <1e-5 <1e-4 <.001 <.010 <.100 <.250 <.500 <.750 <1.00 =1= \n+\n+ 10 20 30 40 50 60 70 80 90\n+ =========+=========+=========+=========+=========+=========+=========+=========+=========+\n+ Sp8 FPWNGLQIHMMGIII---------------------------------------------------------------------------\n+ Sp17 FPWNGLQIHMMGIIIIIIIIIIIIIIIIII------------------------------------------------------------\n+ Sp10 FPWNGLQIHMMGIIIIIIIIIII</spa'..b's=c11> \n+ Similarity Scores: \n+ </pre>\n+ </body>\n+</html>\n'

diff -r 2a156ec81e7a -r e379c0202766 test-data/example.002.AA.out.phy
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.002.AA.out.phy Wed Nov 20 22:30:36 2024 +0000

@@ -0,0 +1,9 @@
+ 6 19
+Sp17         LIGFLLLWQGLDLNKMPVF
+Sp10         V--IMLAWLGLEINMMVII
+Sp8          Y-GIVLPWNGLQIHMMGII
+Sp33         A-GLHMAWGGLEINKQAIL
+Sp6          L-GIYLAWLGLEINMMAII
+Sp26         L-GLFLAWLGLEINMMAQI
+
+

diff -r 2a156ec81e7a -r e379c0202766 test-data/example.002.AA.phy
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.002.AA.phy Wed Nov 20 22:30:36 2024 +0000

@@ -0,0 +1,8 @@
+ 6 60
+Sp17         --------FAYTAPD---LLLIGFLLKTVA-T-FG--DTWF-----QLWQGLDLNKMPVF
+Sp10         ----------DPAVL----FV--IMLGTIT-K-FS--SEWF-----FAWLGLEINMMVII
+Sp8          ----------GLGKV---IVY-GIVLGTKS-DQFSNWVVWL-----FPWNGLQIHMMGII
+Sp33         -----------PTIL---NIA-GLHMETDI-N-FS--LAWF-----QAWGGLEINKQAIL
+Sp6          ----------ASGAI---LTL-GIYLFTLC-AVIS--VSWY-----LAWLGLEINMMAII
+Sp26         AAAAAAAA----ALL---TYL-GLFLGTDY-----EN---FAAAAANAWLGLEINMMAQI
+

diff -r 2a156ec81e7a -r e379c0202766 test-data/example.002.AA.report.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.002.AA.report.html Wed Nov 20 22:30:36 2024 +0000

b'@@ -0,0 +1,54 @@\n+<!DOCTYPE html>\n+<html><head>\n+ <meta http-equiv="Content-Type" content="text/html;charset=ISO-8859-1" />\n+ <title>trimAl v1.5.0 Summary</title>\n+ <style type="text/css" media="all">\n+ #b { background-color: #3366ff; }\n+ #r { background-color: #cc0000; }\n+ #g { background-color: #33cc00; }\n+ #p { background-color: #ff6666; }\n+ #m { background-color: #cc33cc; }\n+ #o { background-color: #ff9900; }\n+ #c { background-color: #46C7C7; }\n+ #y { background-color: #FFFF00; }\n+ .sel { background-color: #B9B9B9; }\n+ .nsel { background-color: #E9E9E9; }\n+ .c1 { background-color: #FFFBF2; }\n+ .c2 { background-color: #FFF8CC; }\n+ .c3 { background-color: #FAF0BE; }\n+ .c4 { background-color: #F0EAD6; }\n+ .c5 { background-color: #F3E5AB; }\n+ .c6 { background-color: #F4C430; }\n+ .c7 { background-color: #C2B280; color: white; }\n+ .c8 { background-color: #DAA520; color: white; }\n+ .c9 { background-color: #B8860B; color: white; }\n+ .c10 { background-color: #918151; color: white; }\n+ .c11 { background-color: #967117; color: white; }\n+ .c12 { background-color: #6E5411; color: white; }\n+ </style>\n+ </head>\n+\n+ <body>\n+ <pre>\n+ Selected Sequences: 6 /Selected Residues: 19\n+ Deleted Sequences: 0 /Deleted Residues: 41\n+\n+ Gaps Scores: =0= <.001 <.050 <.100 <.150 <.200 <.250 <.350 <.500 <.750 <1.00 =1= \n+ Similarity Scores: =0= <1e-6 <1e-5 <1e-4 <.001 <.010 <.100 <.250 <.500 <.750 <1.00 =1= \n+\n+ 10 20 30 40 50 60\n+ =========+=========+=========+=========+=========+=========+\n+ Sp17 --------FAYTAPD---LLLIGFLLKTVA-T-FG--DTWF-----QLWQGLDLNKMPVF\n+ Sp10 ----------DPAVL----FV--IMLGTIT-K-FS--SEWF-----FAWLGLEINMMVII\n+ Sp8 ----------GLGKV---IVY-GIVLGTKS-DQFSNWVVWL-----FPWNGLQIHM</'..b'pan class=nsel> \n+\n+ Gaps Scores: \n+ Similarity Scores: \n+ </pre>\n+ </body>\n+</html>\n'

diff -r 2a156ec81e7a -r e379c0202766 test-data/example.002.AA.stats.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.002.AA.stats.txt Wed Nov 20 22:30:36 2024 +0000

@@ -0,0 +1,216 @@
+| Residue   % Gaps    Gap Score   |
+| Number                          |
++----------------------------------------------+
+      0 83.33333333 0.1666666667
+      1 83.33333333 0.1666666667
+      2 83.33333333 0.1666666667
+      3 83.33333333 0.1666666667
+      4 83.33333333 0.1666666667
+      5 83.33333333 0.1666666667
+      6 83.33333333 0.1666666667
+      7 83.33333333 0.1666666667
+      8 83.33333333 0.1666666667
+      9 83.33333333 0.1666666667
+     10 33.33333333 0.6666666667
+     11 16.66666667 0.8333333333
+     12          0       1
+     13          0       1
+     14          0       1
+     15        100       0
+     16        100       0
+     17        100       0
+     18 16.66666667 0.8333333333
+     19          0       1
+     20          0       1
+     21 83.33333333 0.1666666667
+     22 16.66666667 0.8333333333
+     23          0       1
+     24          0       1
+     25          0       1
+     26          0       1
+     27          0       1
+     28          0       1
+     29          0       1
+     30        100       0
+     31 16.66666667 0.8333333333
+     32 66.66666667 0.3333333333
+     33 16.66666667 0.8333333333
+     34 16.66666667 0.8333333333
+     35 66.66666667 0.3333333333
+     36 66.66666667 0.3333333333
+     37 16.66666667 0.8333333333
+     38 16.66666667 0.8333333333
+     39 16.66666667 0.8333333333
+     40          0       1
+     41 83.33333333 0.1666666667
+     42 83.33333333 0.1666666667
+     43 83.33333333 0.1666666667
+     44 83.33333333 0.1666666667
+     45 83.33333333 0.1666666667
+     46          0       1
+     47          0       1
+     48          0       1
+     49          0       1
+     50          0       1
+     51          0       1
+     52          0       1
+     53          0       1
+     54          0       1
+     55          0       1
+     56          0       1
+     57          0       1
+     58          0       1
+     59          0       1
+
+| Number of          | Cumulative % Cumulative | Number of Gaps   % Gaps   Gap Score  |
+| Residues % Length | NumberResid.    Length    |   per Column   per Column per Column |
++-------------------------------+---------------------------------------+--------------------------------------------------+
+  27 45         27 45         0 0          1
+  9 15         36 60         1 0.1666666667 0.8333333333
+  1 1.666666667 37 61.66666667 2 0.3333333333 0.6666666667
+  3 5          40 66.66666667 4 0.6666666667 0.3333333333
+  16 26.66666667 56 93.33333333 5 0.8333333333 0.1666666667
+  4 6.666666667 60 100        6 1          0
+
+| Residue Similarity  |
+| Number     Value    |
++----------------------------+
+  0     0
+  1     0
+  2     0
+  3     0
+  4     0
+  5     0
+  6     0
+  7     0
+  8     0
+  9     0
+  10    5.53110965e-07
+  11    1.646922465e-05
+  12    0.0006768687163
+  13    1.008950312e-05
+  14    0.0002165469632
+  15    0
+  16    0
+  17    0
+  18    2.547356235e-05
+  19    3.554812429e-05
+  20    0.000239324916
+  21    0
+  22    1
+  23    0.004173502792
+  24    1.045452791e-05
+  25    0.17306979
+  26    1.390550642e-05
+  27    1
+  28    4.909260952e-06
+  29    4.015034392e-06
+  30    0
+  31    3.165722228e-05
+  32    4.141910495e-07
+  33    0.01769078523
+  34    0.01232499164
+  35    0.0001380086615
+  36    5.576576978e-10
+  37    1.25446204e-05
+  38    5.194381811e-05
+  39    1
+  40    0.004842269234
+  41    0
+  42    0
+  43    0
+  44    0
+  45    0
+  46    2.948553856e-06
+  47    0.0006762341363
+  48    1
+  49    5.273301213e-06
+  50    1
+  51    1
+  52    0.01518695708
+  53    0.2151376605
+  54    0.02632254921
+  55    0.0008615002735
+  56    0.0174868498
+  57    0.000106244057
+  58    0.001373802545
+  59    0.007171744481
+
+| Number of          | Cumulative % Cumulative |   Similarity   |
+| Residues % Length | NumberResid.    Length    |     Value      |
++-------------------------------+---------------------------------------+----------------+
+  6 10.00000015 6 10.00000015 1
+  1 1.666666754 7 11.66666672 0.2151376605
+  1 1.666666754 8 13.33333403 0.17306979
+  1 1.666666754 9 15.0000006 0.02632254921
+  1 1.666666754 10 16.66666716 0.01769078523
+  1 1.666666754 11 18.33333373 0.0174868498
+  1 1.666666754 12 20.0000003 0.01518695708
+  1 1.666666754 13 21.66666687 0.01232499164
+  1 1.666666754 14 23.33333343 0.007171744481
+  1 1.666666754 15 25         0.004842269234
+  1 1.666666754 16 26.66666806 0.004173502792
+  1 1.666666754 17 28.33333313 0.001373802545
+  1 1.666666754 18 30.00000119 0.0008615002735
+  1 1.666666754 19 31.66666627 0.0006768687163
+  1 1.666666754 20 33.33333433 0.0006762341363
+  1 1.666666754 21 34.9999994 0.000239324916
+  1 1.666666754 22 36.66666746 0.0002165469632
+  1 1.666666754 23 38.33333254 0.0001380086615
+  1 1.666666754 24 40.0000006 0.000106244057
+  1 1.666666754 25 41.66666567 5.194381811e-05
+  1 1.666666754 26 43.33333373 3.554812429e-05
+  1 1.666666754 27 44.99999881 3.165722228e-05
+  1 1.666666754 28 46.66666687 2.547356235e-05
+  1 1.666666754 29 48.33333194 1.646922465e-05
+  1 1.666666754 30 50         1.390550642e-05
+  1 1.666666754 31 51.66666508 1.25446204e-05
+  1 1.666666754 32 53.33333611 1.045452791e-05
+  1 1.666666754 33 55.00000119 1.008950312e-05
+  1 1.666666754 34 56.66666627 5.273301213e-06
+  1 1.666666754 35 58.33333135 4.909260952e-06
+  1 1.666666754 36 60.00000238 4.015034392e-06
+  1 1.666666754 37 61.66666746 2.948553856e-06
+  1 1.666666754 38 63.33333254 5.53110965e-07
+  1 1.666666754 39 64.99999762 4.141910495e-07
+  1 1.666666754 40 66.66666865 5.576576978e-10
+  20 33.33333433 60 100        0
+
+## MaxIdentity 0.4474
+#> MaxIdentity Get the maximum identity value for any pair of sequences in the alignment
+
+## AverageIdentity 0.3056
+#> AverageIdentity Average identity between all sequences
+
+## Identity sequences matrix
+Sp17   1.0000     0.2750     0.2093     0.2750     0.2683     0.2000
+Sp10   0.2750     1.0000     0.4000     0.4054     0.4474     0.3269
+Sp8    0.2093     0.4000     1.0000     0.2500     0.4000     0.2075
+Sp33   0.2750     0.4054     0.2500     1.0000     0.3421     0.2745
+Sp6    0.2683     0.4474     0.4000     0.3421     1.0000     0.3019
+Sp26   0.2000     0.3269     0.2075     0.2745     0.3019     1.0000
+
+## AverageMostSimilarIdentity 0.3837
+#> AverageMostSimilarIdentity Average identity between most similar pair-wise sequences
+
+## Identity for most similar pair-wise sequences matrix
+Sp17   0.2750 Sp10
+Sp10   0.4474 Sp6
+Sp8    0.4000 Sp10
+Sp33   0.4054 Sp10
+Sp6    0.4474 Sp10
+Sp26   0.3269 Sp10
+
+## MaxOverlap 1.0000
+#> MaxOverlap Get the maximum overlap value for any pair of sequences in the alignment
+
+## AverageOverlap 0.8723
+#> AverageOverlap Average overlap between all sequences
+
+## Overlap sequences matrix
+Sp17   1.0000     0.8750     0.9250     0.9000     0.9250     0.7250
+Sp10   1.0000     1.0000     1.0000     0.9714     1.0000     0.7714
+Sp8    0.9250     0.8750     1.0000     0.9000     0.9500     0.7750
+Sp33   1.0000     0.9444     1.0000     1.0000     1.0000     0.8056
+Sp6    0.9737     0.9211     1.0000     0.9474     1.0000     0.7632
+Sp26   0.6591     0.6136     0.7045     0.6591     0.6591     1.0000

diff -r 2a156ec81e7a -r e379c0202766 test-data/example.005.AA.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.005.AA.fasta Wed Nov 20 22:30:36 2024 +0000

@@ -0,0 +1,24 @@
+>Sp8
+FPWNGLQIHMMGIII---------------------------------------------
+------------------------------
+
+>Sp17
+FPWNGLQIHMMGIIIIIIIIIIIIIIIIII------------------------------
+------------------------------
+
+>Sp10
+FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII---------------
+------------------------------
+
+>Sp26
+FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+------------------------------
+
+>Sp33
+FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+IIIIIIIIIIIIIII---------------
+
+>Sp6
+FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+

diff -r 2a156ec81e7a -r e379c0202766 test-data/example.005.AA.out.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.005.AA.out.fasta Wed Nov 20 22:30:36 2024 +0000

diff -r 2a156ec81e7a -r e379c0202766 test-data/example.005.AA.out.gappyout.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.005.AA.out.gappyout.fasta Wed Nov 20 22:30:36 2024 +0000

@@ -0,0 +1,12 @@
+>Sp8
+FPWNGLQIHMMGIII---------------
+>Sp17
+FPWNGLQIHMMGIIIIIIIIIIIIIIIIII
+>Sp10
+FPWNGLQIHMMGIIIIIIIIIIIIIIIIII
+>Sp26
+FPWNGLQIHMMGIIIIIIIIIIIIIIIIII
+>Sp33
+FPWNGLQIHMMGIIIIIIIIIIIIIIIIII
+>Sp6
+FPWNGLQIHMMGIIIIIIIIIIIIIIIIII

diff -r 2a156ec81e7a -r e379c0202766 test-data/example.005.AA.out.overlaptrim.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.005.AA.out.overlaptrim.fasta Wed Nov 20 22:30:36 2024 +0000

@@ -0,0 +1,12 @@
+>Sp8
+FPWNGLQIHMMGIII
+>Sp17
+FPWNGLQIHMMGIII
+>Sp10
+FPWNGLQIHMMGIII
+>Sp26
+FPWNGLQIHMMGIII
+>Sp33
+FPWNGLQIHMMGIII
+>Sp6
+FPWNGLQIHMMGIII

diff -r 2a156ec81e7a -r e379c0202766 test-data/example.005.AA.out.phylip
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.005.AA.out.phylip Wed Nov 20 22:30:36 2024 +0000

@@ -0,0 +1,9 @@
+ 6 60
+Sp8          FPWNGLQIHMMGIII---------------------------------------------
+Sp17         FPWNGLQIHMMGIIIIIIIIIIIIIIIIII------------------------------
+Sp10         FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII---------------
+Sp26         FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+Sp33         FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+Sp6          FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+
+

diff -r 2a156ec81e7a -r e379c0202766 test-data/example.005.AA.report.gappyout.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.005.AA.report.gappyout.html Wed Nov 20 22:30:36 2024 +0000

b'@@ -0,0 +1,52 @@\n+<!DOCTYPE html>\n+<html><head>\n+ <meta http-equiv="Content-Type" content="text/html;charset=ISO-8859-1" />\n+ <title>trimAl v1.5.0 Summary</title>\n+ <style type="text/css" media="all">\n+ #b { background-color: #3366ff; }\n+ #r { background-color: #cc0000; }\n+ #g { background-color: #33cc00; }\n+ #p { background-color: #ff6666; }\n+ #m { background-color: #cc33cc; }\n+ #o { background-color: #ff9900; }\n+ #c { background-color: #46C7C7; }\n+ #y { background-color: #FFFF00; }\n+ .sel { background-color: #B9B9B9; }\n+ .nsel { background-color: #E9E9E9; }\n+ .c1 { background-color: #FFFBF2; }\n+ .c2 { background-color: #FFF8CC; }\n+ .c3 { background-color: #FAF0BE; }\n+ .c4 { background-color: #F0EAD6; }\n+ .c5 { background-color: #F3E5AB; }\n+ .c6 { background-color: #F4C430; }\n+ .c7 { background-color: #C2B280; color: white; }\n+ .c8 { background-color: #DAA520; color: white; }\n+ .c9 { background-color: #B8860B; color: white; }\n+ .c10 { background-color: #918151; color: white; }\n+ .c11 { background-color: #967117; color: white; }\n+ .c12 { background-color: #6E5411; color: white; }\n+ </style>\n+ </head>\n+\n+ <body>\n+ <pre>\n+ Selected Sequences: 6 /Selected Residues: 30\n+ Deleted Sequences: 0 /Deleted Residues: 60\n+\n+ Gaps Scores: =0= <.001 <.050 <.100 <.150 <.200 <.250 <.350 <.500 <.750 <1.00 =1= \n+\n+ 10 20 30 40 50 60 70 80 90\n+ =========+=========+=========+=========+=========+=========+=========+=========+=========+\n+ Sp8 FPWNGLQIHMMGIII---------------------------------------------------------------------------\n+ Sp17 FPWNGLQIHMMGIIIIIIIIIIIIIIIIII------------------------------------------------------------\n+ Sp10 FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII<span'..b'=sel> \n+\n+ Gaps Scores: \n+ </pre>\n+ </body>\n+</html>\n'

diff -r 2a156ec81e7a -r e379c0202766 test-data/example.005.AA.report.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.005.AA.report.html Wed Nov 20 22:30:36 2024 +0000

b'@@ -0,0 +1,52 @@\n+<!DOCTYPE html>\n+<html><head>\n+ <meta http-equiv="Content-Type" content="text/html;charset=ISO-8859-1" />\n+ <title>trimAl v1.5.0 Summary</title>\n+ <style type="text/css" media="all">\n+ #b { background-color: #3366ff; }\n+ #r { background-color: #cc0000; }\n+ #g { background-color: #33cc00; }\n+ #p { background-color: #ff6666; }\n+ #m { background-color: #cc33cc; }\n+ #o { background-color: #ff9900; }\n+ #c { background-color: #46C7C7; }\n+ #y { background-color: #FFFF00; }\n+ .sel { background-color: #B9B9B9; }\n+ .nsel { background-color: #E9E9E9; }\n+ .c1 { background-color: #FFFBF2; }\n+ .c2 { background-color: #FFF8CC; }\n+ .c3 { background-color: #FAF0BE; }\n+ .c4 { background-color: #F0EAD6; }\n+ .c5 { background-color: #F3E5AB; }\n+ .c6 { background-color: #F4C430; }\n+ .c7 { background-color: #C2B280; color: white; }\n+ .c8 { background-color: #DAA520; color: white; }\n+ .c9 { background-color: #B8860B; color: white; }\n+ .c10 { background-color: #918151; color: white; }\n+ .c11 { background-color: #967117; color: white; }\n+ .c12 { background-color: #6E5411; color: white; }\n+ </style>\n+ </head>\n+\n+ <body>\n+ <pre>\n+ Selected Sequences: 6 /Selected Residues: 60\n+ Deleted Sequences: 0 /Deleted Residues: 30\n+\n+ Gaps Scores: =0= <.001 <.050 <.100 <.150 <.200 <.250 <.350 <.500 <.750 <1.00 =1= \n+\n+ 10 20 30 40 50 60 70 80 90\n+ =========+=========+=========+=========+=========+=========+=========+=========+=========+\n+ Sp8 FPWNGLQIHMMGIII---------------------------------------------------------------------------\n+ Sp17 FPWNGLQIHMMGIIIIIIIIIIIIIIIIII------------------------------------------------------------\n+ Sp10 FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII<span'..b' class=sel> \n+\n+ Gaps Scores: \n+ </pre>\n+ </body>\n+</html>\n'

diff -r 2a156ec81e7a -r e379c0202766 test-data/example.005.AA.report.overlaptrim.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.005.AA.report.overlaptrim.html Wed Nov 20 22:30:36 2024 +0000

b'@@ -0,0 +1,52 @@\n+<!DOCTYPE html>\n+<html><head>\n+ <meta http-equiv="Content-Type" content="text/html;charset=ISO-8859-1" />\n+ <title>trimAl v1.5.0 Summary</title>\n+ <style type="text/css" media="all">\n+ #b { background-color: #3366ff; }\n+ #r { background-color: #cc0000; }\n+ #g { background-color: #33cc00; }\n+ #p { background-color: #ff6666; }\n+ #m { background-color: #cc33cc; }\n+ #o { background-color: #ff9900; }\n+ #c { background-color: #46C7C7; }\n+ #y { background-color: #FFFF00; }\n+ .sel { background-color: #B9B9B9; }\n+ .nsel { background-color: #E9E9E9; }\n+ .c1 { background-color: #FFFBF2; }\n+ .c2 { background-color: #FFF8CC; }\n+ .c3 { background-color: #FAF0BE; }\n+ .c4 { background-color: #F0EAD6; }\n+ .c5 { background-color: #F3E5AB; }\n+ .c6 { background-color: #F4C430; }\n+ .c7 { background-color: #C2B280; color: white; }\n+ .c8 { background-color: #DAA520; color: white; }\n+ .c9 { background-color: #B8860B; color: white; }\n+ .c10 { background-color: #918151; color: white; }\n+ .c11 { background-color: #967117; color: white; }\n+ .c12 { background-color: #6E5411; color: white; }\n+ </style>\n+ </head>\n+\n+ <body>\n+ <pre>\n+ Selected Sequences: 6 /Selected Residues: 15\n+ Deleted Sequences: 0 /Deleted Residues: 75\n+\n+ Gaps Scores: =0= <.001 <.050 <.100 <.150 <.200 <.250 <.350 <.500 <.750 <1.00 =1= \n+\n+ 10 20 30 40 50 60 70 80 90\n+ =========+=========+=========+=========+=========+=========+=========+=========+=========+\n+ Sp8 FPWNGLQIHMMGIII---------------------------------------------------------------------------\n+ Sp17 FPWNGLQIHMMGIIIIIIIIIIIIIIIIII------------------------------------------------------------\n+ Sp10 FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII<span'..b'n> \n+\n+ Gaps Scores: \n+ </pre>\n+ </body>\n+</html>\n'

diff -r 2a156ec81e7a -r e379c0202766 test-data/example.009.AA.out.notrim.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.009.AA.out.notrim.fasta Wed Nov 20 22:30:36 2024 +0000

@@ -0,0 +1,16 @@
+>Csa004271
+----------------------------MYMAMGHFFDRDDVALKNISEYFKECSEEERE
+HANKMIEFHNKRGGTTTYFPIKAPGSFDPANFNTIKAMNCALALEVNVNKSLLALHE--T
+ANGDPEFQDFIEANFLHEQVDAIKKLKDYITNLKLVG---TGLGEFLFDKHFKSS----
+>LcaH
+---SSQNFHQDCEAAINRQINLELYASYVYLSMAYYFDRDDQALHNFAKFFRHQSHEERE
+HAEKLMKLQNQRGGRIFLQDVRKPDRDEWG--SGVEALECALQLEKSVNQSLLDLHKLCS
+DHNDPHLCDFIETHYLDEQVKSIKELADWVTNLRRMGAPQNGMAEYLFDKHTLGKES-S
+>Mmu024661
+MTAPSQNYHQDAEAAINRQINLELYASYVYLSMSCYFDRDDVALKNFAKYFLHQSHEERE
+HAEKLMKLQNQRGGRIFLQDIKKPDRDDWE--SGLNAMECALHLEKSVNQSLLELHKLAT
+DKNDPHLCDFIETYYLSEQVKSIKELGDHVTNLRKMGAPEAGMAEYLFDKHTLGHGDES
+>Ola20972
+---ESQNYHRDCEAAINRMVNMELFASYTYTSMAFYFDRDDVALPGFSHFFKENSHEEKE
+HADKLLSFQNKRGGRIFLQDVKKPERDEWG--SGLEAMQCALQLEKNVNQALLDLHKVAS
+DHKDPHMCDFLETHYLNEQVESIKKIGDHITNLTRMDAHTNKMAEYLFDKHTLGSKS--

diff -r 2a156ec81e7a -r e379c0202766 test-data/trimmed_example.009.AA.mega
--- a/test-data/trimmed_example.009.AA.mega Mon Nov 18 07:06:34 2024 +0000
+++ b/test-data/trimmed_example.009.AA.mega Wed Nov 20 22:30:36 2024 +0000

@@ -1,5 +1,5 @@
#MEGA
-!Title ./test-data/example.009.AA.fasta;
+!Title /tmp/saskia/tmpk459g5o_/files/1/8/2/dataset_182865f6-cd70-425d-9a26-7a7fa9974877.dat;
!Format DataType=protein NSeqs=9 Nsites=174 indel=- CodeTable=Standard;

#Csa004271

diff -r 2a156ec81e7a -r e379c0202766 trimal.xml
--- a/trimal.xml Mon Nov 18 07:06:34 2024 +0000
+++ b/trimal.xml Wed Nov 20 22:30:36 2024 +0000

[

b'@@ -1,28 +1,82 @@\n-<tool id="trimal" name="trimAl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">\n+<tool id="trimal" name="trimAl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0" license="MIT">\n <description>for automated alignment trimming</description>\n <macros>\n <token name="@TOOL_VERSION@">1.5.0</token>\n- <token name="@VERSION_SUFFIX@">0</token>\n+ <token name="@VERSION_SUFFIX@">1</token>\n </macros>\n+ <edam_topics>\n+ <edam_topic>topic_3293</edam_topic> \n+ <edam_topic>topic_0080</edam_topic> \n+ </edam_topics>\n+ <edam_operations>\n+ <edam_operation>operation_3192</edam_operation> \n+ </edam_operations>\n <xrefs>\n <xref type="bio.tools">trimal</xref>\n </xrefs>\n <requirements>\n <requirement type="package" version="@TOOL_VERSION@">trimal</requirement>\n </requirements>\n- <command detect_errors="exit_code"><![CDATA[ \n- trimal -in \'$in\' -out \'$trimmed_output\' -htmlout \'$html_summary\' ${out_format_selector}\n- #if $trimming_mode.mode_selector == "custom"\n- -gapthreshold $trimming_mode.gapthreshold\n- -simthreshold $trimming_mode.simthreshold\n- -cons $trimming_mode.cons\n- #else:\n- $trimming_mode.mode_selector\n- #end if\n+ <command detect_errors="aggressive"><![CDATA[\n+\n+trimal -in \'$in\'\n+-out \'$trimmed_output\'\n+${out_format_selector}\n+\n+#unless $trimming_mode.mode_selector == "manual"\n+ -htmlout \'$html_summary\'\n+#end unless\n+\n+#if $trimming_mode.mode_selector == "custom"\n+ -gapthreshold $trimming_mode.gapthreshold\n+ -simthreshold $trimming_mode.simthreshold\n+ -cons $trimming_mode.cons\n+\n+ #if $trimming_mode.w\n+ -w $trimming_mode.w\n+ #else\n+ #if $trimming_mode.gw\n+ -gw $trimming_mode.gw\n+ #end if\n+ #if $trimming_mode.sw\n+ -sw $trimming_mode.sw\n+ #end if\n+ #if $trimming_mode.cw\n+ -cw $trimming_mode.cw\n+ #end if\n+ #end if\n+#else if $trimming_mode.mode_selector == "manual"\n+ #if $trimming_mode.selectcols\n+ -selectcols { $trimming_mode.selectcols }\n+ #end if\n+ #if $trimming_mode.selectseqs\n+ -selectseqs { $trimming_mode.selectseqs }\n+ #end if\n+#else\n+ $trimming_mode.mode_selector\n+#end if\n+\n+#if $resoverlap\n+ -resoverlap $resoverlap\n+#end if\n+#if $seqoverlap\n+ -seqoverlap $seqoverlap\n+#end if\n+\n+#if $statistics\n+-sgc\n+-sgt\n+-ssc\n+-sst\n+-sident\n+-soverlap\n+| tee \'$statsout\'\n+#end if\n+\n \n ]]></command>\n <inputs>\n- <param argument="-in" type="data" format="fasta,clustal,pir,phylip,nexus,mega" label="Alignment file (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip)" />\n+ <param argument="-in" type="data" format="fasta,clustal,pir,phylip,nexus,mega,txt" label="Alignment file (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip)" />\n <conditional name="trimming_mode">\n <param name="mode_selector" type="select" label="Select trimming mode from the list">\n <option value="-nogaps">nogaps - remove all positions with gaps in the alignment.</option>\n@@ -31,7 +85,8 @@\n <option value="-strict">strict - combine gappyout trimming with subsequent trimming based on an automatically selected similarity threshold. </option>\n <option value="-strictplus">strictplus - very similar to the strict method but the final step of the algorithm is slightly different. </option>\n <option value="-automated1">automated1 - heuristic approach to determine the optimal automatic method for trimming a given alignment. </option>\n- <option value="custom">custom mode - eliminates a specified set of columns defined by the user.</option>\n+ <option value="custom">custom mode - define trimming parameters yourself.</option>\n+ <option value="manual">manual mode - specify columns or sequences to remove</op'..b'hreshold" value="0.75" />\n+ <param name="simthreshold" value="0.8" />\n+ <param name="cons" value="5" />\n+ <param name="conthreshold" value="0.5" />\n+ <param name="clusters" value="4" />\n+ <param name="maxidentity" value="0.8" />\n+ <param name="out_format_selector" value="-nexus" />\n+ <output name="trimmed_output" file="custom_trimmed_example.009.AA.nexus" ftype="nexus"/>\n+ <output name="html_summary" file="custom_trimmed_example.009.AA.html" ftype="html"/>\n+ </test>\n+ <test expect_num_outputs="2">\n+ <param name="in" value="example.005.AA.fasta"/>\n+ <param name="mode_selector" value="custom" />\n+ <param name="gapthreshold" value="0.5" />\n+ <param name="simthreshold" value="0.5" />\n+ <param name="conthreshold" value="0.5" />\n+ <param name="gw" value="3"/>\n+ <param name="sw" value="4"/>\n+ <param name="cw" value="5"/>\n+ <output name="trimmed_output" file="custom_trimmed_window_example.005.AA.fasta" ftype="fasta"/>\n+ <output name="html_summary" file="custom_trimmed_window_example.009.AA.html" ftype="html"/>\n+ </test>\n+ <test expect_num_outputs="3">\n+ <param name="in" value="example.002.AA.phy" ftype="phylip"/>\n+ <param name="mode_selector" value="-strict"/>\n+ <param name="statistics" value="true"/>\n+ <output name="trimmed_output" file="example.002.AA.out.phy" ftype="phylip" lines_diff="0"/>\n+ <output name="html_summary" file="example.002.AA.report.html" ftype="html" lines_diff="0"/>\n+ <output name="statsout" file="example.002.AA.stats.txt" ftype="txt" lines_diff="0"/>\n+ </test>\n+ <test expect_num_outputs="2">\n+ <param name="in" value="example.005.AA.fasta" ftype="fasta"/>\n+ <param name="mode_selector" value="-nogaps"/>\n+ <param name="resoverlap" value="0.8"/>\n+ <param name="seqoverlap" value="6"/>\n+ <output name="trimmed_output" file="example.005.AA.out.overlaptrim.fasta" ftype="fasta" lines_diff="0"/>\n+ <output name="html_summary" file="example.005.AA.report.overlaptrim.html" ftype="html" lines_diff="0"/>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <param name="in" value="example.009.AA.fasta" ftype="fasta"/>\n+ <param name="mode_selector" value="manual"/>\n+ <param name="selectcols" value="2,4,7-9"/>\n+ <param name="selectseqs" value="1,3,5-7"/>\n+ <output name="trimmed_output" file="example.009.AA.out.notrim.fasta" ftype="fasta" lines_diff="0"/>\n </test>\n </tests>\n <help><![CDATA[\n@@ -113,19 +244,19 @@\n \n - getting the complementary alignment (columns that were trimmed),\n - to compute statistics from the alignment,\n-- to select the output file format, \n-- to get a summary of trimAl\'s trimming in HTML and SVG formats, \n+- to select the output file format,\n+- to get a summary of trimAl\'s trimming in HTML and SVG formats,\n - and many other options.\n \n-TrimAl webpage: https://trimal.readthedocs.io \n+TrimAl webpage: https://trimal.readthedocs.io\n \n License\n -------\n-This program is free software: you can redistribute it and/or modify \n-it under the terms of the GNU General Public License as published by \n+This program is free software: you can redistribute it and/or modify\n+it under the terms of the GNU General Public License as published by\n the Free Software Foundation, the last available version.\n ]]></help>\n <citations>\n- <citation type="doi">doi:10.1093/bioinformatics/btp348</citation>\n+ <citation type="doi">10.1093/bioinformatics/btp348</citation>\n </citations>\n-</tool>\n\\ No newline at end of file\n+</tool>\n'