Mercurial > repos > iuc > spaln
changeset 2:dd0cd2319ae5 draft
"planemo upload for repository https://github.com/ogotoh/spaln commit c06dea51e720899c3245d203c3a0abc9f179583f"
| author | iuc |
|---|---|
| date | Fri, 19 Nov 2021 10:09:15 +0000 |
| parents | 37b5e1f0b544 |
| children | 32c11a4b5dbf |
| files | list_spaln_tables.xml macros.xml spaln.xml test-data/output1.bed12 test-data/output1.tabular test-data/output1_gff_genes.gff3 test-data/output1_gff_matches.gff3 test-data/output2.tabular |
| diffstat | 8 files changed, 51 insertions(+), 47 deletions(-) [+] |
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--- a/list_spaln_tables.xml Thu Jul 16 07:57:10 2020 -0400 +++ b/list_spaln_tables.xml Fri Nov 19 10:09:15 2021 +0000 @@ -78,7 +78,7 @@ <output name="output"> <assert_contents> <has_line_matching expression="5\t4\tActinopteri\tcynosemi\tFish_mdl\tCynoglossus semilaevis" /> - <has_line_matching expression="30\t7\tEukaryota\tzea_mays\tMagnolio\tZea mays" /> + <has_line_matching expression="30\t7\tEukaryota\tzea_mays\tAngiosp\tZea mays" /> </assert_contents> </output> </test> @@ -94,7 +94,7 @@ <output name="output"> <assert_contents> <has_line_matching expression="5\t4\tActinopteri\tcynosemi\tFish_mdl\tCynoglossus semilaevis" /> - <has_line_matching expression="30\t7\tEukaryota\tzea_mays\tMagnolio\tZea mays" /> + <has_line_matching expression="30\t7\tEukaryota\tzea_mays\tAngiosp\tZea mays" /> </assert_contents> </output> </test>
--- a/macros.xml Thu Jul 16 07:57:10 2020 -0400 +++ b/macros.xml Fri Nov 19 10:09:15 2021 +0000 @@ -1,3 +1,3 @@ <macros> - <token name="@TOOL_VERSION@">2.4.03</token> + <token name="@TOOL_VERSION@">2.4.6</token> </macros> \ No newline at end of file
--- a/spaln.xml Thu Jul 16 07:57:10 2020 -0400 +++ b/spaln.xml Fri Nov 19 10:09:15 2021 +0000 @@ -38,6 +38,8 @@ #if str($adv.max_gene_length).strip() != '' -XG'${adv.max_gene_length}' #end if + $adv.format_remote_queries + $adv.salvage_mode #end if '$genome' '$query' >'$output1' ]]></command> @@ -90,6 +92,8 @@ <param argument="-yL" name="min_intron_len" type="integer" value="30" label="Minimum expected length of intron" /> <param argument="-yZ" name="intron_potential_weight" type="integer" value="0" label="Weight for intron potential" /> <param argument="-XG" name="max_gene_length" type="text" label="Reset maximum expected gene size, suffix k or M is effective" /> + <param argument="-yX" name="format_remote_queries" type="boolean" checked="false" truevalue="-yX" falsevalue="" label="Format for remote queries" help="More sensitive but less economic than the default" /> + <param argument="-XS" name="salvage_mode" type="boolean" checked="false" truevalue="-XS" falsevalue="" label="Activate salvage mode" help="Examine all positively scored blocks. Considerably slow." /> </when> </conditional> </inputs>
--- a/test-data/output1.bed12 Thu Jul 16 07:57:10 2020 -0400 +++ b/test-data/output1.bed12 Fri Nov 19 10:09:15 2021 +0000 @@ -1,2 +1,2 @@ track name=Spaln description="NP_001121846.1" useScore=1 -scaffold_1 16 10418 NP_001121846.1 530 + 16 10418 255,0,0 16 46,33,122,127,33,4,127,33,6,18,15,11,13,24,24,24, 0,111,401,7107,7546,7642,7721,7908,8278,8849,8963,9050,9959,10028,10212,10378 +scaffold_1 16 10418 NP_001121846.1 355 + 16 10418 255,0,0 16 46,30,122,127,33,4,127,33,6,18,15,11,13,24,24,24, 0,288,401,7107,7546,7642,7721,7908,8278,8849,8963,9050,9959,10028,10212,10378
--- a/test-data/output1.tabular Thu Jul 16 07:57:10 2020 -0400 +++ b/test-data/output1.tabular Fri Nov 19 10:09:15 2021 +0000 @@ -1,18 +1,18 @@ # rID gID %id ExonL MisMch Unpair ref_l ref_r tgt_l tgt_r eScore IntrnL iScore Sig3/I Sig5/T # - X P DiNuc -NP_001121846.1 scaffold_1 21.43 46 11 0 1 14 17 62 79.7 0 0.0 66.40 0.90 0 0 0 0 . -NP_001121846.1 scaffold_1 12.50 33 8 3 15 27 128 160 -4.3 65 -23.9 -5.20 10.70 0 0 0 1 GT.AG -NP_001121846.1 scaffold_1 68.29 122 13 0 28 68 418 539 210.5 257 -0.1 16.10 6.60 0 0 0 1 GT.AG -NP_001121846.1 scaffold_1 64.29 127 15 0 69 110 7124 7250 187.0 6584 -24.3 14.60 17.80 0 0 0 0 GT.AG -NP_001121846.1 scaffold_1 9.09 33 10 0 111 121 7563 7595 11.0 312 -4.2 5.70 5.20 0 0 0 1 GT.AG -NP_001121846.1 scaffold_1 0.00 4 2 0 122 123 7659 7662 21.2 63 -6.4 7.90 13.90 0 0 0 1 GT.AG -NP_001121846.1 scaffold_1 20.45 127 31 2 124 165 7738 7864 21.7 75 5.0 11.80 13.20 0 0 0 2 GT.AG -NP_001121846.1 scaffold_1 9.09 33 10 0 166 176 7925 7957 26.1 60 1.0 7.20 9.70 0 0 0 0 GT.AG -NP_001121846.1 scaffold_1 50.00 6 1 0 177 178 8295 8300 29.4 337 -9.5 8.90 10.80 0 0 0 0 GT.AG -NP_001121846.1 scaffold_1 16.67 18 5 0 179 184 8866 8883 31.0 565 -7.7 12.00 17.60 0 0 0 0 GT.AG -NP_001121846.1 scaffold_1 0.00 15 5 0 185 189 8980 8994 30.3 96 11.1 15.90 9.10 0 0 0 0 GT.AG -NP_001121846.1 scaffold_1 0.00 11 4 0 190 193 9067 9077 27.0 72 -4.0 7.10 7.60 0 0 0 0 GT.AG -NP_001121846.1 scaffold_1 25.00 13 3 0 194 197 9976 9988 28.5 898 -22.1 6.80 15.40 0 0 0 2 GT.AG -NP_001121846.1 scaffold_1 37.50 24 5 0 198 205 10045 10068 27.5 56 3.7 7.70 5.10 0 0 0 0 GT.AG -NP_001121846.1 scaffold_1 25.00 24 6 0 206 213 10229 10252 38.3 160 -6.9 13.10 12.60 0 0 0 0 GT.AG -NP_001121846.1 scaffold_1 20.00 24 6 1 214 222 10395 10418 23.3 142 0.3 12.40 12.60 0 0 0 0 GT.AG -@ scaffold_1 + ( 17 10418 ) NP_001121846.1 222 ( 1 222 ) S: 627.0 =: 36.5 C: 97.3 T#: 135 T-: 6 B#: 0 B-: 0 X: 0 Nexn: 16 +NP_001121846.1 scaffold_1 23.53 46 10 2 1 15 17 62 7.1 0 0.0 6.64 0.09 0 0 0 0 . +NP_001121846.1 scaffold_1 14.29 30 8 2 16 27 305 334 0.6 242 -1.6 0.99 0.40 0 0 0 1 GT.AG +NP_001121846.1 scaffold_1 65.85 122 14 0 28 68 418 539 20.7 83 -0.1 1.61 0.65 0 0 0 1 GT.AG +NP_001121846.1 scaffold_1 64.29 127 15 0 69 110 7124 7250 18.7 6584 -2.5 1.45 1.77 0 0 0 0 GT.AG +NP_001121846.1 scaffold_1 9.09 33 10 0 111 121 7563 7595 1.1 312 -0.4 0.56 0.51 0 0 0 1 GT.AG +NP_001121846.1 scaffold_1 0.00 4 2 0 122 123 7659 7662 2.1 63 -0.7 0.78 1.38 0 0 0 1 GT.AG +NP_001121846.1 scaffold_1 20.00 127 31 3 124 165 7738 7864 2.2 75 0.5 1.17 1.32 0 0 0 2 GT.AG +NP_001121846.1 scaffold_1 9.09 33 10 0 166 176 7925 7957 2.6 60 0.1 0.71 0.96 0 0 0 0 GT.AG +NP_001121846.1 scaffold_1 50.00 6 1 0 177 178 8295 8300 2.9 337 -1.0 0.88 1.07 0 0 0 0 GT.AG +NP_001121846.1 scaffold_1 16.67 18 5 0 179 184 8866 8883 3.1 565 -0.8 1.20 1.75 0 0 0 0 GT.AG +NP_001121846.1 scaffold_1 0.00 15 5 0 185 189 8980 8994 3.0 96 1.1 1.58 0.90 0 0 0 0 GT.AG +NP_001121846.1 scaffold_1 0.00 11 4 0 190 193 9067 9077 2.7 72 -0.4 0.70 0.75 0 0 0 0 GT.AG +NP_001121846.1 scaffold_1 25.00 13 3 0 194 197 9976 9988 2.8 898 -2.2 0.67 1.54 0 0 0 2 GT.AG +NP_001121846.1 scaffold_1 37.50 24 5 0 198 205 10045 10068 2.8 56 0.4 0.77 0.51 0 0 0 0 GT.AG +NP_001121846.1 scaffold_1 25.00 24 6 0 206 213 10229 10252 3.8 160 -0.7 1.30 1.25 0 0 0 0 GT.AG +NP_001121846.1 scaffold_1 20.00 24 6 1 214 222 10395 10418 4.6 142 0.0 1.24 3.54 0 0 0 0 GT.AG +@ scaffold_1 + ( 17 10418 ) NP_001121846.1 [1:222] ( 1 222 ) S: 420.1 =: 36.5 C: 97.3 T#: 135 T-: 8 B#: 0 B-: 0 X: 0 Nexn: 16 HC: 0.0
--- a/test-data/output1_gff_genes.gff3 Thu Jul 16 07:57:10 2020 -0400 +++ b/test-data/output1_gff_genes.gff3 Fri Nov 19 10:09:15 2021 +0000 @@ -1,20 +1,20 @@ ##gff-version 3 ##sequence-region scaffold_1 1 59940 -scaffold_1 ALN gene 17 10418 627 + . ID=gene00001;Name=scaffold_1_5 -scaffold_1 ALN mRNA 17 10418 627 + . ID=mRNA00001;Parent=gene00001;Name=scaffold_1_5 -scaffold_1 ALN cds 17 62 79 + 0 ID=cds00001;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 1 14 + -scaffold_1 ALN cds 128 160 -4 + 2 ID=cds00002;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 15 27 + -scaffold_1 ALN cds 418 539 210 + 2 ID=cds00003;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 28 68 + -scaffold_1 ALN cds 7124 7250 187 + 0 ID=cds00004;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 69 110 + -scaffold_1 ALN cds 7563 7595 11 + 2 ID=cds00005;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 111 121 + +scaffold_1 ALN gene 17 10418 420 + . ID=gene00001;Name=scaffold_1_5 +scaffold_1 ALN mRNA 17 10418 420 + . ID=mRNA00001;Parent=gene00001;Name=scaffold_1_5 +scaffold_1 ALN cds 17 62 71 + 0 ID=cds00001;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 1 15 + +scaffold_1 ALN cds 305 334 5 + 2 ID=cds00002;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 16 27 + +scaffold_1 ALN cds 418 539 207 + 2 ID=cds00003;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 28 68 + +scaffold_1 ALN cds 7124 7250 186 + 0 ID=cds00004;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 69 110 + +scaffold_1 ALN cds 7563 7595 10 + 2 ID=cds00005;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 111 121 + scaffold_1 ALN cds 7659 7662 21 + 2 ID=cds00006;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 122 123 + scaffold_1 ALN cds 7738 7864 21 + 1 ID=cds00007;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 124 165 + -scaffold_1 ALN cds 7925 7957 26 + 0 ID=cds00008;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 166 176 + +scaffold_1 ALN cds 7925 7957 25 + 0 ID=cds00008;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 166 176 + scaffold_1 ALN cds 8295 8300 29 + 0 ID=cds00009;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 177 178 + -scaffold_1 ALN cds 8866 8883 31 + 0 ID=cds00010;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 179 184 + +scaffold_1 ALN cds 8866 8883 30 + 0 ID=cds00010;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 179 184 + scaffold_1 ALN cds 8980 8994 30 + 0 ID=cds00011;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 185 189 + -scaffold_1 ALN cds 9067 9077 27 + 0 ID=cds00012;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 190 193 + +scaffold_1 ALN cds 9067 9077 26 + 0 ID=cds00012;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 190 193 + scaffold_1 ALN cds 9976 9988 28 + 1 ID=cds00013;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 194 197 + scaffold_1 ALN cds 10045 10068 27 + 0 ID=cds00014;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 198 205 + scaffold_1 ALN cds 10229 10252 38 + 0 ID=cds00015;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 206 213 + -scaffold_1 ALN cds 10395 10418 23 + 0 ID=cds00016;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 214 222 + +scaffold_1 ALN cds 10395 10418 46 + 0 ID=cds00016;Parent=mRNA00001;Name=scaffold_1_5;Target=NP_001121846.1 214 222 +
--- a/test-data/output1_gff_matches.gff3 Thu Jul 16 07:57:10 2020 -0400 +++ b/test-data/output1_gff_matches.gff3 Fri Nov 19 10:09:15 2021 +0000 @@ -1,18 +1,18 @@ ##gff-version 3 ##sequence-region scaffold_1 1 59940 -scaffold_1 ALN nucleotide_to_protein_match 17 62 79 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 1 14 +;Gap=D1 M14 -scaffold_1 ALN nucleotide_to_protein_match 128 160 -4 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 15 27 +;Gap=M5 I3 M1 D1 M4 -scaffold_1 ALN nucleotide_to_protein_match 418 539 210 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 28 68 +;Gap=M41 -scaffold_1 ALN nucleotide_to_protein_match 7124 7250 187 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 69 110 +;Gap=M42 -scaffold_1 ALN nucleotide_to_protein_match 7563 7595 11 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 111 121 +;Gap=M11 +scaffold_1 ALN nucleotide_to_protein_match 17 62 71 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 1 15 +;Gap=D1 M13 I1 M1 +scaffold_1 ALN nucleotide_to_protein_match 305 334 5 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 16 27 +;Gap=M6 I2 M4 +scaffold_1 ALN nucleotide_to_protein_match 418 539 207 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 28 68 +;Gap=M41 +scaffold_1 ALN nucleotide_to_protein_match 7124 7250 186 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 69 110 +;Gap=M42 +scaffold_1 ALN nucleotide_to_protein_match 7563 7595 10 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 111 121 +;Gap=M11 scaffold_1 ALN nucleotide_to_protein_match 7659 7662 21 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 122 123 +;Gap=M2 scaffold_1 ALN nucleotide_to_protein_match 7738 7864 21 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 124 165 +;Gap=M14 D1 M7 I2 M19 D1 -scaffold_1 ALN nucleotide_to_protein_match 7925 7957 26 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 166 176 +;Gap=M11 +scaffold_1 ALN nucleotide_to_protein_match 7925 7957 25 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 166 176 +;Gap=M11 scaffold_1 ALN nucleotide_to_protein_match 8295 8300 29 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 177 178 +;Gap=M2 -scaffold_1 ALN nucleotide_to_protein_match 8866 8883 31 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 179 184 +;Gap=M6 +scaffold_1 ALN nucleotide_to_protein_match 8866 8883 30 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 179 184 +;Gap=M6 scaffold_1 ALN nucleotide_to_protein_match 8980 8994 30 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 185 189 +;Gap=M5 -scaffold_1 ALN nucleotide_to_protein_match 9067 9077 27 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 190 193 +;Gap=M4 +scaffold_1 ALN nucleotide_to_protein_match 9067 9077 26 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 190 193 +;Gap=M4 scaffold_1 ALN nucleotide_to_protein_match 9976 9988 28 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 194 197 +;Gap=M4 scaffold_1 ALN nucleotide_to_protein_match 10045 10068 27 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 198 205 +;Gap=M8 scaffold_1 ALN nucleotide_to_protein_match 10229 10252 38 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 206 213 +;Gap=M8 -scaffold_1 ALN nucleotide_to_protein_match 10395 10418 23 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 214 222 +;Gap=M5 I1 M3 +scaffold_1 ALN nucleotide_to_protein_match 10395 10418 46 + . ID=match00001;Name=scaffold_1_5;Target=NP_001121846.1 214 222 +;Gap=M5 I1 M3
--- a/test-data/output2.tabular Thu Jul 16 07:57:10 2020 -0400 +++ b/test-data/output2.tabular Fri Nov 19 10:09:15 2021 +0000 @@ -1,7 +1,7 @@ # rID gID %id ExonL MisMch Unpair ref_l ref_r tgt_l tgt_r eScore IntrnL iScore Sig3/I Sig5/T # - X P DiNuc -NP_001121846.1 scaffold_1 11.11 91 24 0 1 27 17 107 54.8 0 0.0 66.40 5.40 0 0 0 0 . -NP_001121846.1 scaffold_1 65.85 122 14 0 28 68 418 539 210.7 310 -20.3 17.40 8.60 0 0 0 1 GT.AG -NP_001121846.1 scaffold_1 64.29 127 15 0 69 110 7124 7250 188.0 6584 -33.9 16.50 16.90 0 0 0 0 GT.AG -NP_001121846.1 scaffold_1 28.57 147 30 0 111 152 44187 44333 28.7 36936 -44.6 10.00 9.60 0 0 0 1 GT.AG -NP_001121846.1 scaffold_1 20.55 221 52 3 153 222 44595 44815 23.4 261 -18.9 14.00 9.60 0 0 0 1 GT.AG -@ scaffold_1 + ( 17 44815 ) NP_001121846.1 222 ( 1 222 ) S: 349.5 =: 37.8 C: 98.6 T#: 135 T-: 3 B#: 0 B-: 0 X: 0 Nexn: 5 +NP_001121846.1 scaffold_1 10.00 91 24 3 1 27 17 107 5.5 0 0.0 6.64 0.58 0 0 0 0 . +NP_001121846.1 scaffold_1 65.85 122 14 0 28 68 418 539 21.2 310 -1.7 1.88 0.83 0 0 0 1 GT.AG +NP_001121846.1 scaffold_1 64.29 127 15 0 69 110 7124 7250 18.9 6584 -3.1 1.77 1.71 0 0 0 0 GT.AG +NP_001121846.1 scaffold_1 24.49 147 30 7 111 152 44187 44333 3.0 36936 -4.2 1.03 1.02 0 0 0 1 GT.AG +NP_001121846.1 scaffold_1 18.75 221 52 10 153 222 44595 44815 4.8 261 -1.6 1.50 3.36 0 0 0 1 GT.AG +@ scaffold_1 + ( 17 44815 ) NP_001121846.1 [1:222] ( 1 222 ) S: 324.7 =: 37.8 C: 98.6 T#: 135 T-: 20 B#: 0 B-: 0 X: 0 Nexn: 5 HC: 0.0