| Next changeset 1:3b18022a7613 (2020-11-26) |
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Commit message:
planemo upload commit dd9bf5d878d54362e928a834956feedf082960f3 |
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added:
test-data/fastaFilteringTest_IN.fasta test-data/fastaFilteringTest_OUT1.fasta test-data/fastaFilteringTest_OUT2.fasta test-data/geneticFiltering.in test-data/geneticFilteringBad.out test-data/geneticFilteringGood.out test-data/length5Filtering.in test-data/length5FilteringBad.out test-data/length5FilteringGood.out validate_fasta_database.xml |
| b |
| diff -r 000000000000 -r 48c2271171f2 test-data/fastaFilteringTest_IN.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastaFilteringTest_IN.fasta Thu Sep 14 16:15:15 2017 -0400 |
| [ |
| @@ -0,0 +1,84 @@ +>MCHU - Calmodulin - Human, rabbit, bovine, rat, and chicken +ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTID +FPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREA +DIDGDGQVNYEEFVQMMTAK* +>gi||||5524211gbAAD44166.1 cytochrome b [Elephas maximus maximus] +LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV +EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG +LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL +GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX +IENY +>gi||||5523211gbAAD44166.1 cytochrome b [Elephas maximus maximus] +LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV +EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG +LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL +GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX +IENY +>gi||||5524201gbAAD44166.1 cytochrome b [Elephas maximus maximus] +LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV +EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG +LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL +GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX +IENY +>gi||||5524212gbAAD44166.1 cytochrome b [Elephas maximus maximus] +LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV +EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG +LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL +GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX +IENY +>gi||||5523511gbAAD44166.1 cytochrome b [Elephas maximus maximus] +LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV +EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG +LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL +GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX +IENY +>gi||||5524299gbAAD44166.1 cytochrome b [Elephas maximus maximus] +LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV +EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG +LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL +GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX +IENY +>gi||||5524871gbAAD44166.1 cytochrome b [Elephas maximus maximus] +LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV +EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG +LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL +GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX +IENY +>gi||||5524741gbAAD44166.1 cytochrome b [Elephas maximus maximus] +LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV +EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG +LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL +GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX +IENY +>sp|Q01912|1A1C_VIGRR 1-aminocyclopropane-1-carboxylate synthase (Fragment) OS=Vigna radiata var. radiata GN=ACS5 PE=2 SV=1 +QMGLAENQLTSDLVEDWILNNPEASICTPEGINDFRAIANFQDYHGLAEFRNAVAKFMAR +TRGNRITFDPDRIVMSGGATGAHEVTAFCLADPGEAFLVPIPYYPGFDRDLRWRTGVKLV +PVMCDSSNNFVLTKEALEDAYEKAREDNIRVKGLLITNPSNPLGTIMDRKTLRTVVSFIN +EKRIHLVCDEIYAATVFSQPGFISIAEILEDETDIECDRNLVHIVYSLSKDMGFPGFRVG +IIYSYNDAVVNCARKMSSFGLVSTQTQYLLASMLNDDEFVERFLAESAKRLAQRFRVFTG +GLAKVGIKCLQSNAGLFVWMDLRQLLKKPTFDSETELWKVIIHEVKINVSPGYSFHCTEP +GWFRVCFA +>sp|B9K206|1A1D_AGRVS 1-aminocyclopropane-1-carboxylate deaminase OS=Agrobacterium vitis (strain S4 / ATCC BAA-846) GN=acdS PE=3 SV=1 +MLDAFDRYPLTFGPTPIEKLERLTDHLGGKVQLYAKREDCNSGLAFGGNKLRKLEYIIPD +AIASGADTLVSIGGVQSNHTRMVAAVAAKIGFKCRLVQEAWVPHEDAVYDRVGNIMLSRI +MGADVRLVDDGFDIGIRRSWEEAIEEVKAAGGKPYAIPAGASVHKYGGLGYVGFAEEVRA +QEAALGFAFDYIVVCTVTGSSHAGMAVGFAKDGRADHVIGIDASFTPDQTRAQVLEIAQR +TADLVKLGREMRPEDIVLVEDYAYPVYGVPSEETKDAIRLVGRLEGMITDPVYEGKSMQG +MIDLVKKGYFPEGSKVLYAHLGGAPALNGYGYAFRNG +>sp|A3ME84|1A1D_BURM7 1-aminocyclopropane-1-carboxylate deaminase OS=Burkholderia mallei (strain NCTC 10247) GN=acdS PE=3 SV=1 +MNLQKFSRYPLTFGPTPIQPLKRLSAHLGGKVELYAKRDDCNSGLAFGGNKTRKLEYLIP +DALAQGCDTLVSIGGIQSNQTRQVAAVAAHLGMKCVLVQENWVNYHDAVYDRVGNIQMSR +MMGADVRLVPDGFDIGFRKSWEDALADVRARGGKPYAIPAGCSDHPLGGLGFVGFAEEVR +AQEAELGFQFDYVVVCSVTGSTQAGMVVGFAADGRADRVIGVDASAKPAQTREQILRIAK +HTADRVELGRDITSADVVLDERFGGPEYGLPNEGTLEAIRLCAKLEGVLTDPVYEGKSMH +GMIEKVRLGEFPAGSKVLYAHLGGVPALNAYSFLFRDG +>sp|Q62CE3|1A1D_BURMA 1-aminocyclopropane-1-carboxylate deaminase OS=Burkholderia mallei (strain ATCC 23344) GN=acdS PE=3 SV=1 +MNLQKFSRYPLTFGPTPIQPLKRLSAHLGGKVELYAKRDDCNSGLAFGGNKTRKLEYLIP +DALAQGCDTLVSIGGIQSNQTRQVAAVAAHLGMKCVLVQENWVNYHDAVYDRVGNIQMSR +MMGADVRLVPDGFDIGFRKSWEDALADVRARGGKPYAIPAGCSDHPLGGLGFVGFAEEVR +AQEAELGFQFDYVVVCSVTGSTQAGMVVGFAADGRADRVIGVDASAKPAQTREQILRIAK +HTADRVELGRDITSADVVLDERFGGPEYGLPNEGTLEAIRLCAKLEGVLTDPVYEGKSMH +GMIEKVRLGEFPAGSKVLYAHLGGVPALNAYSFLFRDG +>BAB62851.1 bcr/abl e8a2 fusion protein, partial [Homo sapiens] from GenBank +LLYKPVDRVTRSTLVLHDLLKHTPASHPDHPLLQDALRISQNFLSSINEEITPRRQSMTVKKGEGEDRMK +ASSTRKRLLLMEEALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITK \ No newline at end of file |
| b |
| diff -r 000000000000 -r 48c2271171f2 test-data/fastaFilteringTest_OUT1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastaFilteringTest_OUT1.fasta Thu Sep 14 16:15:15 2017 -0400 |
| [ |
| @@ -0,0 +1,36 @@ +>MCHU - Calmodulin - Human, rabbit, bovine, rat, and chicken +ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTID +FPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREA +DIDGDGQVNYEEFVQMMTAK* +>sp|Q01912|1A1C_VIGRR 1-aminocyclopropane-1-carboxylate synthase (Fragment) OS=Vigna radiata var. radiata GN=ACS5 PE=2 SV=1 +QMGLAENQLTSDLVEDWILNNPEASICTPEGINDFRAIANFQDYHGLAEFRNAVAKFMAR +TRGNRITFDPDRIVMSGGATGAHEVTAFCLADPGEAFLVPIPYYPGFDRDLRWRTGVKLV +PVMCDSSNNFVLTKEALEDAYEKAREDNIRVKGLLITNPSNPLGTIMDRKTLRTVVSFIN +EKRIHLVCDEIYAATVFSQPGFISIAEILEDETDIECDRNLVHIVYSLSKDMGFPGFRVG +IIYSYNDAVVNCARKMSSFGLVSTQTQYLLASMLNDDEFVERFLAESAKRLAQRFRVFTG +GLAKVGIKCLQSNAGLFVWMDLRQLLKKPTFDSETELWKVIIHEVKINVSPGYSFHCTEP +GWFRVCFA +>sp|B9K206|1A1D_AGRVS 1-aminocyclopropane-1-carboxylate deaminase OS=Agrobacterium vitis (strain S4 / ATCC BAA-846) GN=acdS PE=3 SV=1 +MLDAFDRYPLTFGPTPIEKLERLTDHLGGKVQLYAKREDCNSGLAFGGNKLRKLEYIIPD +AIASGADTLVSIGGVQSNHTRMVAAVAAKIGFKCRLVQEAWVPHEDAVYDRVGNIMLSRI +MGADVRLVDDGFDIGIRRSWEEAIEEVKAAGGKPYAIPAGASVHKYGGLGYVGFAEEVRA +QEAALGFAFDYIVVCTVTGSSHAGMAVGFAKDGRADHVIGIDASFTPDQTRAQVLEIAQR +TADLVKLGREMRPEDIVLVEDYAYPVYGVPSEETKDAIRLVGRLEGMITDPVYEGKSMQG +MIDLVKKGYFPEGSKVLYAHLGGAPALNGYGYAFRNG +>sp|A3ME84|1A1D_BURM7 1-aminocyclopropane-1-carboxylate deaminase OS=Burkholderia mallei (strain NCTC 10247) GN=acdS PE=3 SV=1 +MNLQKFSRYPLTFGPTPIQPLKRLSAHLGGKVELYAKRDDCNSGLAFGGNKTRKLEYLIP +DALAQGCDTLVSIGGIQSNQTRQVAAVAAHLGMKCVLVQENWVNYHDAVYDRVGNIQMSR +MMGADVRLVPDGFDIGFRKSWEDALADVRARGGKPYAIPAGCSDHPLGGLGFVGFAEEVR +AQEAELGFQFDYVVVCSVTGSTQAGMVVGFAADGRADRVIGVDASAKPAQTREQILRIAK +HTADRVELGRDITSADVVLDERFGGPEYGLPNEGTLEAIRLCAKLEGVLTDPVYEGKSMH +GMIEKVRLGEFPAGSKVLYAHLGGVPALNAYSFLFRDG +>sp|Q62CE3|1A1D_BURMA 1-aminocyclopropane-1-carboxylate deaminase OS=Burkholderia mallei (strain ATCC 23344) GN=acdS PE=3 SV=1 +MNLQKFSRYPLTFGPTPIQPLKRLSAHLGGKVELYAKRDDCNSGLAFGGNKTRKLEYLIP +DALAQGCDTLVSIGGIQSNQTRQVAAVAAHLGMKCVLVQENWVNYHDAVYDRVGNIQMSR +MMGADVRLVPDGFDIGFRKSWEDALADVRARGGKPYAIPAGCSDHPLGGLGFVGFAEEVR +AQEAELGFQFDYVVVCSVTGSTQAGMVVGFAADGRADRVIGVDASAKPAQTREQILRIAK +HTADRVELGRDITSADVVLDERFGGPEYGLPNEGTLEAIRLCAKLEGVLTDPVYEGKSMH +GMIEKVRLGEFPAGSKVLYAHLGGVPALNAYSFLFRDG +>BAB62851.1 bcr/abl e8a2 fusion protein, partial [Homo sapiens] from GenBank +LLYKPVDRVTRSTLVLHDLLKHTPASHPDHPLLQDALRISQNFLSSINEEITPRRQSMTVKKGEGEDRMK +ASSTRKRLLLMEEALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITK |
| b |
| diff -r 000000000000 -r 48c2271171f2 test-data/fastaFilteringTest_OUT2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastaFilteringTest_OUT2.fasta Thu Sep 14 16:15:15 2017 -0400 |
| [ |
| @@ -0,0 +1,48 @@ +>gi||||5524211gbAAD44166.1 cytochrome b [Elephas maximus maximus] +LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV +EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG +LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL +GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX +IENY +>gi||||5523211gbAAD44166.1 cytochrome b [Elephas maximus maximus] +LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV +EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG +LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL +GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX +IENY +>gi||||5524201gbAAD44166.1 cytochrome b [Elephas maximus maximus] +LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV +EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG +LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL +GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX +IENY +>gi||||5524212gbAAD44166.1 cytochrome b [Elephas maximus maximus] +LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV +EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG +LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL +GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX +IENY +>gi||||5523511gbAAD44166.1 cytochrome b [Elephas maximus maximus] +LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV +EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG +LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL +GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX +IENY +>gi||||5524299gbAAD44166.1 cytochrome b [Elephas maximus maximus] +LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV +EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG +LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL +GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX +IENY +>gi||||5524871gbAAD44166.1 cytochrome b [Elephas maximus maximus] +LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV +EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG +LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL +GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX +IENY +>gi||||5524741gbAAD44166.1 cytochrome b [Elephas maximus maximus] +LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV +EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG +LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL +GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX +IENY |
| b |
| diff -r 000000000000 -r 48c2271171f2 test-data/geneticFiltering.in --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/geneticFiltering.in Thu Sep 14 16:15:15 2017 -0400 |
| b |
| @@ -0,0 +1,8 @@ +>generic|001 +ACTGACTG +>generic|002 +ACUGACUG +>generic|003 +MKMMMMM +>generic|004 +MKMMMMMX \ No newline at end of file |
| b |
| diff -r 000000000000 -r 48c2271171f2 test-data/geneticFilteringBad.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/geneticFilteringBad.out Thu Sep 14 16:15:15 2017 -0400 |
| b |
| @@ -0,0 +1,6 @@ +>generic|001 +ACTGACTG +>generic|002 +ACUGACUG +>generic|004 +MKMMMMMX \ No newline at end of file |
| b |
| diff -r 000000000000 -r 48c2271171f2 test-data/geneticFilteringGood.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/geneticFilteringGood.out Thu Sep 14 16:15:15 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>generic|003 +MKMMMMM \ No newline at end of file |
| b |
| diff -r 000000000000 -r 48c2271171f2 test-data/length5Filtering.in --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/length5Filtering.in Thu Sep 14 16:15:15 2017 -0400 |
| b |
| @@ -0,0 +1,6 @@ +>generic|001 +MMMMMMMMMM +>generic|002 +MMMMM +>generic|003 +MMMM \ No newline at end of file |
| b |
| diff -r 000000000000 -r 48c2271171f2 test-data/length5FilteringBad.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/length5FilteringBad.out Thu Sep 14 16:15:15 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>generic|003 +MMMM \ No newline at end of file |
| b |
| diff -r 000000000000 -r 48c2271171f2 test-data/length5FilteringGood.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/length5FilteringGood.out Thu Sep 14 16:15:15 2017 -0400 |
| b |
| @@ -0,0 +1,4 @@ +>generic|001 +MMMMMMMMMM +>generic|002 +MMMMM \ No newline at end of file |
| b |
| diff -r 000000000000 -r 48c2271171f2 validate_fasta_database.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/validate_fasta_database.xml Thu Sep 14 16:15:15 2017 -0400 |
| [ |
| @@ -0,0 +1,106 @@ +<tool id="validate_fasta_database" name="Validate FASTA Database" version="0.1.4"> + <requirements> + <requirement type="package" version="1.0">validate-fasta-database</requirement> + </requirements> + <stdio> + <exit_code range="1" level="fatal" description="Invalid FASTA headers detected, was asked to fail"/> + </stdio> + <command detect_errors="exit_code"><![CDATA[ + validate-fasta-database + '$inFasta' + '$goodFastaOut' + '$badFastaOut' + '$crashIfInvalid' + '$checkIsProtein' + '$customLetters' + '$checkHasAccession' + '$minimumLength' + ]]></command> + <inputs> + <param type="data" name="inFasta" format="fasta" label="Select input FASTA dataset"/> + <param type="boolean" name="crashIfInvalid" + label="Fail job if invalid FASTA headers detected?" + value="false"/> + <param type="boolean" name="checkIsProtein" + label="Ensure that sequence is a valid amino acid sequence?" + help="Checks that sequence only contains the 20 essential amino + acids (and optional non-standard AAs), and checks that is not DNA or RNA" + value="true"/> + <param type="text" name="customLetters" value="" + label="Optional: add one letter codes for any non-standard amino acids that you are using. " + help="Anything that is not an upper case letter [A-Z] will be ignored."/> + <param type="boolean" name="checkHasAccession" + label="Only pass sequences with accession numbers?" + value="false"/> + <param type="integer" name="minimumLength" + label="Minimum length for sequences to pass" + value="0"/> + </inputs> + <outputs> + <data name="goodFastaOut" format="fasta" label="Validate FASTA ${on_string}: passed"/> + <data name="badFastaOut" format="fasta" label="Validate FASTA ${on_string}: failed"/> + </outputs> + <tests> + <!-- test general filtering --> + <test> + <param name="inFasta" value="fastaFilteringTest_IN.fasta"/> + <output name="goodFastaOut" file="fastaFilteringTest_OUT1.fasta" /> + <output name="badFastaOut" file="fastaFilteringTest_OUT2.fasta" /> + </test> + + <!--test filtering out genetic sequences and bad protein sequences--> + <test> + <param name="inFasta" value="geneticFiltering.in"/> + <param name="checkIsProtein" value="true"/> + <output name="goodFastaOut" file="geneticFilteringGood.out"/> + <output name="badFastaOut" file="geneticFilteringBad.out"/> + </test> + + <test> + <param name="inFasta" value="length5Filtering.in"/> + <param name="minimumLength" value="5"/> + <output name="goodFastaOut" file="length5FilteringGood.out"/> + <output name="badFastaOut" file="length5FilteringBad.out"/> + </test> + </tests> + <help> + +<![CDATA[ +**Notes** + +Takes a FASTA database and validates the headers using the Compomics (developers of SearchGUI and PeptideShaker) schema. +Custom FASTA databases may be in an invalid format, which causes SearchGUI to crash. + +**Output** + +The main output of this tool, "Validate FASTA: Passed Sequences", is a FASTA database that can be run through SearchGUI without error. +The failed sequences may be examined for typos and other errors. + +In addition, the tool will print the databases assigned by the Compomics utility (i.e., UniProt), for a quick check of the validity of the custom FASTA database. + +Sequences that may cause the tool to report an exception are those that are not valid examples of the following formats: + * UniProt, + * SwissProt (starts with ">sw|" or ">SW|") + * NCBI (starts with ">gi|" or ">GI|") + * Halobacterium from Max Planck (starts with "OE") + * H Influenza, from Novartis (starts with ">hflu_") + * C Trachomatis (starts with ">C.tr\_" or "C\_trachomatis\_") + * M Tuberculosis (starts with ">M. tub") + * Saccharomyces Genome Database (contains "SGDID") + * Genome translation (ex. ">dm345\_3L-sense [2343534-234353938]") + * Genome Annotation Framework for Flexible Analysis (GAFFA) (starts with ">GAFFA") + * UPS (contains "\_HUMAN\_UPS") + +Many sequences are reported as Generic, which may or may not allow for extraction of the accession number. +]]> + </help> + <citations> + <citation type="bibtex"> + @misc{fastaValidationTool, + author = {The GalaxyP Team}, + date = {22 June 2017}, + title = {FASTA Database Validation Tool} + } + </citation> + </citations> +</tool> |