Mercurial > repos > iuc > fastga
changeset 0:57121595e33c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastga commit 6504da2141da78f7cadb90a2a00e8744b1e0377a
| author | iuc |
|---|---|
| date | Fri, 20 Feb 2026 07:47:05 +0000 |
| parents | |
| children | |
| files | fastga.xml fastga_macros.xml test-data/chrM_HGvMM.paf test-data/chrM_HGvMM.psl test-data/chrM_hg38.fa.gz test-data/chrM_mm39.fa.gz test-data/pafmS_options.paf test-data/pafx.paf |
| diffstat | 8 files changed, 248 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastga.xml Fri Feb 20 07:47:05 2026 +0000 @@ -0,0 +1,217 @@ +<tool id="fastga" name="FastGA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>align whole genomes</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 + '${output_settings.out.format}' + #if str( $output_settings.out.format ) == "-paf": + #if str( $output_settings.out.cigar_string ) != "no": + '${output_settings.out.cigar_string}' + #end if + #if str( $output_settings.out.cs_string ) != "no": + '${output_settings.out.cs_string}' + #end if + #end if + $use_soft_mask + $use_sym_seeding + -f${adaptive_seed_count_cutoff} + -c${minimum_seed_coverage} + -s${new_seed_threshold} + -l${minimum_alignment_length} + -i${minimum_alignment_identity} + 'input1.${input1.ext}' 'input2.${input2.ext}' + #if str( $output_settings.out.format ) != "-1:output": + > output + #end if + ]]></command> + <inputs> + <param name="input1" type="data" label="FASTA sequence" format="fasta,fasta.gz"/> + <param name="input2" type="data" label="FASTA sequence" format="fasta,fasta.gz"/> + <param name="use_soft_mask" type="boolean" label="Use soft mask information if available (-M)" checked="false" truevalue="-M" falsevalue=""/> + <param name="use_sym_seeding" type="boolean" label="Use symmetric seeding (-S)" checked="false" truevalue="-S" falsevalue=""/> + <param name="adaptive_seed_count_cutoff" type="integer" label="Adaptive seed count cutoff (-f)" value="10" min="0" max="255"/> + <param name="minimum_seed_coverage" type="integer" label="Minimum seed chain coverage in both genomes (-c)" value="85" min="0"/> + <param name="new_seed_threshold" type="integer" label="Threshold for starting a new seed chain (-s)" value="1000" min="0"/> + <param name="minimum_alignment_length" type="integer" label="Minimum alignment length (-l)" value="100" min="0"/> + <param name="minimum_alignment_identity" type="float" label="Minimum alignment identity (-i)" value="0.7" min="0.55" max="0.99999999999999994"/> + <section name="output_settings" expanded="False" title="Output"> + <conditional name="out"> + <param name="format" type="select" label="Specify the output format"> + <option value="-paf" selected="true">paf (-paf)</option> + <option value="-psl">psl (-psl)</option> + <option value="-1:output">1aln (-1)</option> + </param> + <when value="-paf"> + <param name="cigar_string" type="select" label="Use CIGAR string?"> + <option value="no" selected="true">No CIGAR string</option> + <option value="-pafx">CIGAR string with X's (-pafx)</option> + <option value="-pafm">CIGAR string with ='s (-pafm)</option> + </param> + <param name="cs_string" type="select" label="Use CS string?"> + <option value="no" selected="true">No CS string</option> + <option value="-pafs">CS string in short form (-pafs)</option> + <option value="-pafS">CS string in long form (-pafS)</option> + </param> + </when> + <when value="-psl"/> + <when value="-1:output"/> + </conditional> + </section> + </inputs> + <outputs> + <data name="output" format="paf" from_work_dir="output"> + <change_format> + <when input="output_settings.out.format" value="-paf" format="paf"/> + <when input="output_settings.out.format" value="-psl" format="psl"/> + <when input="output_settings.out.format" value="-1:output" format="txt"/> + </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"/> + <section name="output_settings"> + <conditional name="out"> + <param name="format" value="-paf"/> + </conditional> + </section> + <output name="output" 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"/> + <section name="output_settings"> + <conditional name="out"> + <param name="format" value="-psl"/> + </conditional> + </section> + <output name="output" file="chrM_HGvMM.psl" ftype="psl"/> + </test> + <test expect_num_outputs="1"> + <param name="input1" value="chrM_hg38.fa.gz"/> + <param name="input2" value="chrM_mm39.fa.gz"/> + <section name="output_settings"> + <conditional name="out"> + <param name="format" value="-paf"/> + <param name="cigar_string" value="-pafx"/> + </conditional> + </section> + <output name="output" file="pafx.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="use_soft_mask" value="True"/> + <param name="use_sym_seeding" value="True"/> + <param name="adaptive_seed_count_cutoff" value="9"/> + <param name="minimum_seed_coverage" value="100"/> + <param name="new_seed_threshold" value="750"/> + <param name="minimum_alignment_length" value="90"/> + <param name="minimum_alignment_identity" value="0.6"/> + <section name="output_settings"> + <conditional name="out"> + <param name="format" value="-paf"/> + <param name="cigar_string" value="-pafm"/> + <param name="cs_string" value="-pafS"/> + </conditional> + </section> + <output name="output" file="pafmS_options.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"/> + <section name="output_settings"> + <conditional name="out"> + <param name="format" value="-1:output"/> + </conditional> + </section> + </test> + </tests> + <help><![CDATA[ + +FastGA compares two high-quality genomes and outputs a ``.1aln``, ``.paf``, or ``.psl`` file containing all local alignments found. + +It is based on a novel adaptive seed finding algorithm as well as the first wave-based local aligner developed for daligner (2012). + +FastGA uses a number of temporary, hidden files such as ONEcode genome databases (.1gdb) and genome indices (.gix) to achieve its high speed and space efficiency. + +----- + +Input +***** + +This tool takes two ``fasta`` or ``fasta.gz`` input files to align. + +It is a core assumption of FastGA that the input genomes are nearly complete and are of high quality (Q40 or better). + +FastGA is not commutative by default (see *Use symmetric seeding* below). + +----- + +Options +******* + + =============================== ======== =========== =========================== + **Option** **Flag** **Default** **Description** + ------------------------------- -------- ----------- --------------------------- + Use soft mask information -M False Use soft-masked regions if + present in the input FASTA + Use symmetric seeding -S False Enables symmetric seeding + (not recommended) + Adaptive seed count cutoff -f 10 Range: 0–255 + Minimum seed chain coverage -c 85 Range: ≥ 0 + Threshold for new seed chain -s 1000 Range: ≥ 0 + Minimum alignment length -l 100 Range: ≥ 0 + Minimum alignment identity -i 0.7 Range: 0.55–<1.0 + =============================== ======== =========== =========================== + +----- + +Output +****** + +**Output format** + + ========== ======== =========== =============================== + **Format** **Flag** **Default** **Notes** + ---------- -------- ----------- ------------------------------- + PAF -paf Yes + PSL -psl No + 1ALN -1 No Output is nondeterministic + ========== ======== =========== =============================== + +**CIGAR string options** + +(available only when output format is PAF) + + ============================== ======== =========== + **Option** **Flag** **Default** + ------------------------------ -------- ----------- + No CIGAR string Yes + CIGAR string with X's -pafx No + CIGAR string with ='s -pafm No + ============================== ======== =========== + +**CS string options** + +(available only when output format is PAF) + + ============================== ======== =========== + **Option** **Flag** **Default** + ------------------------------ -------- ----------- + No CS string Yes + CS string (short form) -pafs No + CS string (long form) -pafS No + ============================== ======== =========== + +]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastga_macros.xml Fri Feb 20 07:47:05 2026 +0000 @@ -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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrM_HGvMM.paf Fri Feb 20 07:47:05 2026 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrM_HGvMM.psl Fri Feb 20 07:47:05 2026 +0000 @@ -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, 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pafmS_options.paf Fri Feb 20 07:47:05 2026 +0000 @@ -0,0 +1,2 @@ +chrM 16569 576 3105 + chrM 16299 0 2547 2013 2651 255 dv:f:.2040 df:i:638 cg:Z:14M1I2M1I10M1I1M1D20M1I2M1I1M1I3M2D33M1I3M1D3M1I2M1I2M1D2M1D34M1D3M1D2M2I3M1I4M1I4M1D2M2I8M1D3M1D1M1D3M2D9M2I94M4I5M2D49M1I2M1D3M1D6M1I8M1I1M1D4M1I4M1D10M3I14M1I2M1D6M1I1M1D8M2I4M2D3M2D3M1I12M1D7M1I4M1D3M1D7M1I75M1D129M4D32M1I7M1I3M1D20M1D60M1D19M1I5M1D13M1I100M6I7M1D3M2D8M1I1M1D4M2D5M1D72M1D31M2D2M1I3M1I1M1I27M1I4M1D6M2I3M1I4M1D8M1D1M1D4M1D21M1D18M1D3M1D4M1D11M1I1M1D29M1D3M1I7M1D4M1I46M2I5M1D2M1D18M1D7M1I36M1D2M1I47M1I3M1D36M1D4M1I3M1D27M1I23M1D5M1I2M1I5M1D14M1D4M1I2M2I25M5D4M4D5M1I3M1I59M1I13M1I5M1D2M1I5M1D3M1I8M2D27M1D3M1I26M2D7M1I12M7I1M1I3M1D7M2D3M3D10M1D7M1I2M1D23M5D6M1I27M1I1M1I3M1D15M1I1M1D18M1I3M1D1M1D137M1I1M1D36M1D4M1I76M1D3M1I2M2I4M1D4M3D14M1I1M1D9M1D3M1I3M1D5M1I7M1I28M1I4M1D9M1D11M1I5M1I17M1D6M1D4M1I8M3D52M1I2M1D17M1D132M cs:Z:=GTT*at=ATGTAGCTTA+c*ac=T+c*acat=CAAAGCAA+t=A-g=CACTGAAAATG*ct=TTAGA*tc=GG+g*ac=T+c=A+c=AT*tc-gt=A*tc=CCCATAAACA*ca=A*at=AGGTTTGGTCCT*ga=GCCTT+t*ac=TA-a=TTA+g*ac=T+c=T*at-g=AG-g=TAA*ag=ATTACACATGCAA*ag=C*ca=TCC*actcaggtat=CC*ga=GTG-t=A*agat-a=TC+ac=CCT+c=TAAA+t=CA*tctc-t=AC+ga=T*tc=AAAA*tgtg-t=AA*gc-g=A-g=AG*gc-gt=ATCAAGCAC+gc=A*tgtc=AA*atagtc=AGCT*tc=AA*ga=AC*ag=C*ct=T*ta=GCCTAGCCACACCCCCACGGGA*cata=CAGCAGTGAT*at=AA*tcac=TT*at=AGCAATAAACGAAAGTTT*ga=ACTAAG*tc=TAT+acta=ACC*tc=C-tt=AGGGTTGGT*ac=AATTTCGTGCCAGCCACCGCGGTCA*tc=ACGATTAACCCAA+g*at=C-t=AAT-t=A*tgcatatg=C+c=GGCGTAAA+g=A-c=GTGT+t*ctat=A*cg-t=AT*ac=A*actcacacac=T+ccc*ac=AATA*ga=A*agtc=TAAAA+c=TC-c=A*ac=CT*tg=A+g=T-a=TGT*ga=AAAA+ac=T*tc=CA-tt=GTT-ag=GAC+a=C*ta=AAA*cttacg=A*ac=TA-a=CGAAAGT+g*agac=TT-c=TA*ga-t=CAT*ta=T*ac=T+g=AA*tc=ACAC*ga=A*ct=AGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCC*ac=TAAACCT*ac=AA*tc=A*ag=TTAAAT*tc-t=AACAAAACT*agtc=T*tc=GCCAGA*gaac=ACTAC*tg=AGCCA*tc=AGCTTAAAACTCAAAGGAC*tc=TGGCGGT*ag=CTT*tc=ATATCC*ac=TCTAGAGGAGCCTGTTCT*ag=TAATCGATAAACCCCG*ca=TC*ta=ACCTCACCA*tc=CTCTTGCT-aatt=CAGCCTATATACCGCCATCTTCAGCAAACCCT+g=A*atag=AAGG+c=TA*tc-t=AAAGTAAGC*agac=AAG*at=A*tc=C*ac=A-a=C*ag=TAAA*ag=ACGTTAGGTCAAGGTGTAGCC*ac=ATGA*agag=TGG*gc=AAGAAATGGGCTACATTTTCT-t=A*tcacacac=AGAA*ca=A*tc=TAC*tg=ATA+g=CCCTT-t=ATGAAACT*at=AAGG+g*at=C*tg=AAGG*at=GGATTTAG*tc=AGTAAA*tc=TAAGA*ag=TAGAG*at=GCTTA*ag=TTGAA*tcta=G*ag=GC*acac=TGAAG*tcag=CG*ct=ACACACCGCCCGTCACCCTCCTCAA*ag=T*taat=A*ac=TT*ac=A+aaggac=A*ct=TTAAC-a=TAA-tt=AA*tctctc=CTA+c=G-a=CAT*ct-cg=T*ta=TAT-g=AGAGGAGA*tc=AAGTCGTAACA*at=GGTAAG*ctag=TACTGGAAAGTG*tcga=CTTGGA*actg=AA*tc=CA*tg=AGTGTAGCTTAA*tc=A*tc-t=AAAGCA*tc=C*tcgaga=C*ct=TACAC*ctct=AG*ag=AGATTTCA-tg=AC+t*ct=AA+c=T+t=GA*ac=C*ag=CTCTGA*ag=CTAA*ta=CCTAGCCC*tc=A+a*ga=CCC-t=AC*at=C*ac=A+cc*at=TA+c=TA*actc-t=A*tg=AC*ta=A*tctc-a=T-a=TA*agac-t=CAAA*ac=CATTTA*tc=CC*ta=A*ca=TAAA-a=GTAT*ta=GG*ac=GA*at=AGAAATT-c=G*ta=A-c=A*tc=CT-a=GG*ac=GC*ta=ATAGA+t=A-c=TAGTACCGCAAGGGAAAGATGAAA*ga=A*ct=TA-a=T*ta=A+c*ac=AAG*tc=A*at-g=AA*ct=A+t=AGCAA*ag=GA*tc=TAA*ac=CC*tc=T*ga=TACCTT*tc=TGCATAATGAA*ct=TAACTAGAA+at=AACTT-c=T*ag-a=C*ta=A*agag=AGA*agtctc=A*ca=AGCTA-g=A*ag=ACCCC+c=GAAACCA*ag=ACGAGCTACCTAA*ag=AACA*agtc=T*tata=A*ta=GA*ag-t=CA+c=AC*tc=CGTCTATGT*ga=GCAAAATAGTG*ag=GAAGATTT*ta=TAGGTAGAGG*tc=GA+c=AAA-g=CCTA*ac=CGAGC*tc=TGGTGATAGCTGGTT*agct=CCAA*ag=A*at=A-t=GAAT+c=TTA-a=GTTCAA*tc=TTTAAA*ct=TTGC*tcac=A*ac=A*ag=AAC+c*acat=C*at=AAATC*acacacatat=GTAA*ga=TTTA-g=A*tc=T*ag=T+t=AG+t=CCAAA-a=GAGG*ga=ACAGCTCTT-c=TGGA+c=AC+ta=GGAAAAAACCTT*tgat=A*tg=AG*ta=GA*ag=TAA-ttaac=AAAA-cagc=TTT*ta=A+c=ACC+c=AT*ta=GTAGGCCTAAAAGCAGCCACCAAT*at=AAGAAAGCGTTCAAGCTCAACA*tcacac=A*ac=T*tatc=C+t=AA*tata=AAT*tc=CCA*ta=A+c=AT*ta=TA-c=AC+t*cg=AACT-t=CCT+c=A*ac=AC*tctc=AA-aa=TTGG*gatctc=AATCTAT*ac=AC*tctc=TATAGA*ta=G-c=AAC+t=A*ca=TGTTAGTAT*ga=AGTAACA*at=GAA*tata=C-ca=ATTCTCC+t*acgc=GCATA*ca=GC*gc=T+gcgtcag=A+t=TAA-c=AAC*ta=C*gt=G-at=AAC-cat=TG*tatc=A*ga=TTAA-t=CAG*ac=C*tc=A+a=TA-g*gt=C*at=A*tc=AATCA*caac=C*ta=A*tc=AA*ag=T*ac=AT-ccacc=TAT*at=AC+c*tc=TC*ta=CTGT*tc=AACCCAACAC*ca=GG*ac=ATGC+t=C+a=TAA-a=GGAAAG*ag=T*ctca=AAAAA+a=G-a=TAAAAGGAACTCGGCAAA+t=C*atat-g=A-a=CCCCGCCTGTTTACCAAAAACATCACCTCTAGCAT*tc=AC*ac=AGTATTAGAGGCAC*tc=GCCTGCCCAGTGAC*taac=A*at=GTTTAACGGCCGCGGTA*tc=CCT*ga=ACCGTGCAAAGGTAGCATAATCACTTGTTCCTTAA*ta=TAGGGAC+c=T-a=G*ct=ATGAA*ct=GGCT*acac=ACGAGGGT*ct=CA*ag=CTGTCTCTTA-t=CTTT+t=AA*tc=CAGTGAAATTGACCT*tgtc=C*ac=GTGAAGAGGC*tg=G*agac=ATA*taac=A*tc=A*agtc=AAGACGAGAAGACCCTATGGAGCTT*at=AATT-a=TAT+t=AA+tg=C*tata=A-t=C*taag=T-tta=A*tctc=TA*tatc=AAACC*tc=A+c=A-t=GG*ct=CC*at=AAA-a=CTA+c*tc=A*ga-t=A*tcacat=G+c*ta=TT*ga=AAA+a=TTTCGGTTGGGG*tc=GACCTCGGAG*ac=A*tg=AA+c*acac=AA-t=CCTCCGA*agtc-g=A*tg=TA*tc=A*atcg=CTA+a=GACTT+c=AC*ac=AGTCAAAG*tcag=AA*ac=T-c=A*acct=ATA-t=CT*tc=A+a=TTGA*ct=CCA-gat=ATA*tatc=TTGA*tc=CAACGGA*ca=CAAGTTACCCTAGGGATAACAGCGCAATCCTATT+c=TA-a=GAGT*tc=CATATC*ga=ACAAT-t=AGGGTTTACGACCTCGATGTTGGATCAGGACATCCC*ag=ATGGTG*tc=AG*acac=GCTATTAA*ta=GGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGGAG*ct=AATCCAGGTCGGTTTCTATCTA +chrM 16569 3112 16269 + chrM 16299 2553 15674 9864 13607 255 dv:f:.2502 df:i:3743 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pafx.paf Fri Feb 20 07:47:05 2026 +0000 @@ -0,0 +1,2 @@ +chrM 16569 596 3105 + chrM 16299 18 2547 1999 2631 255 dv:f:.2032 df:i:632 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