Mercurial > repos > cpt > cpt_progressivemauve
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_progressivemauve/cpt-macros.xml Fri Jun 10 08:41:20 2022 +0000 @@ -0,0 +1,115 @@ +<?xml version="1.0"?> +<macros> + <xml name="gff_requirements"> + <requirements> + <requirement type="package" version="2.7">python</requirement> + <requirement type="package" version="1.65">biopython</requirement> + <requirement type="package" version="2.12.1">requests</requirement> + <yield/> + </requirements> + <version_command> + <![CDATA[ + cd $__tool_directory__ && git rev-parse HEAD + ]]> + </version_command> + </xml> + <xml name="citation/mijalisrasche"> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex">@unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-crr"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {C. Ross}, + title = {CPT Galaxy Tools}, + year = {2020-}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-2020"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {A. Criscione}, + title = {CPT Galaxy Tools}, + year = {2019-2021}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-2020-AJC-solo"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {A. Criscione}, + title = {CPT Galaxy Tools}, + year = {2019-2021}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-clm"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {C. Maughmer}, + title = {CPT Galaxy Tools}, + year = {2017-2020}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="sl-citations-clm"> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {C. Maughmer}, + title = {CPT Galaxy Tools}, + year = {2017-2020}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_progressivemauve/macros.xml Fri Jun 10 08:41:20 2022 +0000 @@ -0,0 +1,58 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package">progressivemauve</requirement> + <requirement type="package" version="3.8.13">python</requirement> + <requirement type="package" version="1.79">biopython</requirement> + <requirement type="package" version="1.2.2">cpt_gffparser</requirement> + <yield/> + </requirements> + </xml> + <token name="@WRAPPER_VERSION@">2.4.0</token> + <xml name="citation/progressive_mauve"> + <citation type="doi">10.1371/journal.pone.0011147</citation> + </xml> + <xml name="citation/gepard"> + <citation type="doi">10.1093/bioinformatics/btm039</citation> + </xml> + + <token name="@XMFA_INPUT@"> + "$xmfa" + </token> + <xml name="xmfa_input" + token_formats="xmfa"> + <param type="data" format="@FORMATS@" name="xmfa" label="XMFA MSA" /> + </xml> + + <token name="@XMFA_FA_INPUT@"> + "$sequences" + </token> + <xml name="xmfa_fa_input"> + <param type="data" format="fasta" name="sequences" label="Sequences in alignment" + help="These sequences should be the SAME DATASET that was used in the progressiveMauve run. Failing that, they should be provided in the same order as in original progressiveMauve run"/> + + </xml> + <xml name="genome_selector"> + <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/> + </xml> + <xml name="gff3_input"> + <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/> + </xml> + <xml name="input/gff3+fasta"> + <expand macro="gff3_input" /> + <expand macro="genome_selector" /> + </xml> + <token name="@INPUT_GFF@"> + "$gff3_data" + </token> + <token name="@INPUT_FASTA@"> + genomeref.fa + </token> + <token name="@GENOME_SELECTOR_PRE@"> + ln -s $genome_fasta genomeref.fa; + </token> + <token name="@GENOME_SELECTOR@"> + genomeref.fa + </token> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_progressivemauve/progressivemauve.xml Fri Jun 10 08:41:20 2022 +0000 @@ -0,0 +1,315 @@ +<?xml version="1.0"?> +<tool id="progressivemauve" name="progressiveMauve" version="19.1.0.0" profile="16.04"> + <description>constructs multiple genome alignments</description> + <macros> + <import>macros.xml</import> + <import>cpt-macros.xml</import> + </macros> + <requirements> + <requirement type="package">progressivemauve</requirement> + </requirements> + <command detect_errors="aggressive"><![CDATA[ +## Symlink files in with correct extensions +#for $file in $sequences: + ln -s $file `basename $file`; +#end for + +progressiveMauve +## Input Options + +#if $apply_backbone: + --apply-backbone=$apply_backbone +#end if +--island-gap-size=$island_gap_size +$mums + +#if $seed_weight: + --seed-weight=$seed_weight +#end if + +#if $max_gapped_aligner_length: + --max-gapped-aligner-length=$max_gapped_aligner_length +#end if + +#if $match_input: + --match-input=$match_input +#end if + +$collinear +--scoring-scheme=$scoring_scheme +$no_weight_scaling + +--max-breakpoint-distance-scale=$max_breakpoint_distance_scale +--conservation-distance-scale=$conservation_distance_scale +$skip_refinement +$skip_gapped_alignment + +#if $bp_dist_estimate_min_score: + --bp-dist-estimate-min-score=$bp_dist_estimate_min_score +#end if + +#if $gap_open: + --gap-open=$gap_open +#end if + +#if $gap_extend: + --gap-extend=$gap_extend +#end if + +#if $weight: + --weight=$weight +#end if + +#if $min_scaled_penalty: + --min-scaled-penalty=$min_scaled_penalty +#end if + +--hmm-p-go-homologous=$hmm_p_go_homologous +--hmm-p-go-unrelated=$hmm_p_go_unrelated +--hmm-identity=$hmm_identity + +$seed_family +$solid_seeds +$coding_seeds +$no_recursion +$disable_backbone + +## Outputs +--output=$output +#if $output_guide_tree: + --output-guide-tree=$output_guide_tree_file +#end if + +#if $output_backbone: + --backbone-output=$output_backbone_file +#end if + +## Sequences +#for file in $sequences: + `basename "${file}"` +#end for + +]]></command> + <inputs> + <param type="data" format="fasta" name="sequences" multiple="True" + label="Select sequences to align" help="in fasta format" /> + <param type="data" format="xmfa" label="Apply Backbone" name="apply_backbone" optional="True" + help="Read an existing sequence alignment in XMFA format and apply backbone statistics to it (--apply-backbone)" /> + + <param type="integer" label="Island gap size" value="20" name="island_gap_size" + help="Alignment gaps above this size in nucleotides are considered to be islands (--island-gap-size)"/> + + <param type="boolean" truevalue="--disable-backbone" falsevalue="" name="disable_backbone" + label="Disable backbone" help="Disable backbone detection (--disable-backbone)" /> + + <param type="boolean" truevalue="True" falsevalue="" name="output_guide_tree" + label="Output Guide Tree" help="Write out the guide tree used for alignment to a file (--output-guide-tree)" /> + + <param type="boolean" truevalue="True" falsevalue="" name="output_backbone" + label="Output Backbone" help="Write out the backbone to a file (--backbone-output)" /> + + <param type="boolean" truevalue="--mums" falsevalue="" label="MUMs" name="mums" + help="Find MUMs only, do not attempt to determine locally collinear blocks (LCBs) (--mums)" /> + + <param type="integer" label="Seed weight" name="seed_weight" value="0" optional="True" + help="Use the specified seed weight for calculating initial anchors (--seed-weight)" /> + + <param type="data" format="tabular" label="Match Input" name="match_input" optional="True" + help="Use specified match file instead of searching for matches (--match-input)" /> + + <!--<param type="file" label="input-id-matrix" help="An identity matrix describing similarity among all pairs of input sequences/alignments (- -input-id-matrix)" />--> + <param type="integer" label="Max gapped aligner length" value="0" optional="True" name="max_gapped_aligner_length" + help="Maximum number of base pairs to attempt aligning with the gapped aligner (--max-gapped-aligner-length)" /> + + <param type="data" format="nhx" label="input-guide-tree" optional="True" name="input_guide_tree" + help="A phylogenetic guide tree in Newick format that describes the order in which sequences will be aligned (--input-guide-tree)" /> + + <param type="boolean" truevalue="--collinear" falsevalue="" label="Collinear inputs" name="collinear" + help="Assume that input sequences are collinear--they have no rearrangements (--collinear)" /> + + <param type="select" label="Scoring scheme" name="scoring_scheme" help="Selects the anchoring score function. (--scoring-scheme)" > + <option value="sp" selected="True">Extant sum-of-pairs (sp)</option> + <option value="ancestral_sp">Sum-of-pairs + Ancestral (ancestral_sp)</option> + <option value="ancestral">Ancestral (ancestral)</option> + </param> + + <param type="boolean" truevalue="--no-weight-scaling" falsevalue="" label="No weight scaling" name="no_weight_scaling" + help="Don't scale LCB weights by conservation distance and breakpoint distance (--no-weight-scaling)" /> + + <param type="float" min="0" max="1" label="max-breakpoint-distance-scale" value="0.5" name="max_breakpoint_distance_scale" + help="Set the maximum weight scaling by breakpoint distance. (--max-breakpoint-distance-scale)" /> + + <param type="float" min="0" max="1" label="conservation-distance-scale" value="0.5" name="conservation_distance_scale" + help="Scale conservation distances by this amount. (--conservation-distance-scale)" /> + + <param type="boolean" truevalue="--skip-refinement" falsevalue="" label="Skip refinement" name="skip_refinement" + help="Do not perform iterative refinement (--skip-refinement)" /> + <param type="boolean" truevalue="--skip-gapped-alignment" falsevalue="" label="Skip gapped alignment" name="skip_gapped_alignment" + help="Do not perform gapped alignment (--skip-gapped-alignment)" /> + <param type="integer" label="BP dist estimate min score" name="bp_dist_estimate_min_score" value="0" optional="True" + help="Minimum LCB score for estimating pairwise breakpoint distance (--bp-dist-estimate-min-score)" /> + + <param type="integer" label="Gap open" name="gap_open" value="0" optional="True" + help="Gap open penalty (--gap-open)" /> + + <param type="select" label="Repeat penalty" name="repeat_penalty" + help="Sets whether the repeat scores go negative or go to zero for highly repetitive sequences. (--repeat-penalty)"> + <option value="negative" selected="True">Negative</option> + <option value="zero">Zero</option> + </param> + + <param type="integer" label="Gap extend" name="gap_extend" value="0" optional="True" + help="Gap extend penalty (--gap-extend)" /> + + <!--<param type="data" label="Substitution matrix" --> + <!--help="Nucleotide substitution matrix in NCBI format (- -substitution-matrix)" />--> + + <param type="integer" label="Weight" name="weight" value="0" optional="True" + help="Minimum pairwise LCB score (--weight)" /> + <param type="integer" label="Min scaled penalty" name="min_scaled_penalty" value="0" optional="True" + help="Minimum breakpoint penalty after scaling the penalty by expected divergence (--min-scaled-penalty)" /> + + <param type="float" label="HMM p go homologous" name="hmm_p_go_homologous" min="0" max="1" value="0.00001" + help="Probability of transitioning from the unrelated to the homologous state (--hmm-p-go-homologous)" /> + <param type="float" label="HMM p go unrelated" name="hmm_p_go_unrelated" min="0" max="1" value="0.000000001" + help="Probability of transitioning from the homologous to the unrelated state (--hmm-p-go-unrelated)" /> + <param type="float" label="HMM identity" name="hmm_identity" min="0" max="1" value="0.7" + help="Expected level of sequence identity among pairs of sequences(--hmm-identity)" /> + + <param type="boolean" truevalue="--seed-family" falsevalue="" label="Seed family" name="seed_family" + help="Use a family of spaced seeds to improve sensitivity (--seed-family)" /> + <param type="boolean" truevalue="--solid-seeds" falsevalue="" label="Solid seeds" name="solid_seeds" + help="Use solid seeds. Do not permit substitutions in anchor matches. (--solid-seeds)" /> + <param type="boolean" truevalue="--coding-seeds" falsevalue="" label="Coding seeds" name="coding_seeds" + help="Use coding pattern seeds. Useful to generate matches coding regions with 3rd codon position degeneracy. (--coding-seeds)" /> + <param type="boolean" truevalue="--no-recursion" falsevalue="" label="No recursion" name="no_recursion" + help="Disable recursive anchor search (--no-recursion)" /> + </inputs> + <outputs> + <data format="xmfa" name="output" label="${tool.name} alignment of ${on_string}"> + <change_format> + <when input="mums" value="--mums" format="tabular" /> + </change_format> + </data> + <data format="nhx" name="output_guide_tree_file" label="${tool.name} alignment of ${on_string}: Guide tree"> + <filter>output_guide_tree</filter> + </data> + <data format="tabular" name="output_backbone_file" label="${tool.name} alignment of ${on_string}: Backbone"> + <filter>output_backbone</filter> + </data> + </outputs> + <tests> + <test> + <param name="sequences" value="phagey.fa,karma.fa" /> + <output name="output" file="1.xmfa" lines_diff="20"/> + </test> + <test> + <param name="sequences" value="merged.fa" /> + <output name="output" file="2.xmfa" lines_diff="20"/> + </test> + <test> + <param name="sequences" value="merged.fa" /> + <param name="output_guide_tree" value="True" /> + <output name="output" file="3.xmfa" lines_diff="20"/> + <output name="output_guide_tree_file" file="3.nhx" /> + </test> + <test> + <param name="sequences" value="merged.fa" /> + <param name="mums" value="True" /> + <output name="output" file="4.mums" compare="sim_size" delta="1000"/> + </test> + <test> + <param name="sequences" value="merged.fa" /> + <param name="match_input" value="4.mums" /> + <output name="output" file="5.xmfa" lines_diff="24"/> + </test> + </tests> + <help><![CDATA[ +What it does +============ + +Mauve is a system for efficiently constructing multiple genome alignments in +the presence of large-scale evolutionary events such as rearrangement and +inversion. Multiple genome alignment provides a basis for research into +comparative genomics and the study of evolutionary dynamics. Aligning whole +genomes is a fundamentally different problem than aligning short sequences. + +Mauve has been developed with the idea that a multiple genome aligner should +require only modest computational resources. It employs algorithmic techniques +that scale well in the amount of sequence being aligned. For example, a pair of +Y. pestis genomes can be aligned in under a minute, while a group of 9 +divergent Enterobacterial genomes can be aligned in a few hours. + + +Example Usage +============= + ++-----------------------------------+-------------+ +| Usage | Notes | ++===================================+=============+ +| Align genomes |Simply | +| |select as | +| |many fasta | +| |files with | +| |one or more | +| |sequences as | +| |necessary | ++-----------------------------------+-------------+ +| Align genomes but also save |Use the | +| the guide tree and produce a |**Output | +| backbone file |Guide Tree** | +| |and **Output | +| |Backbone** | +| |options | ++-----------------------------------+-------------+ +| Align genomes, but do not |Use the | +| detect forced alignment of |**Disable | +| unrelated sequences |backbone** | +| |option | ++-----------------------------------+-------------+ +| Detect forced alignment of |Use the | +| unrelated sequence in the |**Apply | +| alignment produced |Backbone** | +| in previous example, use |option and | +| custom Homology HMM transition |specify the | +| parameters. |XMFA file | +| |produced | +| |in the | +| |previous | +| |example | ++-----------------------------------+-------------+ +| Compute ungapped |Use the | +| local-multiple alignments among |**MUMs** | +| the input sequences |option | ++-----------------------------------+-------------+ +| Compute an alignment of the |Set the | +| same genomes, using previously |**Match | +| computed local-multiple |Input** to | +| alignments |the tabular | +| |MUMs file | +| |produced in | +| |the previous | +| |example | ++-----------------------------------+-------------+ +| Set a minimum scaled |Use the | +| breakpoint penalty to cope with |**Min Scaled | +| the case where most genomes |Penalty** and| +| are aligned correctly, but manual |set to a | +| inspection reveals that |value like | +| a divergent genome has too |5000 | +| many predicted rearrangements. | | ++-----------------------------------+-------------+ +| Globally align a set of |Use the | +| collinear virus |**Colinear**,| +| genomes, using seed families |**Seed | +| to improve anchoring sensitivity |Family** | +| in regions below 70% sequence |options | +| identity. | | ++-----------------------------------+-------------+ + +]]></help> + <citations> + <expand macro="citation/progressive_mauve" /> + <expand macro="citation/mijalisrasche" /> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_progressivemauve/test-data/1.gff3 Fri Jun 10 08:41:20 2022 +0000 @@ -0,0 +1,25 @@ +##gff-version 3 +##sequence-region karma 1 1 +karma progressiveMauve match 83032 140930 . - . ID=phagey;target=phagey +karma progressiveMauve match_part 83032 83041 50.0 + . Parent=phagey +karma progressiveMauve match_part 83042 83051 60.0 + . Parent=phagey +karma progressiveMauve match_part 83060 83069 60.0 + . Parent=phagey +karma progressiveMauve match_part 83070 83079 40.0 + . Parent=phagey +karma progressiveMauve match_part 83080 83089 40.0 + . Parent=phagey +karma progressiveMauve match_part 83108 83117 40.0 + . Parent=phagey +karma progressiveMauve match_part 83125 83134 70.0 + . Parent=phagey +karma progressiveMauve match_part 83144 83153 60.0 + . Parent=phagey +karma progressiveMauve match_part 83154 83163 40.0 + . Parent=phagey +karma progressiveMauve match_part 83164 83173 70.0 + . Parent=phagey +karma progressiveMauve match_part 83196 83205 40.0 + . Parent=phagey +karma progressiveMauve match_part 83206 83215 30.0 + . Parent=phagey +karma progressiveMauve match_part 140791 140800 40.0 + . Parent=phagey +karma progressiveMauve match_part 140801 140810 20.0 + . Parent=phagey +karma progressiveMauve match_part 140811 140820 60.0 + . Parent=phagey +karma progressiveMauve match_part 140821 140830 50.0 + . Parent=phagey +karma progressiveMauve match_part 140831 140840 50.0 + . Parent=phagey +karma progressiveMauve match_part 140841 140850 60.0 + . Parent=phagey +karma progressiveMauve match_part 140851 140860 20.0 + . Parent=phagey +karma progressiveMauve match_part 140861 140870 50.0 + . Parent=phagey +karma progressiveMauve match_part 140871 140880 40.0 + . Parent=phagey +karma progressiveMauve match_part 140906 140915 80.0 + . Parent=phagey
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_progressivemauve/test-data/1.mums Fri Jun 10 08:41:20 2022 +0000 @@ -0,0 +1,409 @@ +FormatVersion 3 +SequenceCount 2 +Sequence0File test-data/merged.fa +Sequence0Length 159457 +Sequence1File test-data/merged.fa +Sequence1Length 221828 +MatchCount 402 +23 9997 10291 0x9c7f540 0 0 +23 118799 199132 0x9c7f588 0 0 +23 26654 -52948 0x9c7f5c8 0 0 +23 126561 47160 0x9c7f610 0 0 +23 110233 -209064 0x9c7f650 0 0 +23 134387 175263 0x9c7f690 0 0 +23 93373 -185643 0x9c7f700 0 0 +23 6917 167993 0x9c7f740 0 0 +23 47238 48379 0x9c7f780 0 0 +23 8742 -150092 0x9c7f7c0 0 0 +23 144337 65631 0x9c7f800 0 0 +23 138300 -100263 0x9c7f890 0 0 +23 62837 -15551 0x9c7f8d0 0 0 +23 135219 16958 0x9c7f910 0 0 +23 19156 -18956 0x9c7f950 0 0 +23 109152 -48925 0x9c7f990 0 0 +23 76438 -161554 0x9c7f9d0 0 0 +23 71190 -46655 0x9c7fa10 0 0 +23 157575 -160188 0x9c7fa50 0 0 +23 143476 -94179 0x9c7fb20 0 0 +23 87012 169379 0x9c7fb60 0 0 +23 121064 43686 0x9c7fba0 0 0 +23 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_progressivemauve/test-data/1.nhx Fri Jun 10 08:41:20 2022 +0000 @@ -0,0 +1,1 @@ +(seq2:0.476132,seq1:0.476132);
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_progressivemauve/test-data/1.xmfa Fri Jun 10 08:41:20 2022 +0000 @@ -0,0 +1,7037 @@ +#FormatVersion Mauve1 +#Sequence1File dataset_662720.dat +#Sequence1Format FastA +#Sequence2File dataset_662721.dat +#Sequence2Format FastA +#BackboneFile /galaxy/database/files/000/663/dataset_663935.dat.bbcols +> 1:3292-131680 - dataset_662720.dat +tctacgaatacgggctctagcctctcctatagtctctgtgaaggttagcataccttcgacctgttctatttttaact--t +tgccttaaaaggctcggagaacccgagttcctggcgataagattctaatagttgttcagtttggtatt-ttagcgcatcc +ctcgtctgtacattgtttggcttacctacgtactgataccctgcaacttccctcagatgcttactcattgcttcgatatc +cataagctcctcctattccatatataaacggattgtatttttattattaaacagcatgatctgataagaaccgccaggcc +cttgaggaattacgcgcattttatagtttcctagttcatctttaggaatttttaaatggccggcacccataccaaagata +tagtccccgtccattgatacataggaactgattaattcctcataagggtttacagatgcagatacaccatctaccgattc +tagctttacctgtttaattactttacctgtaatgttctcatccataattaagtctaaaataagcttactgtcccgtacac 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_progressivemauve/test-data/2.xmfa Fri Jun 10 08:41:20 2022 +0000 @@ -0,0 +1,6309 @@ +#FormatVersion Mauve1 +#Sequence1File dataset_662722.dat +#Sequence1Entry 1 +#Sequence1Format FastA +#Sequence2File dataset_662722.dat +#Sequence2Entry 2 +#Sequence2Format FastA +#BackboneFile /galaxy/database/files/000/662/dataset_662723.dat.bbcols +> 1:83043-149557 - dataset_662722.dat +acagtagtacctaacccgactccgaatatagttgtgtaatccttattcttgttcagtctaaaactaatcgcagtaggtaa +gttggccttaatccgcccgcttacaatatctgcactaggatactgggtagccaccactaaatgtatacctgttttc-ctt +gccttctgccctaaccgagcaatataatcttctacccctttgtcaacagcacgtaaatctgcatattcatctacaataca +cactagatagggtaacggctcctccgctacttcattatacaaagataacaacttcgtacctttttccttcataagagcat +atcgcttatccatctccattgtcagccctgctaatacttggcaagcttctttagcatctgtcactacgtctagtacgtgt +ggactatcctcatacttacttagctctaccatagccgggtcaatcataataaactgtagcttttcaggtggatacattaa 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_progressivemauve/test-data/3.nhx Fri Jun 10 08:41:20 2022 +0000 @@ -0,0 +1,1 @@ +(seq2:0.476132,seq1:0.476132);
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_progressivemauve/test-data/3.xmfa Fri Jun 10 08:41:20 2022 +0000 @@ -0,0 +1,6309 @@ +#FormatVersion Mauve1 +#Sequence1File dataset_662722.dat +#Sequence1Entry 1 +#Sequence1Format FastA +#Sequence2File dataset_662722.dat +#Sequence2Entry 2 +#Sequence2Format FastA +#BackboneFile /galaxy/database/files/000/662/dataset_662724.dat.bbcols +> 1:83043-149557 - dataset_662722.dat +acagtagtacctaacccgactccgaatatagttgtgtaatccttattcttgttcagtctaaaactaatcgcagtaggtaa +gttggccttaatccgcccgcttacaatatctgcactaggatactgggtagccaccactaaatgtatacctgttttc-ctt +gccttctgccctaaccgagcaatataatcttctacccctttgtcaacagcacgtaaatctgcatattcatctacaataca +cactagatagggtaacggctcctccgctacttcattatacaaagataacaacttcgtacctttttccttcataagagcat +atcgcttatccatctccattgtcagccctgctaatacttggcaagcttctttagcatctgtcactacgtctagtacgtgt +ggactatcctcatacttacttagctctaccatagccgggtcaatcataataaactgtagcttttcaggtggatacattaa 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_progressivemauve/test-data/4.mums Fri Jun 10 08:41:20 2022 +0000 @@ -0,0 +1,409 @@ +FormatVersion 3 +SequenceCount 2 +Sequence0File dataset_742014.dat +Sequence0Length 159457 +Sequence1File dataset_742014.dat +Sequence1Length 221828 +MatchCount 402 +23 9997 10291 0x10c62b0 0 0 +23 118799 199132 0x1110520 0 0 +23 26654 -52948 0x1110580 0 0 +23 126561 47160 0x11105f0 0 0 +23 110233 -209064 0x1110650 0 0 +23 134387 175263 0x11106b0 0 0 +23 93373 -185643 0x1110770 0 0 +23 6917 167993 0x11107d0 0 0 +23 47238 48379 0x1110830 0 0 +23 8742 -150092 0x1110890 0 0 +23 144337 65631 0x11108f0 0 0 +23 138300 -100263 0x11109f0 0 0 +23 62837 -15551 0x1110a50 0 0 +23 135219 16958 0x1110ab0 0 0 +23 19156 -18956 0x1110b10 0 0 +23 109152 -48925 0x1110b70 0 0 +23 76438 -161554 0x1110bd0 0 0 +23 71190 -46655 0x1110c30 0 0 +23 157575 -160188 0x1110c90 0 0 +23 143476 -94179 0x1110e10 0 0 +23 87012 169379 0x1110e70 0 0 +23 121064 43686 0x1110ed0 0 0 +23 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_progressivemauve/test-data/5.xmfa Fri Jun 10 08:41:20 2022 +0000 @@ -0,0 +1,6315 @@ +#FormatVersion Mauve1 +#Sequence1File dataset_742014.dat +#Sequence1Entry 1 +#Sequence1Format FastA +#Sequence2File dataset_742014.dat +#Sequence2Entry 2 +#Sequence2Format FastA +#Sequence3File dataset_742014.dat +#Sequence3Entry 3 +#Sequence3Format FastA +#Sequence4File dataset_742014.dat +#Sequence4Entry 4 +#Sequence4Format FastA +#BackboneFile /galaxy/database/files/000/742/dataset_742016.dat.bbcols +> 1:83043-149557 - dataset_742014.dat +acagtagtacctaacccgactccgaatatagttgtgtaatccttattcttgttcagtctaaaactaatcgcagtaggtaa +gttggccttaatccgcccgcttacaatatctgcactaggatactgggtagccaccactaaatgtatacctgttttc-ctt +gccttctgccctaaccgagcaatataatcttctacccctttgtcaacagcacgtaaatctgcatattcatctacaataca +cactagatagggtaacggctcctccgctacttcattatacaaagataacaacttcgtacctttttccttcataagagcat +atcgcttatccatctccattgtcagccctgctaatacttggcaagcttctttagcatctgtcactacgtctagtacgtgt 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+-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_progressivemauve/test-data/karma.fa Fri Jun 10 08:41:20 2022 +0000 @@ -0,0 +1,3699 @@ +>karma +gggctctgggcgaagttttgtgggactactatgacttgcattatttcaagcgcaagcggt +ccgagtggaagtaccaaagatttgctttggtttatcaacaacttgccgacgcggcctcgg +acacctccatcgcgtccaagtttcagacctacgatcacctgccccacctggagccgaagg +tgctcaaggcccggcttgacgcgggtcacgccgacgagcgcgggcggccgattccggacc +gcaaggagcacttccggcgggtggtggtcagcgtcgactcggccaacaagcccggcgccc +gcaacgactacagcgtcgcccaggtctggggggagacccacgcccgcaagcactacctga +tctaccaggagcgcaagaaggtcgacatcaccggcctgaccgagatgatcgagcgggtgg +ccaagcgctacgaggtcgacgccatcctggtcgaagacaagggcaacggcaccgcctaca +tccaggcgcggggccagaccgacagccagcggcggctcgccccggccccgatcgaggcga +tccaggtcccgagcacctattccaaggagttccgcttcaacgagatcgtcccgatgatcg +aggccggcgaggtcttcctgccgggcaaggccccgtggctcgacctgctgatccgcgaaa +tcggtcagttccccgaaggcgcccatgacgaccaagtcgacgccatgacgcagtacctcc +gctgggccaagtccaagcgcacgcggttcggcgcgcgcaaggtcggctcgatgggctgac 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_progressivemauve/test-data/merged.fa Fri Jun 10 08:41:20 2022 +0000 @@ -0,0 +1,6360 @@ +>phagey +tggtattacaagagagaaaggaagtaatcgatatgcaacagacagcagctaagaacacac +aaccagaaggtttacatctttacatggcaattggatcgtatgagtcggccattaacaaat +atgcgcacccatataatcctggttactggaataagtataagaaactaaaacagaaaatcc +ttcagtggcagcagcaaatcagttaatacatagaagaagggttagaggagggaaaggaaa +tgggaacaggattaaatgaacaattcgtagatgacatcgtgaaactaacgaaagaagcgg +gttcaaaagtggaggcagtattaaaggtgatgagttatctttcagctgagtattatgtaa +tagacgcagacattgtaccagacccggataactacttgtacgaaagagatatattccata +tggataatgagacagaatttcttttagaagaaacatttaataaggaggacaattaaatgg +aagtaaatggggatgttatcctaggcggggttgcggcttttgtactttactcgtggttac +tatacaacagaggatacagaaaaggttcggatgacgcggccactattatactagatcgca +tggaggaagtctttgagttatcagaagaagacaaggagtatagaagaaaaatgcagggag +gtaaataatatgtatgaaaatgtgttagacgttatcaattgtagaacaaaagaggtagcg +gagaaactattcgattattttgcttcagaagggtataccgtgtcattagctggtgcggag 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_progressivemauve/test-data/phagey.fa Fri Jun 10 08:41:20 2022 +0000 @@ -0,0 +1,2661 @@ +>phagey +tggtattacaagagagaaaggaagtaatcgatatgcaacagacagcagctaagaacacac +aaccagaaggtttacatctttacatggcaattggatcgtatgagtcggccattaacaaat +atgcgcacccatataatcctggttactggaataagtataagaaactaaaacagaaaatcc +ttcagtggcagcagcaaatcagttaatacatagaagaagggttagaggagggaaaggaaa +tgggaacaggattaaatgaacaattcgtagatgacatcgtgaaactaacgaaagaagcgg +gttcaaaagtggaggcagtattaaaggtgatgagttatctttcagctgagtattatgtaa +tagacgcagacattgtaccagacccggataactacttgtacgaaagagatatattccata +tggataatgagacagaatttcttttagaagaaacatttaataaggaggacaattaaatgg +aagtaaatggggatgttatcctaggcggggttgcggcttttgtactttactcgtggttac +tatacaacagaggatacagaaaaggttcggatgacgcggccactattatactagatcgca +tggaggaagtctttgagttatcagaagaagacaaggagtatagaagaaaaatgcagggag +gtaaataatatgtatgaaaatgtgttagacgttatcaattgtagaacaaaagaggtagcg +gagaaactattcgattattttgcttcagaagggtataccgtgtcattagctggtgcggag 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