| Previous changeset 3:1650a97189be (2017-11-17) Next changeset 5:17e61517c166 (2018-08-31) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7 |
|
modified:
minimap2.xml |
|
added:
test-data/mini_reads.fq test-data/mini_reads.paf |
| b |
| diff -r 1650a97189be -r 6f50f36e4481 minimap2.xml --- a/minimap2.xml Fri Nov 17 08:11:42 2017 -0500 +++ b/minimap2.xml Tue Aug 07 07:59:53 2018 -0400 |
| b |
| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="minimap2" name="Map with minimap2" version="2.5" profile="17.01"> +<tool id="minimap2" name="Map with minimap2" version="2.5+gx1" profile="17.01"> <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description> <requirements> <requirement type="package" version="2.5">minimap2</requirement> @@ -13,7 +13,7 @@ #else: ln -f -s '$reference_source.ref_file.fields.path' reference.fa && #end if - minimap2 -a + minimap2 -x $analysis_type_selector ## indexing options #if $indexing_options.k: @@ -100,21 +100,29 @@ #else if $fastq_input.fastq_input_selector == 'paired': '$fastq_input.fastq_input1' '$fastq_input.fastq_input2' #else if $fastq_input.fastq_input_selector == 'paired_collection': - '$fastq_input.fastq_input1.forward' '$fastq_input.fastq_input1.reverse' + '$fastq_input.fastq_input1.forward' '$fastq_input.fastq_input1.reverse' #end if - | samtools sort - -@\${GALAXY_SLOTS:-2} - -O $io_options.output_format - #if $io_options.output_format == 'CRAM': + #if $io_options.output_format == 'BAM': + -a + | samtools sort + -@\${GALAXY_SLOTS:-2} + -O $io_options.output_format + -o '$alignment_output' + #else if $io_options.output_format == 'CRAM': + -a + | samtools sort + -@\${GALAXY_SLOTS:-2} + -O $io_options.output_format --reference reference.fa --output-fmt-option no_ref + -o '$alignment_output' #end if - -o '$alignment_output' + > '$alignment_output' ]]> </command> <inputs> <conditional name="reference_source"> - <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below"> + <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below. If you would like to perform self-mapping select `history` here, then choose your input file as reference."> <option value="cached">Use a built-in genome index</option> <option value="history">Use a genome from history and build index</option> </param> @@ -128,7 +136,7 @@ </param> </when> <when value="history"> - <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" /> + <param name="ref_file" type="data" format="fasta,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference" /> </when> </conditional> <section name="indexing_options" title="Indexing options"> @@ -200,9 +208,10 @@ </param> </section> <section name="io_options" title="Set advanced output options" help="Sets -Q, -L, -R, -c, --cs and -K options." expanded="False"> - <param name="output_format" type="select" label="Produce BAM or CRAM file?"> + <param name="output_format" type="select" label="Select an output format"> <option value="BAM">BAM</option> <option value="CRAM">CRAM</option> + <option value="paf">paf</option> </param> <param argument="-Q" type="boolean" truevalue="-Q" falsevalue="" optional="true" label="don't output base quality"/> <param argument="-L" type="boolean" truevalue="-L" falsevalue="" optional="true" label="write CIGAR with >65535 ops to the CG tag" help="Useful for very long reads in SAM/BAM format"/> @@ -235,6 +244,7 @@ </conditional> </actions> <change_format> + <when input="io_options.output_format" value="paf" format="tabular" /> <when input="io_options.output_format" value="CRAM" format="cram" /> </change_format> </data> @@ -302,6 +312,16 @@ <param name="analysis_type_selector" value="sr"/> <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="2" /> </test> + <test> + <!-- test paf output --> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" ftype="fastqsanger" value="mini_reads.fq" /> + <param name="fastq_input_selector" value="single"/> + <param name="fastq_input1" ftype="fastqsanger" value="mini_reads.fq" /> + <param name="analysis_type_selector" value="ava-ont"/> + <param name="output_format" value="paf"/> + <output name="alignment_output" ftype="tabular" file="mini_reads.paf" /> + </test> </tests> <help> |
| b |
| diff -r 1650a97189be -r 6f50f36e4481 test-data/mini_reads.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mini_reads.fq Tue Aug 07 07:59:53 2018 -0400 |
| b |
| b'@@ -0,0 +1,100 @@\n+@m140213_230323_42129_c100520410120000001823082509281362_s1_X0/247/0_9332\n+CCACACCAAAGAGAGAGATTCAGCAATGCTCGAAGAGATGGACGGCGTTAAGTTTACGCCGATAACCCCAGACTCCGGGCTTACACTCTGAAAACATTCAGCTCACCAGCGTTACGCCCCGTTCTATCAACAAACCGCACCGTCAAGAAACGCTCCACCACCGTCGATAGTCAGCGATGCATGAGGATGGCGACCGTAAATTCCCGCCGGCCGCCCAATGCCAGCGCCACGTAAGCACCAGTGTCAGCAAAAGATACCCCCAAACCGCCGGCCGTCTGCCAGTAGCGTTCACCCTTCACACAACGTGCCGCACCAACCTCGCACTGACCGCTTTCACCGACGACATAACAAAGCGATTCGTGATATTTCACTTTCGACTTCAAGCGAGACGATTACCCGGCCCTGGTCGCGCCCGGCCAGTATGAATAGTCCTGTCAATGCAGGCAAAAACCGCCCCCAGTGAGCGACTTCACCTCACAAACATGCGCGCCACACCCAGCTAAAGAACTCTCCACCATCTGCCAGACAATGTCCCGGCGCACCGCCAAGTTCAAGTGAAACCGATGCCACGGCGAGACTCCCCGGGCCACCAACAGCCGCCTCCGCAGGGCAAAACCCACCGTGGCGTAAACAGCGTGGTTTGCGAAATATATGTTCGCCAAGCGAGCGGCCATCCAGCACCCGGCGATAAAATCCGCAGGCGGCGCGACGGGTTATCGGGCCCGCCGCCTTTCCTCAACACACGCGAAGTCCATCGCAAACCACAGCGCGGCAGCACCGCTTTGCAGCCACCAGCGACAACTCGGCGCTACATGATAGCAAAGCGGAACGCCGCCGCGCACAGGCGGGCCGGAAGAGCCAAAGACGCTTGCGACCTGTCGCGCCGCGCCTCCAACGGTTGCTCCGCAAATTCCGTCGCCGCCTTACCGGCGTCAGATGCTGGCGCAACAGCCCCGTCCCCGCCCGCACGAACGGTGAGGTGAAATGCTGGCCGGTATTATCGACCAGGCTCAGCGCCCGACGCAGAGTCGGCCCGCCACTTTCGCACAGCCTGTGGGCCACCACGCATCATCCTTCAATCATTTATCCGTTACCACACCACCTGACGCAGGTAATAGAACGTCCACCCACCAGATCGCTTTGTCCGCCATCACCGCACAATACTTATACGCCATCGGGATTCGCGATCACATGTCGCATCTTACGGCATCCCACATGCCGTGGCAACGTAATGATCTCCACGTCGAACAGTTTTTCGTCTTTAGTCGGCTCATACCCGCCCGGCACCGGCGCACGCCCAGACGACTCTTCATTTCCCAGCCCCCACGGACGATGAAACTTTTTGCTCCCATCGAAACCGGGAAAATTCCATATGACCCACACGCGCAAAACACCGGCGCCTTTTACGGCTACACGTAGATCTCTCACGCAAATGCTGGTTCTTTTGCAACAGCAGTTGTGGTGACAGAGTTTGATCTCCCATCGCAGCGTGTGGCTGTCGACGCGTTTCTGCGAAGCTCGCAAGCCGTTACCGACGTTTTCCATCATCGCATCCGGTTAACTTGAAAAACGCGCCAGGCCACGCTTCAGGTAATCACAAAGACCCGTACCTTCCAAAAGACGCCAGATCAACGCGACGCGCAAGACGTCTCAAGCTTTCCTGCACTCTTTGTGGCCAGAACATAAATAAGTCCGAGGCGTACCATTCCGCGTGAAACCCGATCACGCATAAATCCACAACCTGTCCCACCCATCAAGGCAGATTTCAAATAAAGTGGTTACCGTCCAGCTCCAGTGTTAGAGTCATGGGATCAGGAAAAACGGGAATATTGCGAACCACTGATACCGCGCTCAAAAAGCCAGCCCATTTAGCATCCGACGGAACTAGTGATTTTCCCAGGCACCTTTACACTTACAAACGGGCCAGTGTACCGCGAGTGATGGATCTGTCGCAAGTCGGCCGTTCAAGCGCCTGACGCAGCGCGCCAGGTTTTTCAAGCAGGTCTTCGCCGTTAAACGAGCCGTACGCAGCGCGTCATTCACAAAGCCAATACTCACGGCCGCCCGCCTGCTCGGAAAATCGCCCCCTTGGTCGGATCACTACCAAGGGGAACCTTACCCAGTGTACAATCAGGCAATACCTGCAATAATGTTTGAAAATAAAACGCATCTGTCGGCCGTATTAATAAGTCGACGTCCATCGCCTCTACCGGCACGCCTTGTCCCACACATTTACCGGGCATTCAGTGTCAAATTCGTAATCATTGTTTTTCTCTTTCGTGTTGCTGCCGGACAGAAGCACACCGTCGTGCCAAAAATTAAAATAAGCAGCGTAATTCTTTTAATTCATTGTTTATAAAAAAAAATTATATCTTAGCGTTCCGAACCGAGATTCCGGCAAAGCCACAATTTACCGATAAATGAACAATCGCTAAAGGATATCTAAGATCGTAAAACAGTAGCTTTTGCTTTGCGTAACCGTACTGGATATGCCGGGCGCGGCAGTCAGCGCGGTCAAAAATGGCGCCCGCACTCCATTTAATGCAGCAAGAATCGTGGCATCGACTCGACGGAATTGTTCACGACGCCGCTCGCGCCGCTAAATGAAAACGCTTAAAACGCGATAACTCCCAGCGTTCGCGCGAAACACAGTGTGACGTGAGAGAACGCAAACGCCGGGAGTCGAAGAAAAGGTCAAACGTCCTGCCTGCCATATCGCCCGTGGACGCGTTTCAACCGAGAAAAAGAAGACATTAATTCACACACCTACGGTAACCTCACGTCGCGCAGATTTCTGTTTCTGCATGGCAGAAGCGCGTTACCTGGCCCGCCCGGCTGATACAATGCACTTCACCCTCCGCGCAAAAAGAACGCCGCGCGCCCAGGAACGTAACATACGATCTCGGATTAACCGTAAACGCCATGGCCAGCCGCTGCCGAGAACGCCAGCAAACGCTGATTTACTCAAAGCCGGCATTGGCCACTCGTAAACCCTCCACTCAACGCCGCAATGATGAGCAGATCGAAAAAAGTGGCGATTCAATCCCGGCCGCCGATTCTCAACGGTTCCCAACCGGTCCGGCAAATCATTCGGTCGCGGACGCCATCTCGAGTTAAAACAGGCGCGATCAGTAGCGGCGCGTGGGTGGGAAGGAACTGCCCCACCCTGCCGCGATACCGCCATGCCGACGCTGTGGTCATAAAAGCCGTACCGGGCGCGGGAACTCGTGAAGGTGTTATTACAGCGGCCAAACGGCGAATGTCTTAGAGATGGCGGAACGGCGCAACGAACAGGGCAATGCGGGCTGAAAGCCAAGAAAAAACCTTTTACCCGTGCAGCGATCCCCAGGTGACAGTGATTCAGCTTATCGCCGAACGGGGCGCCGATATTGCGGCCCAGCTGGTTCCGAAGGCAAATTTCGCAAAACTGTACGCGCGGATAATCTCGACCTTCACCCGCGTCACCCAACGCCAGAAGATATTGAACCGAACCTGATATAAGGAGCGCCACGCCCACTCACTGGGCGAACAGCGCTTAACACCGAACGCGGCGCGCGATTGGCCTGGTTGGCTTGCGACCTCTCCCAAGGCAAGCGCGCTAAACTCGCGACTTTCGGCCAAAGCCCACCGGATGCCACTCCACTCAGCGACCCATCACGCTCGGAACTGATTAAATGAAATAAACCCATGCCTAAACGCAGAGAGCCGCCCCTCCGCGCTTACGGCGTGCGGGCGCAGAGGGCAAGAAAACATCATCTCTTCGCGTAAGCAACTCGGAAACACGTATCGCTATCCGCCGCCAGGCAAAAGCGCTTCCGCAGCCGACGCCAGCTGGGAACTCGCCGCCCAGGCAAACCCACGTCAAATGACGCGGATCGGGCTAACGCAAATACCTGGTGCGCGTT'..b'TCCAACCCTGCTCAACTGGAGTTTCAATCGAATCGCTTTCTGCCGTGGCTGCCGACAATACAGTAATTAGCTGGCATTTCTGCTTGGGCTTTCAAGCAAATGCGATGCAACCACAAGGCTGTCTCCGCAATCAAACCGCACCGCATCAACACCGAGCTTCATTCCCACTAATGCATTGCGCGGATAATGCAGCCGTGAAGGATAGCGCTAATGACCAAAAATGTCCAATCTCTCCTACAACAGTATGCCTGCTCCAAAACCGTGGCATAACGCAATTACCTGAATGTCGCGCCATCTTTCAACCAACGAGTACGACTCAAAATCGCCACGCAGGCTGGCATTGCCCAACGTAAACGCCCTCCCGAAATAGACACGCCGATGTCAATACCGCTGTCGGATGACAAAGACTCCTCTTCTGGCACAACCGATCAGACCTCTACTATAAATGCAATAACGCGCTCCTGTTCAAATATTCAAGCGCCAAACGTGAAAAATACACTCCCGCCAGGCATTCACCCGACTCGAGTTTCACACTTTTTCAACTAACGAACGCTAAAGCAGCAGGCGCTACGCCTGATAAATTTATACACAGCTTATCGCCGACCGTAGTGCCCTGCCCCAGTGTGCCGGAAGCAACTCCCGCAACAAATGTCTTTAAAGGACGCACGGGCGATTAAAATGGATCAGTAAAAAGCCTAAACTATGAAATGCCCGCCGCGGGGTTAAAACTCGCGCCGCCCTTTTGAAAAGCGGCACCAGCGGGCGGAAAATGACTGAATAAAGTTTCGTACTATGGCATTTTGTTCATTAAATGCCACATCTTCTACTCTGGCACGTCATGCGGCGCGAGAAAAGCGCCAGTGGATTGCGCTTTCAACAAATCACGGTTACCCCACACCCGCTTCATGCAAAATCTGTACATCGCCAATTTTGCGACGGCGATTCCATCAAGGCTGGTGCCATGCGCCAAAACCTTGCCAAATCAAAAACTGCTTTTTGACATCAAGCACACGTTTGATTTACTAAACCTCCGAGAGCAACAGATCCATATTACCCATCCATGCAGGTGTCTGCGCGATTATTAATTTTACCTTTCTGATCCCGACGCGTCAGCGCAAGCCATTTATCACTGAGGCTATAAAACTGCGGCGCCCCGATGGCGGAAACATCCAGCCGCAGAGAGCCTTCGTTTATTAAGACGAAACATAAGCGGGCGCACGAAAACGCTCACCAAAATCCCAGCCTTCCACCAAAGCATCCAGACTACCAACCAGTATTCAAACCACCCGACAGAAATCTAATCACCCATACATAAGGAGAAGTCAAAGATGGCCACTTAACCGGAACAGCGTTTACAGCATGTGATAAACAGTATCAAGTTACTCATTCGCTTCAAGCTCGTTGTATTGTTGTGAATTAGAATCATAGCACTAGTTCGTACGACTCT\n++\n+(/,..-$+,)$-.)&-+%#*)#\'%%,-#,%-*,/)&//+.**/\'.)-,/),,"*.\',-/\'*-),,-.*-(.\'./\'-+//*,.,--/.,.,././.-//.&&$$\'+-\'./-/-/*&/.../.)(-+--+-+\'.,/./,/--%.,..(\'*#.-+,*,&/,..*(/-/-+,.)*+/%../,./*)-)/..,%.-.\'(,+%.,,+.-..".(..,/.,/.---....*"+-,*,.$$..-+../--,+..,%),)\')&-,+#-.(//.(.,.$-/.-//./-."*&+*.-.##&+\'\')*.)//(.,/+,--.*,.--/--+(//)+./.#\'./,./(.*%+,-"-.,+.-,&-,..-...,,/*,,+.$.../.&.././-/.-/-./,,.),,#--+.&,./)(.+-/.*\'%\'++\'(%&$+..-+*#)+/\'//-+.-.+)+.+.,.*.+..(...*-)*#,.../(./-\',(+/.,---..-.,.\'/),/.+/\'./).,--.#""*)-.)&$-/.*/.--/&%)-#-.+&,(\'-+)/(/)/-*-+-,#/*.-#,.$,(#,--),,.-/,/(#/%,#&/...*-/**-&/\'.**.-(++.-&-)/.\'-/+.,/-#/(./*.*/.(/-.*(,-,&.-\'..\'.(---\'%-.+..%.,*\'/,//)/+*,/)..(.,*..,.-,/*.).&,.,..).*,,-/%./-%-.+,+%("*$,\'$$&#(((\',#&\',...+)+-(%#++"/-,/./,/.,/+-/-/.%/)-,*-.---,+."--"#+(%.#-+\'.(*+../\'/-,/).-.+-,+..$,.-..-,.\'+.\'.,/(+.(//,/.--(.-/&,/./+,//...--+//../)/-.-*-/*/.,,$+*(+&)-$,.).(,,)))&%-+++\'+\'+).#,)-$,/./-)....,,.-,\'$%.)/...,/+--..-.(./-,.*)\'(.(*./.....--%(&.*,.+#,.*..-$\'.,/.*,/-/./)/,-*-+%..-&.&$\'+,"(./,/,.+-.-.&$+.,/++-/%-\'--.\'-++,$))(*)--).,*/.*-*-*...(.,+.,.,,+)(##*%%#*+&*)+"*#*\'&(*\'*(,*--,\'&&&&%&+"*\',&,,\'#(-+"*-*&+"+$%.-.+/.*..#-,.,")*-.+,.++*$-+#.--.(.)+**/&.+//"+-.,**--#-(/,,//$.$/.*/-,/,.\',-+++-#.+.#,.*,#,-)&\',*.*.$&-(-**\'),($-*.(-),(+""&,(,\',+&($,(,.,/.(&/**,/*/-)+)--.,.&-&..+/+-/,/..,/..-(,+/.-/--(%.+-,+/,/,.+.-\'.+..,./.,+.&#*.(-.,&,,,+.*,,(,#..-,/*+*+..-.+/(,,/,*(/-/.,..//,)(,\'\',)&-.-.#(./,..&)--,/(/-)/./+..-*.,-*/&$+-%,.+./...,./),,-+&,.\'),/\'.$.../--/-+-#"/,/./-/(//.//.&..(./.+.&..&&.//&./,-*...\'.,/--*.*&.+."-+,.-.+.(.+).+.*\'..+(#-,*.-.,.-**.,.%++$$$,,+.-*..\',+\',-,/+/./*-+,/+,.,$+-/-\'//+-.-*.\'--..)(+///+.-+*"+.$..,,/.+,//-.).,+*/.,/*\'(.-.*..+-/,,/\'.)+.)%*,./-/.+/."/(.,,.,&+..--",&\'*-,,\'\'+..-+(-*-$,-,/+.,(,+)-*,/,..#+/.-*..-\'-(.&...(.*-*"\'--)&..+(%,-#+(.*\'.-&(,.,,/,\'+((,.,.-(-,-+-/.,."-((++--##$....-/))+,+-.*,,)&--,,-/+\'..)-.*.,,\'/.-.\'\'.././+/,/%.,..#)*//*..$,/.)/.$)(*+)(--,(-+-)++.\',-\'-\',-+,,#)-,*.-/$#...,."(.-/../-++--++-.-.-.%/#*-../.+$-$#-++,.\'..-#-&-),\'--..*,.+.*,*&**.-.*/&../-+)/./+.#)./,,-(.+./.-//-%\'+(-./&)/+/)/)---,/*-/.-.--+/,/.+,(.)),#.(\'\'*.-+&.",,)+,...+-%-&-#(-.)-#-*/.,+..-.&.+%*,..,&.+/,*-.*/$-$.("\'\'.\'+..\',.(.-/...,-%--+.).,/$..$$(.),,./,"-+-.--&#++.,#/./+-..$/,/+..-.%*#+.+//.%(.%(.#.$-)&..,+,-\'.),\',,/./+"/),-,../.,+.$\'-%)###%$*)-+-.".+,..-.%.\'/-.,/./$-.#.)(&/-.//,**#-/&../*,/*)+.++(--&+*%*#*##$(**-.&#+.-../())/,/-/..$.)..+#),&#$)-#-...-,/(-&,-+/.\'-.+././#,/*,.*-##\'.**...*.#\'...,*-$$.+*,...-..,&/./)+-../+//-.\'+#..,..-,.(+....+.&\'.+/*-.),,"$-#%"*$.)\'.(,,$)%.*).),/.//\'*+.).#.+,+//-..*.--,(\n' |
| b |
| diff -r 1650a97189be -r 6f50f36e4481 test-data/mini_reads.paf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mini_reads.paf Tue Aug 07 07:59:53 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +m140213_230323_42129_c100520410120000001823082509281362_s1_X0/1263/0_8655 8655 755 8475 + m140213_230323_42129_c100520410120000001823082509281362_s1_X0/817/0_20440 20440 5798 13009 395 7727 0 tp:A:S cm:i:43 s1:i:294 +m140213_230323_42129_c100520410120000001823082509281362_s1_X0/1447/0_15191 15191 12916 14825 - m140213_230323_42129_c100520410120000001823082509281362_s1_X0/1447/15237_17783 2546 347 2303 152 1985 0 tp:A:S cm:i:15 s1:i:133 |