| Next changeset 1:84f769706f7a (2019-04-02) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab |
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added:
macro.xml mykrobe_genotype.xml test-data/reads.fastq test-data/tb-bradley-probe-set-feb-09-2017.fasta.gz |
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| diff -r 000000000000 -r d783eb846f59 macro.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macro.xml Sat Jan 13 09:02:58 2018 -0500 |
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| @@ -0,0 +1,77 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.5.6">mykrobe</requirement> + </requirements> + </xml> + + <token name="@select_inputs@"> + <![CDATA[ + #set $name='sample' + #set $type='fastq' + ## Adding sample name, indicate specie and inputs fastq(s) files + #if $data_type.type == "paired": + + ln -s '$data_type.fastq_input1' sample_1.fastq && + ln -s '$data_type.fastq_input2' sample_2.fastq && + + + #elif $data_type.type == "collection": + #set $name=str($data_type.fastq_input1.name) + ln -s '$data_type.fastq_input1.forward' '$data_type.fastq_input1.name'_1.fastq && + ln -s '$data_type.fastq_input1.reverse' '$data_type.fastq_input1.name'_2.fastq && + + #elif $data_type.type == "single": + + + #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'): + ln -s '$data_type.fastq_input1' sample.fastq && + + #end if + + #if $data_type.fastq_input1.is_of_type('bam'): + ln -s '$data_type.fastq_input1' sample.bam && + #set $type='bam' + #end if + + #end if + ]]> + </token> + + <xml name="inputs"> + <conditional name="data_type"> + <param name="type" type="select" label="Specify the read type."> + <option value="single">Single-end Data</option> + <option value="paired">Paired-end Data</option> + <option value="collection">Collection Paired-end Data</option> + </param> + <when value="single"> + <param name="fastq_input1" type="data" format="fastqsanger, fastq,fasta,bam" label="Single end read file(s)"/> + </when> + <when value="paired"> + <param name="fastq_input1" type="data" format="fastqsanger, fastq" label="Forward paired-end read file"/> + <param name="fastq_input2" type="data" format="fastqsanger, fastq" label="Reverse paired-end read file"/> + </when> + <when value="collection"> + <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger, fastq" collection_type="paired" /> + </when> + </conditional> + </xml> + + <token name="@ATTRIBUTION@"> + <![CDATA[ + + **MyKrobe predict - Antibiotic resistance predictions** + + Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis + using Bruijn graph. + ]]> + </token> + + <xml name="citation"> + <citations> + <citation type="doi">10.1038/ncomms10063</citation> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r d783eb846f59 mykrobe_genotype.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mykrobe_genotype.xml Sat Jan 13 09:02:58 2018 -0500 |
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| @@ -0,0 +1,64 @@ +<?xml version="1.0" encoding="utf-8"?> +<tool id="mykrobe_genotype" name="mkyrobe genotype" version="0.5.6" > + <description>Antibiotic resistance predictions</description> + <macros> + <import>macro.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"> +<![CDATA[ + @select_inputs@ + + mykrobe genotype + '$name' + '$probe_set' + + #if $kmer: + --kmer $kmer + #end if + + #if $expected_depth: + --expected_depth $expected_depth + #end if + + + -q + -t "\${GALAXY_SLOTS:-1}" + + -1 + #if $type == 'fastq': + *.fastq + #elif $type == 'bam': + *.bam + #else + *.fasta + #end if + > $json +]]> + </command> + <inputs> + <expand macro="inputs" /> + <param name="probe_set" type="data" format="fasta" label="Probe Set"/> + <param name="kmer" argument="--kmer" optional="True" type="integer" min="0" label="Kmer length" value="21" help="default = 21"/> + <param name="expected_depth" argument="--expected_depth" optional="True" type="integer" min="0" label="Expected Depth" help=""/> + </inputs> + <outputs> + <data name="json" format="json" label="JSON prediction"/> + </outputs> + <tests> + <test> + <param name="type" value="single"/> + <param name="fastq_input1" value="reads.fastq"/> + <param name="probe_set" value="tb-bradley-probe-set-feb-09-2017.fasta.gz"/> + <output name="json"> + <assert_contents> + <has_text_matching expression="ref-S315T"/> + </assert_contents> + </output> + </test> + </tests> + <help> +@ATTRIBUTION@ + </help> + <expand macro="citation" /> +</tool> |
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| diff -r 000000000000 -r d783eb846f59 test-data/reads.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads.fastq Sat Jan 13 09:02:58 2018 -0500 |
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| b'@@ -0,0 +1,4140 @@\n+@ERR117639.81080\n+CTGGCCGCGGCCAGTAGGAACATCCCCGGCCAGTCGTCCTCGGTCGGGCTACACAGGGTCACAGTCACAGAATCCGACTGTGGCATATGCCGCGGCCACG\n++\n+CAFFHIIKKJKJKKJMJLKKKJKJJIKIKJMJHMJJHKHJLHMMJKKIKKKGJKJKML@KMJKJJJKLOILLLKII8HHFGKJJKJLJHHKHNGIGIGJE\n+@ERR117639.138514\n+ATCGGTGAAACTGGCCGCGGCCAGTAGGAACATCCCCGGCCAGTCGTCCTCGGTCGGGCTACACAGGGTCACAGTCACAGAATCCGACTGTGGCATATGC\n++\n+BCCHHIIGKJNJEKIILLHKKMKJIJHIKKHJKIJJJKLJLHMFJKEIKJKKJKJKKINKMJIKLJKLOHLJIKIKFLJKIKMJAJLLJIHHGGIGIGJE\n+@ERR117639.605794\n+GGTCACAGTCACAGAATCCGACTGTGGCATATGCCGCGGCCACGTGCACGTGAATATTACGACGACAGTGTCTGGCAAAGGATCACGCGATGCGGGTAGC\n++\n+BAFFHIIKKJKJIKIMKLJKKMKJLLKIKIMNJMKJJKLJKHMIJKKLKJKKJKIFKLKKMIKHJJKHHHIKLKEKLMJFJGM@KJKHHIKHIJIG>BHC\n+@ERR117639.792943\n+TCGGTGAAACTGGCCGCGGTCAGTAGGAACATCCCCGGCCAGTCGTCCTCGGTCGGGCTACACAGGGTCACAGTCACAGAATCCGACTGTGGCATATGCC\n++\n+CCFGHIIKKHNFKKIKLIJKIMKJLJJIKINIHMKJJKLJLKHMJKIIKHKGFKIKGGKKIIIKLJKJHKLIFKCJHHKMIGKJKJLJJEKHKCCJIGGB\n+@ERR117639.826271\n+CAGGGTCACAGTCACAGAATCCGACTGTGGCATATGCCGCGGCCACGTGCACGTGAATATTACGACGACAGTGTCTGGCAAAGGATCACGCGATGCGGGT\n++\n+CCDGJIEKKHKJKKIMILGKKMKJJLJJKKMJKIJJKKLJLICMJKJIKEKJJKIKMLHKMJHH:JKLOKJJDDIDLHKK7GJBGJAFJFKHAJHIIGH/\n+@ERR117639.942680\n+GGCCAGTCGTCCTCGGTTCGGGCTACACAGGGTCACAGTCACAGAATCCGACTGTGGTATATGCCGCGGCCACGTGCACGTGAATATTACGACGACAGTG\n++\n+BCB=HI>KK@NJKHLE*7@KK;>@LFJJEHMG>FJ=<H9<=A<:FE;IHH1>B;6IF6G);<DJG6+G.H899=(A4J221:9.F:A2A1)<?;<D9GH8\n+@ERR117639.1045623\n+GCTACACAGGGTCACAGTCACAGAATCCGACTGTGGCATATGCCGCGGCCACGTGCACGTGAATATTACGACGACAGTGTCTGGCAAAGGATCACGCGAT\n++\n+BA=DHBGFK@NJIJIHKLGIKMKJJJKIKJMJJMJJJKLKKIMKJKKNKLKGJELKKINKIGGHJJKJH8FIIKIKLFGDJGKJLMHJICGC?CAB?JH/\n+@ERR117639.1246224\n+GGCTACACAGGGTCACAGTCACAGAATCCGACTGTGGCATATGCCGCGGCCACGTGCACGTGAATATTACGACGACAGTGTCTGGCAAAGGATCACGCGA\n++\n+BCFFFIKHKINJKKLKILHKKMKJJJHJKJMJLMJJHKHJGKIKJGKNKJKIJKJKGL@KMIKHLJKJOIDKJD?JIHJDJKEJIJGHHHKCGKHIIGC8\n+@ERR117639.1403621\n+CCGGCCAGTCGTCCTCGGTCGGGCTACACAGGGTCACAGTCACAGAATCCGACTGTGGCATATGCCGCGGCCACGTGCACGTGAATATTACGACGACAGT\n++\n+BCEGHIJKKJNJIAFHKLGKKLKHLLJJKHMNK=JJKKLILHHKJLKIK<KIJKLHMLHKMJIJL@KKHGLLLDIJHJJMICJJKJHLFHJHAJHDIGH=\n+@ERR117639.2049300\n+CATCCCCGGCCAGTCGTCCTCGGTCGGGCTACACAGGGTCACAGTCACAGAATCCGACTGTGGCATATGCCGCGGCCACGTGCACGTGAATATTACGACG\n++\n+CBBGHIGKKGNJKJJ=KLKFIMKEJJKJKJNJKMKJFKFJHKH@J6KLGKKKJKLF#LHKMGILLGKKHJLKLK;ILFJKGKMFLJKJJHKH9GH3CHH@\n+@ERR117639.2391080\n+ATCGGTGAAACTGGCCGCGGCCAGTAGGAACATCCCCGGCCAGTCGTCCTCGGTCGGGCTACACAGGGTCACAGTCACAGAATCCGACTGTGGCATATGC\n++\n+BABGHIIKK@KAHKHMKIJKKMGLBIHEKJBJHMJJDKLJLHLIJKONKJKHJEHKGINKJIIKLJKLHKILJKEILHGIJKMJDJHJJEJNGHCDIJJB\n+@ERR117639.2516039\n+AACATCCCCGGCCAGTCGTCCTCGGTCGGGCTACACAGGGTCACAGTCACAGAATCCGACTGTGGCATATGCCGCGGCCACGTGCACGTGAATATTACGA\n++\n+=<F=FI8KCEBFICI+JHG?KAKLIJHJ<JGJ>FEJFKFJ/HL-<9=EDEKFJ?JK,E@K+G9KIJHH@J8KBK9IA9DK?H6JGJFJJE650HI9I>FB\n+@ERR117639.2757526\n+CGGTCGGGCTACACAGGGTCACAGTCACAGAATCCGACTGTGGCATATGCCGCGGCCACGTGCACGTGAATATTACGACGACAGTGTCTGGCAAAGGATC\n++\n+7<66??B@C18CC2HE:L*?CKDI6I<I<HFJKJC=H>B/<KC:JBGIKI;AFI:HC8;A7G-9B@IJC@8I96?7IFBMCH6D5MLLCCK5?H7II4F/\n+@ERR117639.564430\n+TCCTCGGTCGGGCTACACAGGGTCACAGTCACAGAATCCGACTGTGGCATATGCCGCGGCCACGTGCACGTGAATATTACGACGACAGTGTCTGGCAAAG\n++\n+BFBBGHGKNKJIEHJGJMKIDGMFIEKILLKOLKJILIJJKI8K6LKJGKJKEKKJKIKLJFKJJJIKJNJKIJKJLKMKIGKKKHKKJKJKJIIHDFCC\n+@ERR117639.849310\n+GGTCGGGCTACACAGGGTCACAGTCACAGAATCCGACTGTGGCATATGCCGCGGCCACGTGCACGTGAATATTACGACGACAGTGTCTGGCAAAGGATCA\n++\n+@CB>DHKNIJHHHLJIJHCIDDHIIEFIJLHMLKJGKIJM?NLLHJIJKKEKIIHJHLKLJLGJBJMLJFHKGAJILKHKJKIJKKKKJNJKKIIJHCCC\n+@ERR117639.1122299\n+CCCGGCCAGTCGTCCTCGGTCGGGCTACACAGGGTCACAGTCACAGAATCCGACTGTGGCATATGCCGCGGCCACGTGCACGTGAATATTACGACGACAG\n++\n+CJHIIHGGHJFIHLJKJJKIIJMHIEKLLIIHLKJLHIIMKNLMHJKJJKKKNKGJKLHHJLKJJJMJKMKKKJFLLKMFKHHDILKKJNJKKIIHHFBB\n+@ERR117639.1367003\n+ACACAGGGTCACAGTCACAGAATCCGACTGTGGCATATGCCGCGGCCACGTGCACGTGAATATTACGACGACAGTGTCTGGCAAAGGATCACGCGATGCG\n++\n+=5GIGHCINKIJJLJIJECGKHFLKIKILLJOGKJLHGJMKIIKHJKBHKIGLKHHIHIKJHKI=JGKJMJKIKJLIKMKJKLKHFJIFNIKKJIHFFBC\n+@ERR117639.1422311\n+CGGTGAAACTGGCCGCGGCCAGTAGGAACATCCCCGGCCAGTCGTCCTCGGTCGGGCTACACAGGGTCACAGTCACAGAATCCGACTGTGGCATATGCCG\n++\n+C;JD'..b"TAAGGAGCACCACGAAAACGCCCCAACTGGTGGGGCGTAGGCC\n++\n+4H+ADHJAHAEILHMM&KKJMJHIJIKLLLIOK#JJJHLIGNIMHI?BIKIKMKKJMLKLJLKIJCIHJHJKIHILLKMEKKLJIIKIJNJKEIIHHCAC\n+@ERR117639.2299093\n+CGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCTAAGGAGCACCACGAAAACGCCCCAACTGGTGGGGCG\n++\n+CCEDHGGFKHKJGIIIKHKKIMKLJ>JKKJMJLMEJHHGDK;IIJLJJKL;H8KBKL>NKML9HG@BG5KFIFFIJDJHMJHEJIJKHF@KNGFIGIGG=\n+@ERR117639.250496\n+GAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCTAGATCGGAAG\n++\n+BCFGHIIKKJKJKKKKKHKKKFKLLKJIKJHKKMKJIKLIDHMMJKKLKKKAJKLKKINKMLKKLJK9OGIII@EK8-'+?K6DIAHJ7@A5?F,DI4G/\n+@ERR117639.768553\n+TGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCTAAGGAGCACCACGAAAAC\n++\n+CADGHIIKKEKJKIIIKHKKIMKLLLJJKJMGKMJJJKLDLHLIJKKIK<KKJKHFLLHAJGIFI@EK+H'EBF7IGDJICC+BAJ6A?@D>AK7I>JC=\n+@ERR117639.1711220\n+CTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCTAAGGAGCACCACGAAAA\n++\n+=?==FBBJCJ8FEKHIAHEHKJGHBKGEG<BJHFKJHHFJK6IH@L=IKEEIJGHCLLKK+9IKJJHCO,F@J6IDAMKII?HE>BF87+AHI>IHB==E\n+@ERR117639.2314382\n+CTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCTAAGGAGCACCACGAAAA\n++\n+CBCHHGGKKJIJIKBMKLNJKAKEJLKJKHNGHIJJJKHJKHDMJEKNGLAKJGJF@INK7GGKL@HLO8J,D6CIFHJIJ6M8GJL8?FKHIGADEGHB\n+@ERR117639.910209\n+TAACCCTCGGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCT\n++\n+8FJ6DIKGIKF?EKJL@HKB5BDDDIKLJLKCHIJLHC9BKILLFL:JHKEKIKEJ:IILDLKHJKMLGHIKEAJJIKAC?HHIKKFKC8JF@GIF=DC=\n+@ERR117639.1454913\n+CCTAACCCTCGGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTT\n++\n+BFG8H7FGC<=GJ<II;KED2?JFJEH>>C7HFKJ:FIFMEELLFG8JIEK@E=:FKIIE=LIHGJMKJMHAKKJHLKIKK@CDIHIIJBJ8KIIFH=A=\n+@ERR117639.201184\n+GGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCTAAGGAGCACCACGAAAACGCCCCAACTG\n++\n+CBFGHIIKKHNJKKJKKLKIKMKJLJHKCJGJHKKJKKLILIIMJLJIKHKFJKJHKI7GBGIDIJFGOJFLFD7JAMD>GGHJG9LJHFGCIKH5IGCC\n+@ERR117639.926014\n+GATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCTAAGGAGCACCACGAAAACGCCCCAACTGGT\n++\n+@FBIJIFK>AHJJKJAFKKII9JGIIGFGFH>HKGJJGGMKEICKF:@G;HKEKEDKICHKIGJJJCLKBJKKHKIL>MKIKKJIIHIJNHKKGIHG=AC\n+@ERR117639.921294\n+CTCGGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGGCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCTAAGGA\n++\n+B<==FD8GC@8CIFBMDC@?7A2JJJ<GAJBJ>KEJJK==HH;HHGE/=E;98AH6CI@'MLIHL,@9H8FI96,I8FBMC?+85'F-HEACG6H<64G/\n+@ERR117639.2521862\n+CCTAACCCTCGGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTT\n++\n+CCCAFIIKKGIJKKF@JCNKKMKLIJAIK/MJLKJJHKIHLKM=J>GIHKEKFKHH7IKKJIIDGJKKHHLKLK4IFHG5J?MDG9LE7@6I5HC1I.HB\n+@ERR117639.2828692\n+CCTAACCCTCGGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTT\n++\n+CBCGHAGKIH?FKJII;KKICJKIJJJJKDMJJJJJJKGJKI>KJEKJGJAGFE:HLLHKILH@GJKHHGFKDFEKGLG5ICMJGBLL?6=IGK7GCBH@\n+@ERR117639.1754141\n+GAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCTAAGGAGCACC\n++\n+CAG><CF5>A@,AGB+J>KG>JD8JE6-BL8>GE7L-GG>CE87H:BJA?B=J=EJI;K<=L><AJF>GM<<EA>B@D27?N7FK7H13<@K@8I4G6<B\n+@ERR117639.2832771\n+ATCGGAGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCTAAGGAGCACCACGAAAACGCCCCAACTGGTG\n++\n+CBEAH'KG>JDFKKII6HNHKMKJLJJJKJ:NJMJJJKLJLIEKJK/ICEAJBKB6LLKKIIIKIJKCO8I7I@I78JHFJCHJIJAHJJHHGHCBIHAB\n+@ERR117639.823588\n+TGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCTAAGGAGCACCACGAAAACGCCCCAACTGGTGGGGCGTAGG\n++\n+BJHI5H>GHJHJJLJKEMHIKKMFJIKJIIJCLIJLLKIMKILGKJKCJKKKNKKJMCKLHLKJJJMHKMJKIJLLHKGKKJLKKJKEJIEKKIIJFCAC\n+@ERR117639.406517\n+CGATTGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCTAAGGAGCACCACGAAAACGCCCCAACTGGTGGGGCG\n++\n+CCFDHIIKKINJKKKKILJJKMKLJJJKKJJIKMJJKKGJL;MIJLKMKJ;DFGJHCIKKMIGDIJEH@KJEIF?IFFHIJHEJGJLFHFKHKHIGIGHC\n+@ERR117639.566963\n+TGGGACGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCTAAGGAGCACCACGAAAACGCCCCAACTGGTGGGGCGTAGG\n++\n+EHJIGH>KCJ@?8FJIDKHGMJMIJMFLKFKHKKJLDKJMKKLJKHKCIKJKIKK@KHKLJHKHJJMHJNJKIKILLKGKKHLLMJJKJNHKHIIHHFCC\n" 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| diff -r 000000000000 -r d783eb846f59 test-data/tb-bradley-probe-set-feb-09-2017.fasta.gz |
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| Binary file test-data/tb-bradley-probe-set-feb-09-2017.fasta.gz has changed |