Mercurial > repos > galaxy-australia > kmc
comparison macros.xml @ 0:ca2743037241 draft
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
| author | galaxy-australia |
|---|---|
| date | Tue, 27 Sep 2022 05:20:06 +0000 |
| parents | |
| children | c7fda6e88567 |
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| -1:000000000000 | 0:ca2743037241 |
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| 1 <macros> | |
| 2 <token name="@TOOL_VERSION@">3.2.1</token> | |
| 3 <token name="@VERSION_SUFFIX@">0</token> | |
| 4 <xml name="requirements"> | |
| 5 <requirements> | |
| 6 <requirement type="package" version="@TOOL_VERSION@">kmc</requirement> | |
| 7 </requirements> | |
| 8 </xml> | |
| 9 <xml name="stdio"> | |
| 10 <stdio> | |
| 11 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> | |
| 12 <exit_code range="1:" level="fatal" description="Error" /> | |
| 13 </stdio> | |
| 14 </xml> | |
| 15 <xml name="version_command"> | |
| 16 <version_command><![CDATA[ | |
| 17 kmc --version 2>&1 | head -1 | |
| 18 ]]></version_command> | |
| 19 </xml> | |
| 20 <xml name="macro_input"> | |
| 21 <param name="input_file" type="data" format="fasta,fastq,fasta.gz,fastqsanger,fastq.gz,bam" label="Sequence file"/> | |
| 22 </xml> | |
| 23 <xml name="general_option"> | |
| 24 <param argument="exclude_length" type="integer" value="2" label="exclude k-mers occurring less than [value] times (default: 2)"/> | |
| 25 <param argument="exclude_kmer_occurence" type="integer" value="1000000000" label="exclude k-mers occurring more of than [value] times (default: 1e9)"/> | |
| 26 </xml> | |
| 27 <xml name="transform_option"> | |
| 28 <section name="input_opt" title="Input options" expanded="true"> | |
| 29 <expand macro="input_option"/> | |
| 30 </section> | |
| 31 <section name="output_opt" title="Output options" expanded="true"> | |
| 32 <expand macro="none_counter_calculation_option"/> | |
| 33 </section> | |
| 34 </xml> | |
| 35 <xml name="histogram_option"> | |
| 36 <section name="input_opt" title="Input options" expanded="true"> | |
| 37 <expand macro="input_option"/> | |
| 38 </section> | |
| 39 <section name="output_opt" title="Output options" expanded="true"> | |
| 40 <param name="min_kmer_value" argument="-ci" type="integer" value="2" optional="true" label="minimum value of counter to be stored in the output file"/> | |
| 41 <param name="max_kmer_value" argument="-cx" type="integer" value="255" optional="true" label="maximum value of counter to be stored in the output file"/> | |
| 42 </section> | |
| 43 </xml> | |
| 44 <xml name="set_count_option"> | |
| 45 <section name="input_opt" title="Input options" expanded="true"> | |
| 46 <expand macro="input_option"/> | |
| 47 <param argument="kmer_counts_value" type="integer" value="10" label="set all k-mer counts to specific value"/> | |
| 48 </section> | |
| 49 </xml> | |
| 50 <xml name="misc"> | |
| 51 <param name="misc_output" argument="-o" type="select" label="output in KMC or KFF format (default: kmc)"> | |
| 52 <option value="kmc" selected="true">KMC</option> | |
| 53 <option value="kff">KFF</option> | |
| 54 </param> | |
| 55 </xml> | |
| 56 <xml name="dump_option"> | |
| 57 <section name="input_opt" title="Input options" expanded="true"> | |
| 58 <expand macro="input_option"/> | |
| 59 </section> | |
| 60 <section name="output_opt" title="Output options" expanded="true"> | |
| 61 <param name="sort_output" argument="-s" type="boolean" truevalue="true" checked="false" label="sorted output"/> | |
| 62 </section> | |
| 63 </xml> | |
| 64 <xml name="input_option"> | |
| 65 <param name="min_kmer_occurrence" argument="-ci" type="integer" value="3" optional="true" label="exclude k-mers occurring less than x times"/> | |
| 66 <param name="max_kmer_occurrence" argument="-cx" type="integer" value="30" optional="true" label="exclude k-mers occurring more of than x times"/> | |
| 67 </xml> | |
| 68 <xml name="input_option_two"> | |
| 69 <param name="min_kmer_occurrence_two" argument="-ci" type="integer" value="3" label="exclude k-mers occurring less than x times"/> | |
| 70 <param name="max_kmer_occurrence_two" argument="-cx" type="integer" value="30" label="exclude k-mers occurring more of than x times"/> | |
| 71 </xml> | |
| 72 <xml name="simple_operation"> | |
| 73 <param name="select_operation" type="select" label="Simple Operation" help="redefine counter calculation mode for equal k-mers"> | |
| 74 <option value="intersect" selected="true">intersect</option> | |
| 75 <option value="union">union</option> | |
| 76 <option value="kmers_subtract">kmers_subtract</option> | |
| 77 <option value="reverse_kmers_subtract">reverse_kmers_subtract</option> | |
| 78 <option value="counters_subtract">counters_subtract</option> | |
| 79 <option value="reverse_counters_subtract">reverse_counters_subtract</option> | |
| 80 </param> | |
| 81 </xml> | |
| 82 <xml name="counter_calculation_option"> | |
| 83 <param name="min_kmer_occurrence" argument="-ci" type="integer" optional="true" label="exclude k-mers occurring less than x times"/> | |
| 84 <param name="max_kmer_occurrence" argument="-cx" type="integer" optional="true" label="exclude k-mers occurring more of than x times"/> | |
| 85 <param name="max_counter_value" argument="-cs" type="integer" optional="true" label="maximal value of a counter"/> | |
| 86 <param argument="-oc" name="oc" type="select" optional="true" label="Counter Calculation" help="redefine counter calculation mode for equal k-mers"> | |
| 87 <option value="min">min - get lower value of a k-mer counter</option> | |
| 88 <option value="max">max - get upper value of a k-mer counter</option> | |
| 89 <option value="sum">sum - get sum of counters from both databases</option> | |
| 90 <option value="diff">diff - get difference between counters </option> | |
| 91 <option value="left">left - get counter from first datatabase (KMC db one)</option> | |
| 92 <option value="right">right - get counter from second database (KMC db two)</option> | |
| 93 </param> | |
| 94 </xml> | |
| 95 <xml name="none_counter_calculation_option"> | |
| 96 <param name="min_kmer_occurrence" argument="-ci" type="integer" optional="true" label="exclude k-mers occurring less than x times"/> | |
| 97 <param name="max_kmer_occurrence" argument="-cx" type="integer" optional="true" label="exclude k-mers occurring more of than x times"/> | |
| 98 <param name="max_counter_value" argument="-cs" type="integer" optional="true" label="maximal value of a counter"/> | |
| 99 </xml> | |
| 100 <xml name="transform_operation"> | |
| 101 <param name="transform_operation" type="select" optional="true" label="Transform Operation" help="transforms single KMC database to one or more KMC database(s) or text file(s)"> | |
| 102 <option value="sort" >sort - converts database produced by KMC2.x to KMC1.x database format (which contains k-mers in sorted order)</option> | |
| 103 <option value="reduce">reduce - exclude too rare and too frequent k-mers</option> | |
| 104 <option value="compact">compact - remove counters of k-mers</option> | |
| 105 <option value="histogram">histogram - produce histogram of k-mers occurrences</option> | |
| 106 <option value="dump">dump - produce text dump of kmc database</option> | |
| 107 <option value="set_counts">set counts - set all k-mer counts to specific value</option> | |
| 108 </param> | |
| 109 </xml> | |
| 110 </macros> |