Mercurial > repos > iuc > khmer_extract_partitions

comparison macros.xml @ 6:2c763fb18010 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
author iuc
date Wed, 18 Dec 2019 16:00:12 -0500
parents 518ba4a77274
children 98b53d46e851
comparison
equal deleted inserted replaced
5:518ba4a77274 6:2c763fb18010
1 <macros> 1 <macros>
2 <token name="@WRAPPER_VERSION@">3.0.0a1</token> 2 <token name="@WRAPPER_VERSION@">3.0.0a3</token>
3 <token name="@TOOL_VERSION@">+galaxy1</token>
3 <xml name="requirements"> 4 <xml name="requirements">
4 <requirements> 5 <requirements>
5 <requirement type="package" version="@WRAPPER_VERSION@">khmer</requirement> 6 <requirement type="package" version="@WRAPPER_VERSION@">khmer</requirement>
7 <yield/>
6 </requirements> 8 </requirements>
7 </xml> 9 </xml>
8 <xml name="version"> 10 <xml name="version">
9 <version_command><![CDATA[@BINARY@ --version 2>&1 | tail -n 1 | cut -d ' ' -f 2]]></version_command> 11 <version_command><![CDATA[@BINARY@ --version 2>&1 | tail -n 1 | cut -d ' ' -f 2]]></version_command>
10 </xml> 12 </xml>
33 help="ksize, n_tables, a specific tablesize" > 35 help="ksize, n_tables, a specific tablesize" >
34 <option value="simple" selected="true">Hide</option> 36 <option value="simple" selected="true">Hide</option>
35 <option value="specific">Show</option> 37 <option value="specific">Show</option>
36 </param> 38 </param>
37 <when value="simple"> 39 <when value="simple">
38 <param name="tablesize" type="select" label="Sample Type" display="radio"> 40 <param argument="" name="tablesize" type="select" label="Sample Type" display="radio">
39 <option value="1e9" selected="true">Microbial Genome</option> 41 <option value="1e9" selected="true">Microbial Genome</option>
40 <option value="2e9">Animal Transcriptome</option> 42 <option value="2e9">Animal Transcriptome</option>
41 <option value="4e9">Small Animal Genome or Low-Diversity Metagenome</option> 43 <option value="4e9">Small Animal Genome or Low-Diversity Metagenome</option>
42 <option value="16e9">Large Animal Genome</option> 44 <option value="16e9">Large Animal Genome</option>
43 </param> 45 </param>
44 </when> 46 </when>
45 <when value="specific"> 47 <when value="specific">
46 <param name="ksize" type="integer" value="20" label="k-mer size" help="k-mer size to use" /> 48 <param argument="--ksize" name="ksize" type="integer" value="20" label="k-mer size" help="k-mer size to use" />
47 <param name="n_tables" type="integer" min="1" value="4" label="n_tables" help="number of tables to use" /> 49 <param argument="--n_tables" name="n_tables" type="integer" min="1" value="4" label="n_tables" help="number of tables to use" />
48 <param name="tablesize_specific" type="text" value="1000000.0" 50 <param argument="--max-tablesize" name="tablesize_specific" type="text" value="1000000.0"
49 label="tablesize" help="(--max-tablesize) upper bound on the tablesize to use" /> 51 label="tablesize" help="(--max-tablesize) upper bound on the tablesize to use" />
50 </when> 52 </when>
51 </conditional> 53 </conditional>
52 </xml> 54 </xml>
55 <token name="@LINK_SEQUENCES@">
56 <![CDATA[
57 #import re
58 mkdir input/ &&
59 #set gzip=""
60 #for $num, $input in enumerate($inputs)
61 ln -s '${input}' 'input/$re.sub("[^\w\-_.]", "_", $input.element_identifier).$input.ext' &&
62 #if str($input).endswith(".gz"):
63 #set gzip="--gzip"
64 #end if
65 #end for]]></token>
66 <token name="@USE_SEQUENCES@">
67 <![CDATA[
68 #for $num, $input in enumerate($inputs)
69 '../input/$re.sub("[^\w\-_.]", "_", $input.element_identifier).$input.ext'
70 #end for]]></token>
71
53 <xml name="input_sequences_filenames"> 72 <xml name="input_sequences_filenames">
54 <param name="inputs" multiple="true" type="data" format="fasta,fastq" 73 <param name="inputs" multiple="true" type="data" format="fasta,fastq,fasta.gz,fastq.gz"
55 label="Sequences in FASTA or FASTQ format" 74 label="Sequences in FASTA or FASTQ format"
56 help="Put in order of precedence such as longest reads first." /> 75 help="Put in order of precedence such as longest reads first." />
57 </xml> 76 </xml>
58 <xml name="input_sequence_filename"> 77 <xml name="input_sequence_filename">
59 <param name="input_sequence_filename" type="data" format="fasta,fastq" 78 <param name="input_sequence_filename" type="data" format="fasta,fastq"
64 label="the k-mer countgraph to query" 83 label="the k-mer countgraph to query"
65 help="The abundances of the k-mers in the input nucleotide sequence file will be calculated using the kmer counts in this k-mer countgraph." /> 84 help="The abundances of the k-mers in the input nucleotide sequence file will be calculated using the kmer counts in this k-mer countgraph." />
66 </xml> 85 </xml>
67 <xml name="abundance-histogram-output"> 86 <xml name="abundance-histogram-output">
68 <data name="output_histogram_filename" format="txt" 87 <data name="output_histogram_filename" format="txt"
69 label="${tool.name} k-mer abundance histogram. The 88 label="${tool.name} on ${on_string}: k-mer abundance histogram. The
70 columns are: (1) k-mer abundance, (2) k-mer count, (3) 89 columns are: (1) k-mer abundance, (2) k-mer count, (3)
71 cumulative count, (4) fraction of total distinct k-mers." /> 90 cumulative count, (4) fraction of total distinct k-mers." />
72 </xml> 91 </xml>
73 <xml name="output_sequences"> 92 <xml name="output_sequences" token_extension="">
74 <data name="output" format_source="inputs" 93 <collection name="sequences" type="list">
75 label="${tool.name} processed nucleotide sequence file"> 94 <discover_datasets pattern="(?P&lt;name&gt;.*)\.(?P&lt;ext&gt;fast[aq](\.gz)?)\.@EXTENSION@" directory="output" />
76 <discover_datasets pattern="__designation_and_ext__" directory="output" visible="true"/> 95 </collection>
77 </data>
78 </xml> 96 </xml>
79 <xml name="output_sequences_single"> 97 <xml name="output_sequences_single">
80 <data name="output" format_source="input_sequence_filename" 98 <data name="output" format_source="input_sequence_filename"
81 label="${tool.name} processed nucleotide sequence file" /> 99 label="${tool.name} on ${on_string}: processed nucleotide sequence file" />
82 </xml> 100 </xml>
83 <xml name="input_zero"> 101 <xml name="input_zero">
84 <param name="zero" type="boolean" truevalue="" falsevalue="--no-zero" checked="true" 102 <param argument="--no-zero" name="zero" type="boolean" truevalue="" falsevalue="--no-zero" checked="true"
85 help="Output zero count bins (--no-zero)" /> 103 help="Output zero count bins" />
86 </xml> 104 </xml>
87 <xml name="input_bigcount"> 105 <xml name="input_bigcount">
88 <param name="bigcount" type="boolean" truevalue="" falsevalue="--no-bigcount" 106 <param argument="--no-bigcount" name="bigcount" type="boolean" truevalue="" falsevalue="--no-bigcount"
89 checked="true" help="Count k-mers past 255 occurences (--no-bigcount)" /> 107 checked="true" help="Count k-mers past 255 occurences" />
90 </xml> 108 </xml>
91 <token name="@HELP_FOOTER@"><![CDATA[ 109 <token name="@HELP_FOOTER@"><![CDATA[
92 (from the khmer project: http://khmer.readthedocs.org/en/v2.0/ )]]></token> 110 (from the khmer project: http://khmer.readthedocs.org/en/v2.0/ )]]></token>
93 <xml name="software-citation"> 111 <xml name="software-citation">
94 <citation type="doi">10.12688/f1000research.6924.1</citation> 112 <citation type="doi">10.12688/f1000research.6924.1</citation>