Mercurial > repos > iuc > khmer_abundance_distribution

comparison macros.xml @ 10:e699e2747356 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
author iuc
date Thu, 03 Oct 2024 13:45:57 +0000
parents 7624945cacd3
children
comparison
equal deleted inserted replaced
9:7624945cacd3 10:e699e2747356
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">3.0.0a3</token> 2 <token name="@TOOL_VERSION@">3.0.0a3</token>
3 <token name="@VERSION_SUFFIX@">2</token> 3 <token name="@VERSION_SUFFIX@">3</token>
4 <token name="@PROFILE@">20.01</token> 4 <token name="@PROFILE@">20.01</token>
5 <xml name="bio_tools"> 5 <xml name="bio_tools">
6 <xrefs> 6 <xrefs>
7 <xref type="bio.tools">khmer</xref> 7 <xref type="bio.tools">khmer</xref>
8 </xrefs> 8 </xrefs>
32 --n_tables=$parameters.n_tables 32 --n_tables=$parameters.n_tables
33 --max-tablesize="$parameters.tablesize_specific" 33 --max-tablesize="$parameters.tablesize_specific"
34 #end if 34 #end if
35 ]]> 35 ]]>
36 </token> 36 </token>
37 <token name="@THREADS@">--threads \${GALAXY_SLOTS:-4}</token> 37 <token name="@THREADS@">--threads "\${GALAXY_SLOTS:-4}"</token>
38 <xml name="tableinputs"> 38 <xml name="tableinputs">
39 <conditional name="parameters"> 39 <conditional name="parameters">
40 <param name="type" type="select" label="Advanced Parameters" 40 <param name="type" type="select" label="Advanced Parameters"
41 help="ksize, n_tables, a specific tablesize" > 41 help="ksize, n_tables, a specific tablesize" >
42 <option value="simple" selected="true">Hide</option> 42 <option value="simple" selected="true">Hide</option>
43 <option value="specific">Show</option> 43 <option value="specific">Show</option>
44 </param> 44 </param>
45 <when value="simple"> 45 <when value="simple">
46 <param argument="" name="tablesize" type="select" label="Sample Type" display="radio"> 46 <param argument="--max-tablesize" name="tablesize" type="select" label="Sample Type" display="radio">
47 <option value="1e9" selected="true">Microbial Genome</option> 47 <option value="1e9" selected="true">Microbial Genome</option>
48 <option value="2e9">Animal Transcriptome</option> 48 <option value="2e9">Animal Transcriptome</option>
49 <option value="4e9">Small Animal Genome or Low-Diversity Metagenome</option> 49 <option value="4e9">Small Animal Genome or Low-Diversity Metagenome</option>
50 <option value="16e9">Large Animal Genome</option> 50 <option value="16e9">Large Animal Genome</option>
51 </param> 51 </param>
52 </when> 52 </when>
53 <when value="specific"> 53 <when value="specific">
54 <param argument="--ksize" name="ksize" type="integer" value="20" label="k-mer size" help="k-mer size to use" /> 54 <param argument="--ksize" type="integer" value="20" label="k-mer size" help="k-mer size to use" />
55 <param argument="--n_tables" name="n_tables" type="integer" min="1" value="4" label="n_tables" help="number of tables to use" /> 55 <param argument="--n_tables" type="integer" min="1" value="4" label="n_tables" help="number of tables to use" />
56 <param argument="--max-tablesize" name="tablesize_specific" type="text" value="1000000.0" 56 <param argument="--max-tablesize" name="tablesize_specific" type="text" value="1000000.0"
57 label="tablesize" help="(--max-tablesize) upper bound on the tablesize to use" /> 57 label="tablesize" help="(--max-tablesize) upper bound on the tablesize to use" />
58 </when> 58 </when>
59 </conditional> 59 </conditional>
60 </xml> 60 </xml>
88 <param name="input_countgraph_filename" type="data" format="oxlicg" 88 <param name="input_countgraph_filename" type="data" format="oxlicg"
89 label="the k-mer countgraph to query" 89 label="the k-mer countgraph to query"
90 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." /> 90 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." />
91 </xml> 91 </xml>
92 <xml name="abundance-histogram-output"> 92 <xml name="abundance-histogram-output">
93 <data name="output_histogram_filename" format="txt" 93 <data name="output_histogram_filename" format="csv"
94 label="${tool.name} on ${on_string}: k-mer abundance histogram. The 94 label="${tool.name} on ${on_string}: k-mer abundance histogram" />
95 columns are: (1) k-mer abundance, (2) k-mer count, (3)
96 cumulative count, (4) fraction of total distinct k-mers." />
97 </xml> 95 </xml>
96 <token name="@ABUNDANCE_HISTOGRAM_OUTPUT_HELP@"><![CDATA[
97 The columns of the k-mer abundance histogram are: (1) k-mer abundance, (2) k-mer count, (3) cumulative count, (4) fraction of total distinct k-mers.
98 ]]></token>
99
98 <xml name="output_sequences" token_extension=""> 100 <xml name="output_sequences" token_extension="">
99 <collection name="sequences" type="list"> 101 <collection name="sequences" type="list">
100 <discover_datasets pattern="(?P&lt;name&gt;.*)\.(?P&lt;ext&gt;fast[aq](\.gz)?)\.@EXTENSION@" directory="output" /> 102 <discover_datasets pattern="(?P&lt;name&gt;.*)\.(?P&lt;ext&gt;fast[aq](\.gz)?)\.@EXTENSION@" directory="output" />
101 </collection> 103 </collection>
102 </xml> 104 </xml>