Mercurial > repos > iuc > khmer_partition

annotate macros.xml @ 11:bd185cf6bd34 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
author iuc
date Thu, 03 Oct 2024 13:44:33 +0000
parents 02bc1ef43ef7
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
1 <macros>
9
94e459e086bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 14ea2dc5ef36219c908ed64b256794711ce7b902"
iuc
parents: 8
diff changeset
2 <token name="@TOOL_VERSION@">3.0.0a3</token>
11
bd185cf6bd34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
iuc
parents: 10
diff changeset
3 <token name="@VERSION_SUFFIX@">3</token>
9
94e459e086bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 14ea2dc5ef36219c908ed64b256794711ce7b902"
iuc
parents: 8
diff changeset
4 <token name="@PROFILE@">20.01</token>
10
02bc1ef43ef7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 9
diff changeset
5 <xml name="bio_tools">
02bc1ef43ef7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 9
diff changeset
6 <xrefs>
02bc1ef43ef7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 9
diff changeset
7 <xref type="bio.tools">khmer</xref>
02bc1ef43ef7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 9
diff changeset
8 </xrefs>
02bc1ef43ef7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 9
diff changeset
9 </xml>
0
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
10 <xml name="requirements">
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
11 <requirements>
9
94e459e086bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 14ea2dc5ef36219c908ed64b256794711ce7b902"
iuc
parents: 8
diff changeset
12 <requirement type="package" version="@TOOL_VERSION@">khmer</requirement>
8
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
13 <yield/>
0
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
14 </requirements>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
15 </xml>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
16 <xml name="version">
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
17 <version_command><![CDATA[@BINARY@ --version 2>&1 | tail -n 1 | cut -d ' ' -f 2]]></version_command>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
18 </xml>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
19 <xml name="stdio">
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
20 <stdio>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
21 <exit_code range="1:" level="fatal" />
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
22 </stdio>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
23 </xml>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
24 <token name="@TABLEPARAMS@">
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
25 <![CDATA[
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
26 #if $parameters.type == "simple"
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
27 --ksize=20
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
28 --n_tables=4
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
29 --max-tablesize=$parameters.tablesize
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
30 #else
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
31 --ksize=$parameters.ksize
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
32 --n_tables=$parameters.n_tables
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
33 --max-tablesize="$parameters.tablesize_specific"
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
34 #end if
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
35 ]]>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
36 </token>
11
bd185cf6bd34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
iuc
parents: 10
diff changeset
37 <token name="@THREADS@">--threads "\${GALAXY_SLOTS:-4}"</token>
0
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
38 <xml name="tableinputs">
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
39 <conditional name="parameters">
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
40 <param name="type" type="select" label="Advanced Parameters"
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
41 help="ksize, n_tables, a specific tablesize" >
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
42 <option value="simple" selected="true">Hide</option>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
43 <option value="specific">Show</option>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
44 </param>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
45 <when value="simple">
11
bd185cf6bd34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
iuc
parents: 10
diff changeset
46 <param argument="--max-tablesize" name="tablesize" type="select" label="Sample Type" display="radio">
0
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
47 <option value="1e9" selected="true">Microbial Genome</option>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
48 <option value="2e9">Animal Transcriptome</option>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
49 <option value="4e9">Small Animal Genome or Low-Diversity Metagenome</option>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
50 <option value="16e9">Large Animal Genome</option>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
51 </param>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
52 </when>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
53 <when value="specific">
11
bd185cf6bd34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
iuc
parents: 10
diff changeset
54 <param argument="--ksize" type="integer" value="20" label="k-mer size" help="k-mer size to use" />
bd185cf6bd34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
iuc
parents: 10
diff changeset
55 <param argument="--n_tables" type="integer" min="1" value="4" label="n_tables" help="number of tables to use" />
8
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
56 <param argument="--max-tablesize" name="tablesize_specific" type="text" value="1000000.0"
0
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
57 label="tablesize" help="(--max-tablesize) upper bound on the tablesize to use" />
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
58 </when>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
59 </conditional>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
60 </xml>
8
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
61 <token name="@LINK_SEQUENCES@">
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
62 <![CDATA[
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
63 #import re
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
64 mkdir input/ &&
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
65 #set gzip=""
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
66 #for $num, $input in enumerate($inputs)
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
67 ln -s '${input}' 'input/$re.sub("[^\w\-_.]", "_", $input.element_identifier).$input.ext' &&
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
68 #if str($input).endswith(".gz"):
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
69 #set gzip="--gzip"
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
70 #end if
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
71 #end for]]></token>
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
72 <token name="@USE_SEQUENCES@">
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
73 <![CDATA[
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
74 #for $num, $input in enumerate($inputs)
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
75 '../input/$re.sub("[^\w\-_.]", "_", $input.element_identifier).$input.ext'
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
76 #end for]]></token>
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
77
0
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
78 <xml name="input_sequences_filenames">
8
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
79 <param name="inputs" multiple="true" type="data" format="fasta,fastq,fasta.gz,fastq.gz"
0
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
80 label="Sequences in FASTA or FASTQ format"
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
81 help="Put in order of precedence such as longest reads first." />
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
82 </xml>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
83 <xml name="input_sequence_filename">
9
94e459e086bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 14ea2dc5ef36219c908ed64b256794711ce7b902"
iuc
parents: 8
diff changeset
84 <param name="input_sequence_filename" type="data" format="fasta,fastq,fasta.gz,fastq.gz"
0
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
85 label="Sequence in FASTA or FASTQ format" />
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
86 </xml>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
87 <xml name="input_countgraph_filename">
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
88 <param name="input_countgraph_filename" type="data" format="oxlicg"
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
89 label="the k-mer countgraph to query"
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
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." />
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
91 </xml>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
92 <xml name="abundance-histogram-output">
11
bd185cf6bd34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
iuc
parents: 10
diff changeset
93 <data name="output_histogram_filename" format="csv"
bd185cf6bd34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
iuc
parents: 10
diff changeset
94 label="${tool.name} on ${on_string}: k-mer abundance histogram" />
0
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
95 </xml>
11
bd185cf6bd34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
iuc
parents: 10
diff changeset
96 <token name="@ABUNDANCE_HISTOGRAM_OUTPUT_HELP@"><![CDATA[
bd185cf6bd34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
iuc
parents: 10
diff changeset
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.
bd185cf6bd34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
iuc
parents: 10
diff changeset
98 ]]></token>
bd185cf6bd34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
iuc
parents: 10
diff changeset
99
8
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
100 <xml name="output_sequences" token_extension="">
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
101 <collection name="sequences" type="list">
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
102 <discover_datasets pattern="(?P&lt;name&gt;.*)\.(?P&lt;ext&gt;fast[aq](\.gz)?)\.@EXTENSION@" directory="output" />
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
103 </collection>
0
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
104 </xml>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
105 <xml name="output_sequences_single">
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
106 <data name="output" format_source="input_sequence_filename"
8
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
107 label="${tool.name} on ${on_string}: processed nucleotide sequence file" />
0
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
108 </xml>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
109 <xml name="input_zero">
8
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
110 <param argument="--no-zero" name="zero" type="boolean" truevalue="" falsevalue="--no-zero" checked="true"
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
111 help="Output zero count bins" />
0
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
112 </xml>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
113 <xml name="input_bigcount">
8
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
114 <param argument="--no-bigcount" name="bigcount" type="boolean" truevalue="" falsevalue="--no-bigcount"
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents: 7
diff changeset
115 checked="true" help="Count k-mers past 255 occurences" />
0
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
116 </xml>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
117 <token name="@HELP_FOOTER@"><![CDATA[
5
4ff373852ec5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit f30bc6f7e10409dfa0dd65688e60da8b59f12464
iuc
parents: 2
diff changeset
118 (from the khmer project: http://khmer.readthedocs.org/en/v2.0/ )]]></token>
0
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
119 <xml name="software-citation">
7
3f0d5322fe37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
iuc
parents: 5
diff changeset
120 <citation type="doi">10.12688/f1000research.6924.1</citation>
0
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
121 </xml>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
122 <xml name="diginorm-citation">
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
123 <citation type="bibtex">@unpublished{diginorm,
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
124 author = "Brown, C Titus and Howe, Adina and Zhang, Qingpeng and Pyrkosz,
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
125 Alexis B and Brom, Timothy H",
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
126 title = "A Reference-Free Algorithm for Computational Normalization of
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
127 Shotgun Sequencing Data",
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
128 year = "2012",
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
129 eprint = "arXiv:1203.4802",
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
130 url = "http://arxiv.org/abs/1203.4802",
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
131 }</citation></xml>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
132 <xml name="graph-citation">
7
3f0d5322fe37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
iuc
parents: 5
diff changeset
133 <citation type="doi">10.1073/pnas.1121464109</citation>
0
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
134 </xml>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
135 <xml name="counting-citation">
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
136 <citation type="doi">10.1371/journal.pone.0101271</citation>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
137 </xml>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
iuc
parents:
diff changeset
138 </macros>