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comparison macros.xml @ 0:0ebbfc58f889 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
author iuc
date Mon, 05 Aug 2019 15:56:54 -0400
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children 093970f68fa0
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-1:000000000000 0:0ebbfc58f889
1 <macros>
2 <token name="@IDBA_VERSION@">1.1.3</token>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="@IDBA_VERSION@">idba</requirement>
6 <yield/>
7 </requirements>
8 </xml>
9
10 <xml name="main_input">
11 <param argument="--read" type="data" format="fasta" label="Fasta read file. Lower or equal to 600b"/>
12 <param argument="--long_read" type="data" format="fasta" optional="true" label="Fasta long read file. More than 600b"/>
13 </xml>
14
15 <token name="@MAIN_INPUT@">
16 --read '$read'
17 #if $long_read:
18 --long_read '$long_read'
19 #end if
20 </token>
21
22 <xml name="levels_input">
23 <param argument="--read_level_2" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for second level scaffolds"/>
24 <param argument="--read_level_3" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for third level scaffolds"/>
25 <param argument="--read_level_4" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for fourth level scaffolds"/>
26 <param argument="--read_level_5" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for fifth level scaffolds"/>
27 </xml>
28 <token name="@LEVELS_INPUT@">
29 #if $read_level_2:
30 --read_level_2 '$read_level_2'
31 #end if
32 #if $read_level_3:
33 --read_level_3 '$read_level_3'
34 #end if
35 #if $read_level_4:
36 --read_level_4 '$read_level_4'
37 #end if
38 #if $read_level_5:
39 --read_level_5 '$read_level_5'
40 #end if
41 </token>
42
43 <xml name="kmer_options" token_maxk_default="" token_step_default="">
44 <param argument="--mink" type="integer" value="20" max="312" label="Minimum k value. Lower or equal to 312"/>
45 <param argument="--maxk" type="integer" value="@MAXK_DEFAULT@" max="312" label="Maximum k value. Lower or equal to 312"/>
46 <param argument="--step" type="integer" value="@STEP_DEFAULT@" label="Increment of k-mer of each iteration"/>
47 <param argument="--inner_mink" type="integer" value="10" label="Inner minimum k value"/>
48 <param argument="--inner_step" type="integer" value="5" label="Inner increment of k-mer"/>
49 <param argument="--prefix" type="integer" value="3" label="Prefix length used to build sub k-mer table"/>
50 <param argument="--min_count" type="integer" value="2" label="Minimum multiplicity for filtering k-mer when building the graph"/>
51 <param argument="--min_support" type="integer" value="1" label="Minimum supoort in each iteration"/>
52 <param argument="--seed_kmer" type="integer" value="30" label="Seed kmer size for alignment"/>
53 </xml>
54 <token name="@KMER_OPTIONS@">
55 --mink $mink
56 --maxk $maxk
57 --step $step
58 --inner_mink $inner_mink
59 --inner_step $inner_step
60 --prefix $prefix
61 --min_count $min_count
62 --min_support $min_support
63 --seed_kmer $seed_kmer
64 </token>
65
66 <xml name="filter_options">
67 <param argument="--min_contig" type="integer" value="200" label="Minimum size of contig"/>
68 <param argument="--similar" type="float" value="0.95" label="Similarity for alignment"/>
69 <param argument="--max_mismatch" type="integer" value="3" label="Max mismatch of error correction"/>
70 </xml>
71 <token name="@FILTER_OPTIONS@">
72 --min_contig $min_contig
73 --similar $similar
74 --max_mismatch $max_mismatch
75 </token>
76
77 <xml name="min_pairs_filter">
78 <param argument="--min_pairs" type="integer" value="3" label="Minimum number of pairs"/>
79 </xml>
80 <token name="@MIN_PAIRS_FILTER@">
81 --min_pairs $min_pairs
82 </token>
83 <xml name="other_options">
84 <param name="other" type="select" display="checkboxes" multiple="true" label="Other options">
85 <yield/>
86 <option value="--no_local">Do not use local assembly (--no_local)</option>
87 <option value="--no_coverage">Do not iterate on coverage (--no_coverage)</option>
88 <option value="--no_correct">Do not do correction (--no_correct)</option>
89 <option value="--pre_correction">Perform pre-correction before assembly (--pre_correction)</option>
90 </param>
91 </xml>
92 <token name="@OTHER_OPTIONS@">
93 #if $other:
94 ${" ".join(str($other).split(","))}
95 #end if
96 </token>
97
98 <token name="@THREADS@">
99 --num_threads \${GALAXY_SLOTS:-1}
100 </token>
101
102 <xml name="help" token_more_help="">
103 <help><![CDATA[
104 IDBA is an iterative De Bruijn Graph De Novo Assembler for sequence assembly. Most assemblers based on de Bruijn graph build a de Bruijn graph with a specific k-mer size to perform the assembling task. For all of them, it is very crucial to find a specific value of k. If k is too large, there will be a lot of gap problems in the graph. If k is too small, there will a lot of branch problems. IDBA uses not only one specific k but a range of k values to build the iterative de Bruijn graph. It can keep all the information in graphs with different k values.
105
106 @MORE_HELP@
107
108 Input: IDBA-* take interleaved paired end data in the FASTA format as input,
109 i.e. paired-end reads need to be stored in the same FASTA file such that a pair
110 of reads should be in two consecutive lines.
111 In Galaxy paired reads in separate FASTQ files can be converted into interleaved
112 FASTA using the tools:
113
114 * `FASTQ interlacer on paired end read <https://toolshed.g2.bx.psu.edu/view/devteam/fastq_paired_end_interlacer>`_
115 * `Samtools extract FASTA or FASTQ from a SAM file <https://toolshed.g2.bx.psu.edu/view/devteam/fastq_to_fasta>`_
116
117 Note that, IDBA-* assumes that the paired-end reads are in order (->,<-).
118 If your data is in reverse order (<-,->), please convert it by yourself.
119 ]]></help>
120 </xml>
121 <xml name="citations">
122 <citations>
123 <citation type="doi">10.1007/978-3-642-12683-3_28</citation>
124 <yield/>
125 </citations>
126 </xml>
127
128 </macros>