Mercurial > repos > iuc > idba_tran

annotate macros.xml @ 2:03de4e0f84c2 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/idba_ud commit 9c0a7395ca18043ae2dd957f39f47b65c938750a
author iuc
date Thu, 21 Jul 2022 13:34:24 +0000
parents a30d991a3fdd
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
1 <macros>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
2 <token name="@IDBA_VERSION@">1.1.3</token>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
3 <xml name="requirements">
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
4 <requirements>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
5 <requirement type="package" version="@IDBA_VERSION@">idba</requirement>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
6 <yield/>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
7 </requirements>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
8 </xml>
2
03de4e0f84c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 9c0a7395ca18043ae2dd957f39f47b65c938750a
iuc
parents: 0
diff changeset
9 <xml name="bio_tools">
03de4e0f84c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 9c0a7395ca18043ae2dd957f39f47b65c938750a
iuc
parents: 0
diff changeset
10 <xrefs>
03de4e0f84c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 9c0a7395ca18043ae2dd957f39f47b65c938750a
iuc
parents: 0
diff changeset
11 <xref type="bio.tools">idba</xref>
03de4e0f84c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 9c0a7395ca18043ae2dd957f39f47b65c938750a
iuc
parents: 0
diff changeset
12 </xrefs>
03de4e0f84c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 9c0a7395ca18043ae2dd957f39f47b65c938750a
iuc
parents: 0
diff changeset
13 </xml>
0
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
14 <xml name="main_input">
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
15 <param argument="--read" type="data" format="fasta" label="Fasta read file. Lower or equal to 600b"/>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
16 <param argument="--long_read" type="data" format="fasta" optional="true" label="Fasta long read file. More than 600b"/>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
17 </xml>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
18
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
19 <token name="@MAIN_INPUT@">
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
20 --read '$read'
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
21 #if $long_read:
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
22 --long_read '$long_read'
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
23 #end if
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
24 </token>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
25
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
26 <xml name="levels_input">
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
27 <param argument="--read_level_2" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for second level scaffolds"/>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
28 <param argument="--read_level_3" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for third level scaffolds"/>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
29 <param argument="--read_level_4" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for fourth level scaffolds"/>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
30 <param argument="--read_level_5" type="data" format="fasta" optional="true" label="Fasta Paired-end reads for fifth level scaffolds"/>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
31 </xml>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
32 <token name="@LEVELS_INPUT@">
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
33 #if $read_level_2:
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
34 --read_level_2 '$read_level_2'
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
35 #end if
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
36 #if $read_level_3:
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
37 --read_level_3 '$read_level_3'
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
38 #end if
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
39 #if $read_level_4:
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
40 --read_level_4 '$read_level_4'
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
41 #end if
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
42 #if $read_level_5:
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
43 --read_level_5 '$read_level_5'
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
44 #end if
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
45 </token>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
46
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
47 <xml name="kmer_options" token_maxk_default="" token_step_default="">
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
48 <param argument="--mink" type="integer" value="20" max="312" label="Minimum k value. Lower or equal to 312"/>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
49 <param argument="--maxk" type="integer" value="@MAXK_DEFAULT@" max="312" label="Maximum k value. Lower or equal to 312"/>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
50 <param argument="--step" type="integer" value="@STEP_DEFAULT@" label="Increment of k-mer of each iteration"/>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
51 <param argument="--inner_mink" type="integer" value="10" label="Inner minimum k value"/>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
52 <param argument="--inner_step" type="integer" value="5" label="Inner increment of k-mer"/>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
53 <param argument="--prefix" type="integer" value="3" label="Prefix length used to build sub k-mer table"/>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
54 <param argument="--min_count" type="integer" value="2" label="Minimum multiplicity for filtering k-mer when building the graph"/>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
55 <param argument="--min_support" type="integer" value="1" label="Minimum supoort in each iteration"/>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
56 <param argument="--seed_kmer" type="integer" value="30" label="Seed kmer size for alignment"/>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
57 </xml>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
58 <token name="@KMER_OPTIONS@">
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
59 --mink $mink
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
60 --maxk $maxk
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
61 --step $step
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
62 --inner_mink $inner_mink
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
63 --inner_step $inner_step
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
64 --prefix $prefix
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
65 --min_count $min_count
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
66 --min_support $min_support
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
67 --seed_kmer $seed_kmer
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
68 </token>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
69
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
70 <xml name="filter_options">
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
71 <param argument="--min_contig" type="integer" value="200" label="Minimum size of contig"/>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
72 <param argument="--similar" type="float" value="0.95" label="Similarity for alignment"/>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
73 <param argument="--max_mismatch" type="integer" value="3" label="Max mismatch of error correction"/>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
74 </xml>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
75 <token name="@FILTER_OPTIONS@">
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
76 --min_contig $min_contig
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
77 --similar $similar
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
78 --max_mismatch $max_mismatch
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
79 </token>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
80
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
81 <xml name="min_pairs_filter">
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
82 <param argument="--min_pairs" type="integer" value="3" label="Minimum number of pairs"/>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
83 </xml>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
84 <token name="@MIN_PAIRS_FILTER@">
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
85 --min_pairs $min_pairs
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
86 </token>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
87 <xml name="other_options">
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
88 <param name="other" type="select" display="checkboxes" multiple="true" label="Other options">
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
89 <yield/>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
90 <option value="--no_local">Do not use local assembly (--no_local)</option>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
91 <option value="--no_coverage">Do not iterate on coverage (--no_coverage)</option>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
92 <option value="--no_correct">Do not do correction (--no_correct)</option>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
93 <option value="--pre_correction">Perform pre-correction before assembly (--pre_correction)</option>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
94 </param>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
95 </xml>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
96 <token name="@OTHER_OPTIONS@">
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
97 #if $other:
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
98 ${" ".join(str($other).split(","))}
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
99 #end if
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
100 </token>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
101
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
102 <token name="@THREADS@">
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
103 --num_threads \${GALAXY_SLOTS:-1}
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
104 </token>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
105
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
106 <xml name="help" token_more_help="">
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
107 <help><![CDATA[
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
108 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.
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
109
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
110 @MORE_HELP@
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
111
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
112 Input: IDBA-* take interleaved paired end data in the FASTA format as input,
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
113 i.e. paired-end reads need to be stored in the same FASTA file such that a pair
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
114 of reads should be in two consecutive lines.
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
115 In Galaxy paired reads in separate FASTQ files can be converted into interleaved
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
116 FASTA using the tools:
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
117
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
118 * `FASTQ interlacer on paired end read <https://toolshed.g2.bx.psu.edu/view/devteam/fastq_paired_end_interlacer>`_
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
119 * `Samtools extract FASTA or FASTQ from a SAM file <https://toolshed.g2.bx.psu.edu/view/devteam/fastq_to_fasta>`_
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
120
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
121 Note that, IDBA-* assumes that the paired-end reads are in order (->,<-).
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
122 If your data is in reverse order (<-,->), please convert it by yourself.
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
123 ]]></help>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
124 </xml>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
125 <xml name="citations">
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
126 <citations>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
127 <citation type="doi">10.1007/978-3-642-12683-3_28</citation>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
128 <yield/>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
129 </citations>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
130 </xml>
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
131
a30d991a3fdd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff changeset
132 </macros>