Mercurial > repos > iuc > idba_ud

annotate idba_ud.xml @ 2:694b0f55b744 draft

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 665baeb11498ceef8abb1f1da43fe315d2d75b37"
author iuc
date Tue, 04 Aug 2020 05:50:30 -0400
parents 2ed5c0795f99
children 1542a2fffe0c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
1 <tool id="idba_ud" name="IDBA-UD" version="@IDBA_VERSION@+galaxy1">
0
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
iuc
parents:
diff changeset
2 <description>
1
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
3 Iterative de Bruijn Graph Assembler for data with highly uneven depth
0
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
iuc
parents:
diff changeset
4 </description>
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
iuc
parents:
diff changeset
5 <macros>
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
iuc
parents:
diff changeset
6 <import>macros.xml</import>
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
iuc
parents:
diff changeset
7 </macros>
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
iuc
parents:
diff changeset
8 <expand macro="requirements"/>
1
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
9 <command detect_errors="aggressive"><![CDATA[
0
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
iuc
parents:
diff changeset
10 idba_ud
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
iuc
parents:
diff changeset
11
1
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
12 @MAIN_INPUT@
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
13 @LEVELS_INPUT@
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
14 @KMER_OPTIONS@
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
15 @FILTER_OPTIONS@
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
16 --min_pairs $min_pairs
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
17 @OTHER_OPTIONS@
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
18 @THREADS@
0
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
iuc
parents:
diff changeset
19 ]]></command>
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
iuc
parents:
diff changeset
20
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
iuc
parents:
diff changeset
21 <inputs>
1
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
22 <expand macro="main_input"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
23 <expand macro="levels_input"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
24 <expand macro="kmer_options" maxk_default="100" step_default="20"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
25 <expand macro="filter_options"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
26 <expand macro="min_pairs_filter"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
27 <expand macro="other_options">
0
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
iuc
parents:
diff changeset
28 <option value="--no_bubble">Do not merge bubble (--no_bubble)</option>
1
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
29 </expand>
0
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
iuc
parents:
diff changeset
30 </inputs>
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
iuc
parents:
diff changeset
31 <outputs>
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
iuc
parents:
diff changeset
32 <data name="output" from_work_dir="out/scaffold.fa" format="fasta"/>
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
iuc
parents:
diff changeset
33 </outputs>
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
iuc
parents:
diff changeset
34 <tests>
1
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
35 <!-- basic test + check of defaults -->
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
36 <test>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
37 <param name="read" value="merged.fa" ftype="fasta"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
38 <assert_command>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
39 <has_text text="--mink 20" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
40 <has_text text="--maxk 100" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
41 <has_text text="--step 20" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
42 <has_text text="--inner_mink 10" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
43 <has_text text="--inner_step 5" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
44 <has_text text="--prefix 3" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
45 <has_text text="--min_count 2" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
46 <has_text text="--min_support 1" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
47 <has_text text="--seed_kmer 30" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
48 <has_text text="--min_contig 200" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
49 <has_text text="--similar 0.95" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
50 <has_text text="--max_mismatch 3" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
51 <has_text text="--min_pairs 3" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
52 <not_has_text text="--read_level_2" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
53 <not_has_text text="--read_level_3" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
54 <not_has_text text="--read_level_4" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
55 <not_has_text text="--read_level_5" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
56 <not_has_text text="--no_bubble" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
57 <not_has_text text="--no_local" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
58 <not_has_text text="--no_coverage" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
59 <not_has_text text="--no_correct" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
60 <not_has_text text="--pre_correction" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
61 </assert_command>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
62 <output name="output" file="out/scaffold.fa" ftype="fasta"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
63 </test>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
64 <!-- read levels test -->
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
65 <test>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
66 <param name="read" value="merged.fa" ftype="fasta"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
67 <param name="read_level_2" ftype="fasta" value="merged.fa"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
68 <param name="read_level_3" ftype="fasta" value="merged.fa"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
69 <param name="read_level_4" ftype="fasta" value="merged.fa"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
70 <param name="read_level_5" ftype="fasta" value="merged.fa"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
71 <assert_command>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
72 <has_text text="--read_level_2" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
73 <has_text text="--read_level_3" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
74 <has_text text="--read_level_4" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
75 <has_text text="--read_level_5" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
76 </assert_command>
2
694b0f55b744 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 665baeb11498ceef8abb1f1da43fe315d2d75b37"
iuc
parents: 1
diff changeset
77 <output name="output" file="out/scaffold.fa" ftype="fasta" lines_diff="2"/>
1
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
78 </test>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
79 <!-- k-mer options -->
0
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
iuc
parents:
diff changeset
80 <test>
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
iuc
parents:
diff changeset
81 <param name="read" value="merged.fa" ftype="fasta"/>
1
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
82 <param name="mink" value="19"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
83 <param name="maxk" value="99"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
84 <param name="step" value="19"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
85 <param name="inner_mink" value="9"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
86 <param name="inner_step" value="4"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
87 <param name="prefix" value="2"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
88 <param name="min_count" value="1"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
89 <param name="min_support" value="2"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
90 <param name="seed_kmer" value="29"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
91 <assert_command>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
92 <has_text text="--mink 19" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
93 <has_text text="--maxk 99" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
94 <has_text text="--step 19" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
95 <has_text text="--inner_mink 9" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
96 <has_text text="--inner_step 4" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
97 <has_text text="--prefix 2" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
98 <has_text text="--min_count 1" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
99 <has_text text="--min_support 2" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
100 <has_text text="--seed_kmer 29" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
101 </assert_command>
2
694b0f55b744 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 665baeb11498ceef8abb1f1da43fe315d2d75b37"
iuc
parents: 1
diff changeset
102 <output name="output" file="out/scaffold.fa" lines_diff="2"/>
1
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
103 </test>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
104 <!-- filter options -->
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
105 <test>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
106 <param name="read" value="merged.fa" ftype="fasta"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
107 <param name="min_contig" value="199"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
108 <param name="similar" value="0.96"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
109 <param name="max_mismatch" value="2"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
110 <assert_command>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
111 <has_text text="--min_contig 199" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
112 <has_text text="--similar 0.96" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
113 <has_text text="--max_mismatch 2" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
114 </assert_command>
2
694b0f55b744 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 665baeb11498ceef8abb1f1da43fe315d2d75b37"
iuc
parents: 1
diff changeset
115 <output name="output" file="out/scaffold.fa" lines_diff="2"/>
1
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
116 </test>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
117 <!-- min-pairs and other options -->
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
118 <test>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
119 <param name="read" value="merged.fa" ftype="fasta"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
120 <param name="min_pairs" value="2"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
121 <param name="other" value="--no_bubble,--no_local,--no_coverage,--no_correct,--pre_correction"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
122 <assert_command>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
123 <has_text text="--min_pairs 2" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
124 <has_text text="--no_bubble" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
125 <has_text text="--no_local" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
126 <has_text text="--no_coverage" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
127 <has_text text="--no_correct" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
128 <has_text text="--pre_correction" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
129 </assert_command>
2
694b0f55b744 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 665baeb11498ceef8abb1f1da43fe315d2d75b37"
iuc
parents: 1
diff changeset
130 <output name="output" file="out/scaffold.fa" lines_diff="2"/>
0
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
iuc
parents:
diff changeset
131 </test>
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
iuc
parents:
diff changeset
132 </tests>
1
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
133 <expand macro="help" more_help="IDBA-UD is an extension of IDBA algorithm for Short Reads Sequencing data with Highly Uneven Sequencing Depth. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions."/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
134 <expand macro="citations">
0
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
iuc
parents:
diff changeset
135 <citation type="doi">10.1093/bioinformatics/bts174</citation>
1
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents: 0
diff changeset
136 </expand>
0
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
iuc
parents:
diff changeset
137 </tool>