Mercurial > repos > iuc > raven
comparison raven.xml @ 0:33b7d8481a76 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"
author | iuc |
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date | Wed, 18 Nov 2020 19:42:15 +0000 |
parents | |
children | f8564b2d7f63 |
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-1:000000000000 | 0:33b7d8481a76 |
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1 <?xml version="1.0"?> | |
2 <tool id="raven" name="Raven" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> | |
3 <description>De novo assembly of Oxford Nanopore Technologies data</description> | |
4 <macros> | |
5 <import>macros.xml</import> | |
6 </macros> | |
7 | |
8 <expand macro="requirements"/> | |
9 | |
10 <expand macro="version_command"/> | |
11 | |
12 <!--TODO in future version : enable CUDA support for racon polishing--> | |
13 | |
14 <command detect_errors="exit_code"><![CDATA[ | |
15 #if $input_reads.is_of_type("fasta") | |
16 ln -s '$input_reads' ./input.fa && | |
17 #set input = "input.fa" | |
18 #elif $input_reads.is_of_type("fasta.gz") | |
19 ln -s '$input_reads' ./input.fa.gz && | |
20 #set input = "input.fa.gz" | |
21 #elif $input_reads.is_of_type("fastq") | |
22 ln -s '$input_reads' ./input.fq && | |
23 #set input = "input.fq" | |
24 #elif $input_reads.is_of_type("fastq.gz") | |
25 ln -s '$input_reads' ./input.fq.gz && | |
26 #set input = "input.fq.gz" | |
27 #end if | |
28 raven | |
29 $weaken | |
30 --polishing-rounds '$polishing_rounds' | |
31 --match '$match' | |
32 --mismatch '$mismatch' | |
33 --gap '$gap' | |
34 $graphical_fragment_assembly | |
35 --disable-checkpoints | |
36 -t \${GALAXY_SLOTS:-4} | |
37 '$input' | |
38 > '$out_fasta' | |
39 ]]></command> | |
40 <inputs> | |
41 <param name="input_reads" type="data" format="fasta,fastq,fasta.gz,fastq.gz"/> | |
42 <param argument="--weaken" type="boolean" truevalue="--weaken" falsevalue="" label="use larger (k, w); (for use in assembling highly accurate sequences)" checked="false"/> | |
43 <param argument="--polishing-rounds" type="integer" value="2" min="0" label="Number of times racon polishing is invoked"/> | |
44 <param argument="--match" type="integer" value="3"/> | |
45 <param argument="--mismatch" type="integer" value="-5"/> | |
46 <param argument="--gap" type="integer" value="-4" max="-1"/> | |
47 <param argument="--graphical-fragment-assembly" type="boolean" truevalue="--graphical-fragment-assembly out.gfa" falsevalue="" label="output graphical fragment assembly file?" checked="true"/> | |
48 </inputs> | |
49 <outputs> | |
50 <data name="out_gfa" format="gfa1" label="${tool.name} on ${on_string} (Graphical Fragment Assembly)" from_work_dir="out.gfa"> | |
51 <filter>graphical_fragment_assembly</filter> | |
52 </data> | |
53 <data name="out_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA)" /> | |
54 </outputs> | |
55 <tests> | |
56 <test expect_num_outputs="2"> | |
57 <param name="input_reads" ftype="fastq.gz" value="ERA476754.fastq.gz"/> | |
58 <output name="out_gfa" file="raven_gfa_assembly.txt"> | |
59 <assert_contents> | |
60 <has_n_lines n="2"/> | |
61 </assert_contents> | |
62 </output> | |
63 <output name="out_fasta" file="raven_assembly.fasta"> | |
64 <assert_contents> | |
65 <has_n_lines n="2"/> | |
66 </assert_contents> | |
67 </output> | |
68 </test> | |
69 <test expect_num_outputs="1"> | |
70 <param name="input_reads" ftype="fastq.gz" value="ERA476754.fastq.gz"/> | |
71 <param name="graphical_fragment_assembly" value="false"/> | |
72 <output name="out_fasta" file="raven_assembly.fasta"> | |
73 <assert_contents> | |
74 <has_n_lines n="2"/> | |
75 </assert_contents> | |
76 </output> | |
77 </test> | |
78 </tests> | |
79 <help><![CDATA[ | |
80 .. class:: infomark | |
81 | |
82 **What it does** | |
83 | |
84 @WID@ | |
85 | |
86 **Input** | |
87 - fasta / fastq / fasta.gz / fastq.gz data | |
88 | |
89 **Output** | |
90 | |
91 - Assembled genome (FASTA) | |
92 - Graphical fragment assembly (optional) (.txt) | |
93 | |
94 **References** | |
95 | |
96 @REFERENCES@ | |
97 ]]></help> | |
98 <expand macro="citations"/> | |
99 </tool> |