Mercurial > repos > iuc > raven
comparison raven.xml @ 5:5c55448d0f33 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit 7bd5e845f7f0a531d619f66193470127a2a7a7ea
author | iuc |
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date | Sat, 18 May 2024 21:31:16 +0000 |
parents | 3edba9afc9bc |
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4:2b2a352488fa | 5:5c55448d0f33 |
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1 <?xml version="1.0"?> | |
2 <tool id="raven" name="Raven" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> | 1 <tool id="raven" name="Raven" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> |
3 <description>De novo assembly of Oxford Nanopore Technologies data</description> | 2 <description>De novo assembly of Oxford Nanopore Technologies data</description> |
4 <macros> | 3 <macros> |
5 <import>macros.xml</import> | 4 <import>macros.xml</import> |
6 </macros> | 5 </macros> |
7 | |
8 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
9 | |
10 <expand macro="version_command"/> | 7 <expand macro="version_command"/> |
11 | 8 <!--TODO in future version : enable CUDA support for racon polishing--> |
12 <!--TODO in future version : enable CUDA support for racon polishing--> | |
13 | |
14 <command detect_errors="exit_code"><![CDATA[ | 9 <command detect_errors="exit_code"><![CDATA[ |
15 #if $input_reads.is_of_type("fasta") | 10 #if $input_reads.is_of_type("fasta") |
16 ln -s '$input_reads' ./input.fa && | 11 ln -s '$input_reads' ./input.fa && |
17 #set input = "input.fa" | 12 #set input = "input.fa" |
18 #elif $input_reads.is_of_type("fasta.gz") | 13 #elif $input_reads.is_of_type("fasta.gz") |
31 --frequency '$frequency' | 26 --frequency '$frequency' |
32 --polishing-rounds '$polishing_rounds' | 27 --polishing-rounds '$polishing_rounds' |
33 --match '$match' | 28 --match '$match' |
34 --mismatch '$mismatch' | 29 --mismatch '$mismatch' |
35 --gap '$gap' | 30 --gap '$gap' |
31 --kMaxNumOverlaps '$kMaxNumOverlaps' | |
32 --identity $identity | |
33 --min-unitig-size $min_unitig_size | |
34 --use-micromizers $use_micromizers | |
36 $graphical_fragment_assembly | 35 $graphical_fragment_assembly |
37 --disable-checkpoints | 36 --disable-checkpoints |
38 -t \${GALAXY_SLOTS:-4} | 37 -t \${GALAXY_SLOTS:-4} |
39 '$input' | 38 '$input' |
40 > '$out_fasta' | 39 > '$out_fasta' |
42 <inputs> | 41 <inputs> |
43 <param name="input_reads" type="data" format="fasta,fastq,fasta.gz,fastq.gz"/> | 42 <param name="input_reads" type="data" format="fasta,fastq,fasta.gz,fastq.gz"/> |
44 <param argument="--kmer-len" type="integer" value="15" label="Length of minimizers used to find overlaps"/> | 43 <param argument="--kmer-len" type="integer" value="15" label="Length of minimizers used to find overlaps"/> |
45 <param argument="--window-len" type="integer" value="5" label="Length of sliding window from which minimizers are sampled"/> | 44 <param argument="--window-len" type="integer" value="5" label="Length of sliding window from which minimizers are sampled"/> |
46 <param argument="--frequency" type="float" value="0.001" label="Threshold for ignoring most frequent minimizers"/> | 45 <param argument="--frequency" type="float" value="0.001" label="Threshold for ignoring most frequent minimizers"/> |
46 <param argument="--identity" type="float" value="0" label="Threshold for overlap between two reads in order to construct an edge between them" help="If set to zero, this functionality is disabled"/> | |
47 <param argument="--kMaxNumOverlaps" type="integer" value="32" label="Maximum number of overlaps that will be taken during FindOverlapsAndCreatePiles stage"/> | |
48 <param argument="--min-unitig-size" type="integer" value="9999" label="Minimal unitig size"/> | |
49 | |
47 <param argument="--polishing-rounds" type="integer" value="2" min="0" label="Number of times racon polishing is invoked"/> | 50 <param argument="--polishing-rounds" type="integer" value="2" min="0" label="Number of times racon polishing is invoked"/> |
48 <param argument="--match" type="integer" value="3"/> | 51 <param argument="--match" type="integer" value="3"/> |
49 <param argument="--mismatch" type="integer" value="-5"/> | 52 <param argument="--mismatch" type="integer" value="-5"/> |
50 <param argument="--gap" type="integer" value="-4" max="-1"/> | 53 <param argument="--gap" type="integer" value="-4" max="-1"/> |
51 <param argument="--graphical-fragment-assembly" type="boolean" truevalue="--graphical-fragment-assembly out.gfa" falsevalue="" label="output graphical fragment assembly file?" checked="true"/> | 54 <param argument="--graphical-fragment-assembly" type="boolean" truevalue="--graphical-fragment-assembly out.gfa" falsevalue="" label="output graphical fragment assembly file?" checked="true"/> |
55 <param argument="--use-micromizers" type="boolean" truevalue="--use-micromizers" falsevalue="" label="Use micromizers instead of mimizers in graph construction" help="Performance will increase slightly and memory consumption will decrease but results could be slightly worse"/> | |
52 </inputs> | 56 </inputs> |
53 <outputs> | 57 <outputs> |
54 <data name="out_gfa" format="gfa1" label="${tool.name} on ${on_string} (Graphical Fragment Assembly)" from_work_dir="out.gfa"> | 58 <data name="out_gfa" format="gfa1" label="${tool.name} on ${on_string} (Graphical Fragment Assembly)" from_work_dir="out.gfa"> |
55 <filter>graphical_fragment_assembly</filter> | 59 <filter>graphical_fragment_assembly</filter> |
56 </data> | 60 </data> |
57 <data name="out_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA)" /> | 61 <data name="out_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA)"/> |
58 </outputs> | 62 </outputs> |
59 <tests> | 63 <tests> |
60 <test expect_num_outputs="2"> | 64 <test expect_num_outputs="2"> |
61 <param name="input_reads" ftype="fastq.gz" value="ERA476754.fastq.gz"/> | 65 <param name="input_reads" ftype="fastq.gz" value="ERA476754.fastq.gz"/> |
62 <output name="out_gfa"> | 66 <output name="out_gfa"> |
63 <assert_contents> | 67 <assert_contents> |
64 <has_n_lines n="2"/> | 68 <has_n_lines n="2"/> |
65 <has_text_matching expression="^S\tUtg52\t[ATCG]{30000,40000}\tLN:i:36[0-9]{3}\tRC:i:22\nS\tCtg54\t[ATCG]{9000,10000}\tLN:i:9361\tRC:i:4"/> | 69 <has_text_matching expression="^S\tUtg52\t[ATCG]{30000,40000}\tLN:i:36[0-9]{3}\tRC:i:22\tdp:f:8\nS\tCtg54\t[ATCG]{9000,10000}\tLN:i:9361\tRC:i:4"/> |
66 </assert_contents> | 70 </assert_contents> |
67 </output> | 71 </output> |
68 <output name="out_fasta"> | 72 <output name="out_fasta"> |
69 <assert_contents> | 73 <assert_contents> |
70 <has_n_lines n="2"/> | 74 <has_n_lines n="2"/> |
71 <has_text_matching expression="^>Utg52 LN:i:36[0-9]{3} RC:i:22 XO:i:0\n[ATCG]{30000,40000}$"/> | 75 <has_text_matching expression="^>Utg52 LN:i:36[0-9]{3} RC:i:22 XO:i:0\n[ATCG]{30000,40000}$"/> |
72 </assert_contents> | 76 </assert_contents> |
73 </output> | 77 </output> |
74 </test> | 78 </test> |
75 <!-- <test expect_num_outputs="1"> | 79 <!-- <test expect_num_outputs="1"> |
76 <param name="input_reads" ftype="fastq.gz" value="ERA476754.fastq.gz"/> | 80 <param name="input_reads" ftype="fastq.gz" value="ERA476754.fastq.gz"/> |