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comparison raven.xml @ 5:2025c7c40396 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit d6846cd9a2228b677e7bc171e67e85e3f3426a00
author iuc
date Mon, 10 Feb 2025 19:16:14 +0000
parents fe48e5bca42d
children
comparison
equal deleted inserted replaced
4:de622e5acd77 5:2025c7c40396
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 6 <expand macro="xrefs"/>
8 <expand macro="requirements"/> 7 <expand macro="requirements"/>
9
10 <expand macro="version_command"/> 8 <expand macro="version_command"/>
11 9 <!--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[ 10 <command detect_errors="exit_code"><![CDATA[
15 #if $input_reads.is_of_type("fasta") 11 #if $input_reads.is_of_type("fasta")
16 ln -s '$input_reads' ./input.fa && 12 ln -s '$input_reads' ./input.fa &&
17 #set input = "input.fa" 13 #set input = "input.fa"
18 #elif $input_reads.is_of_type("fasta.gz") 14 #elif $input_reads.is_of_type("fasta.gz")
31 --frequency '$frequency' 27 --frequency '$frequency'
32 --polishing-rounds '$polishing_rounds' 28 --polishing-rounds '$polishing_rounds'
33 --match '$match' 29 --match '$match'
34 --mismatch '$mismatch' 30 --mismatch '$mismatch'
35 --gap '$gap' 31 --gap '$gap'
32 --kMaxNumOverlaps '$kMaxNumOverlaps'
33 --identity $identity
34 --min-unitig-size $min_unitig_size
35 --use-micromizers $use_micromizers
36 $graphical_fragment_assembly 36 $graphical_fragment_assembly
37 --disable-checkpoints 37 --disable-checkpoints
38 -t \${GALAXY_SLOTS:-4} 38 -t \${GALAXY_SLOTS:-4}
39 '$input' 39 '$input'
40 > '$out_fasta' 40 > '$out_fasta'
42 <inputs> 42 <inputs>
43 <param name="input_reads" type="data" format="fasta,fastq,fasta.gz,fastq.gz"/> 43 <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"/> 44 <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"/> 45 <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"/> 46 <param argument="--frequency" type="float" value="0.001" label="Threshold for ignoring most frequent minimizers"/>
47 <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"/>
48 <param argument="--kMaxNumOverlaps" type="integer" value="32" label="Maximum number of overlaps that will be taken during FindOverlapsAndCreatePiles stage"/>
49 <param argument="--min-unitig-size" type="integer" value="9999" label="Minimal unitig size"/>
50
47 <param argument="--polishing-rounds" type="integer" value="2" min="0" label="Number of times racon polishing is invoked"/> 51 <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"/> 52 <param argument="--match" type="integer" value="3"/>
49 <param argument="--mismatch" type="integer" value="-5"/> 53 <param argument="--mismatch" type="integer" value="-5"/>
50 <param argument="--gap" type="integer" value="-4" max="-1"/> 54 <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"/> 55 <param argument="--graphical-fragment-assembly" type="boolean" truevalue="--graphical-fragment-assembly out.gfa" falsevalue="" label="output graphical fragment assembly file?" checked="true"/>
56 <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> 57 </inputs>
53 <outputs> 58 <outputs>
54 <data name="out_gfa" format="gfa1" label="${tool.name} on ${on_string} (Graphical Fragment Assembly)" from_work_dir="out.gfa"> 59 <data name="out_gfa" format="gfa1" label="${tool.name} on ${on_string} (Graphical Fragment Assembly)" from_work_dir="out.gfa">
55 <filter>graphical_fragment_assembly</filter> 60 <filter>graphical_fragment_assembly</filter>
56 </data> 61 </data>
57 <data name="out_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA)" /> 62 <data name="out_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA)"/>
58 </outputs> 63 </outputs>
59 <tests> 64 <tests>
60 <test expect_num_outputs="2"> 65 <test expect_num_outputs="2">
61 <param name="input_reads" ftype="fastq.gz" value="ERA476754.fastq.gz"/> 66 <param name="input_reads" ftype="fastq.gz" value="ERA476754.fastq.gz"/>
62 <output name="out_gfa"> 67 <output name="out_gfa">
63 <assert_contents> 68 <assert_contents>
64 <has_n_lines n="2"/> 69 <has_n_lines n="2"/>
65 <has_text_matching expression="^S\tUtg52\t[ATCG]{30000,40000}\tLN:i:36[0-9]{3}\tRC:i:22\nS\tCtg54\t[ATCG]{9000,10000}\tLN:i:9361\tRC:i:4"/> 70 <has_text_matching expression="^S\tUtg52\t[ATCG]{30000,40000}\tLN:i:36[0-9]{3}\tRC:i:22\tdp:f:8\nS\tCtg54\t[ATCG]{9000,10000}\tLN:i:9361\tRC:i:4"/>
66 </assert_contents> 71 </assert_contents>
67 </output> 72 </output>
68 <output name="out_fasta"> 73 <output name="out_fasta">
69 <assert_contents> 74 <assert_contents>
70 <has_n_lines n="2"/> 75 <has_n_lines n="2"/>
71 <has_text_matching expression="^>Utg52 LN:i:36[0-9]{3} RC:i:22 XO:i:0\n[ATCG]{30000,40000}$"/> 76 <has_text_matching expression="^&gt;Utg52 LN:i:36[0-9]{3} RC:i:22 XO:i:0\n[ATCG]{30000,40000}$"/>
72 </assert_contents> 77 </assert_contents>
73 </output> 78 </output>
74 </test> 79 </test>
75 <!-- <test expect_num_outputs="1"> 80 <!-- <test expect_num_outputs="1">
76 <param name="input_reads" ftype="fastq.gz" value="ERA476754.fastq.gz"/> 81 <param name="input_reads" ftype="fastq.gz" value="ERA476754.fastq.gz"/>