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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
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1 <tool id="raven" name="Raven" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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2 <description>De novo assembly of Oxford Nanopore Technologies data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
5
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6 <expand macro="xrefs"/>
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7 <expand macro="requirements"/>
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8 <expand macro="version_command"/>
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9 <!--TODO in future version : enable CUDA support for racon polishing-->
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10 <command detect_errors="exit_code"><![CDATA[
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11 #if $input_reads.is_of_type("fasta")
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12 ln -s '$input_reads' ./input.fa &&
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13 #set input = "input.fa"
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14 #elif $input_reads.is_of_type("fasta.gz")
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15 ln -s '$input_reads' ./input.fa.gz &&
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16 #set input = "input.fa.gz"
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17 #elif $input_reads.is_of_type("fastq")
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18 ln -s '$input_reads' ./input.fq &&
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19 #set input = "input.fq"
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20 #elif $input_reads.is_of_type("fastq.gz")
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21 ln -s '$input_reads' ./input.fq.gz &&
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22 #set input = "input.fq.gz"
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23 #end if
2
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24 raven
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25 --kmer-len '$kmer_len'
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26 --window-len '$window_len'
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27 --frequency '$frequency'
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28 --polishing-rounds '$polishing_rounds'
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29 --match '$match'
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30 --mismatch '$mismatch'
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31 --gap '$gap'
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32 --kMaxNumOverlaps '$kMaxNumOverlaps'
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33 --identity $identity
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34 --min-unitig-size $min_unitig_size
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35 --use-micromizers $use_micromizers
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36 $graphical_fragment_assembly
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37 --disable-checkpoints
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38 -t \${GALAXY_SLOTS:-4}
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39 '$input'
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40 > '$out_fasta'
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41 ]]></command>
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42 <inputs>
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43 <param name="input_reads" type="data" format="fasta,fastq,fasta.gz,fastq.gz"/>
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44 <param argument="--kmer-len" type="integer" value="15" label="Length of minimizers used to find overlaps"/>
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45 <param argument="--window-len" type="integer" value="5" label="Length of sliding window from which minimizers are sampled"/>
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46 <param argument="--frequency" type="float" value="0.001" label="Threshold for ignoring most frequent minimizers"/>
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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"/>
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48 <param argument="--kMaxNumOverlaps" type="integer" value="32" label="Maximum number of overlaps that will be taken during FindOverlapsAndCreatePiles stage"/>
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49 <param argument="--min-unitig-size" type="integer" value="9999" label="Minimal unitig size"/>
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50
0
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51 <param argument="--polishing-rounds" type="integer" value="2" min="0" label="Number of times racon polishing is invoked"/>
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52 <param argument="--match" type="integer" value="3"/>
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53 <param argument="--mismatch" type="integer" value="-5"/>
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54 <param argument="--gap" type="integer" value="-4" max="-1"/>
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55 <param argument="--graphical-fragment-assembly" type="boolean" truevalue="--graphical-fragment-assembly out.gfa" falsevalue="" label="output graphical fragment assembly file?" checked="true"/>
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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"/>
0
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57 </inputs>
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58 <outputs>
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59 <data name="out_gfa" format="gfa1" label="${tool.name} on ${on_string} (Graphical Fragment Assembly)" from_work_dir="out.gfa">
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60 <filter>graphical_fragment_assembly</filter>
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61 </data>
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62 <data name="out_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA)"/>
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63 </outputs>
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64 <tests>
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65 <test expect_num_outputs="2">
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66 <param name="input_reads" ftype="fastq.gz" value="ERA476754.fastq.gz"/>
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67 <output name="out_gfa">
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68 <assert_contents>
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69 <has_n_lines n="2"/>
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70 <has_text_matching expression="^S\tUtg52\t[ATCG]{30000,40000}\tLN:i:36[0-9]{3}\tRC:i:22\tdp:f:8\nS\tCtg54\t[ATCG]{9000,10000}\tLN:i:9361\tRC:i:4"/>
0
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71 </assert_contents>
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72 </output>
1
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73 <output name="out_fasta">
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74 <assert_contents>
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75 <has_n_lines n="2"/>
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76 <has_text_matching expression="^&gt;Utg52 LN:i:36[0-9]{3} RC:i:22 XO:i:0\n[ATCG]{30000,40000}$"/>
0
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77 </assert_contents>
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78 </output>
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79 </test>
1
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80 <!-- <test expect_num_outputs="1">
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81 <param name="input_reads" ftype="fastq.gz" value="ERA476754.fastq.gz"/>
837fd4b0b3fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"
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82 <param name="graphical_fragment_assembly" value="false"/>
1
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83 <output name="out_fasta">
0
837fd4b0b3fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"
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84 <assert_contents>
837fd4b0b3fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"
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85 <has_n_lines n="2"/>
1
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86 <has_text_matching expression="^>Utg52 LN:i:36[0-9]{3} RC:i:22 XO:i:0\n[ATCG]{30000,40000}$"/>
0
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87 </assert_contents>
837fd4b0b3fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"
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88 </output>
1
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89 </test> -->
0
837fd4b0b3fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"
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90 </tests>
837fd4b0b3fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"
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91 <help><![CDATA[
837fd4b0b3fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"
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92 .. class:: infomark
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93
837fd4b0b3fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"
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94 **What it does**
837fd4b0b3fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"
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95
837fd4b0b3fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"
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96 @WID@
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97
837fd4b0b3fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"
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98 **Input**
837fd4b0b3fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"
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99 - fasta / fastq / fasta.gz / fastq.gz data
837fd4b0b3fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"
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100
837fd4b0b3fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"
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101 **Output**
837fd4b0b3fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"
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102
837fd4b0b3fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"
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103 - Assembled genome (FASTA)
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104 - Graphical fragment assembly (optional) (.txt)
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105
837fd4b0b3fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"
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106 **References**
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107
837fd4b0b3fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"
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108 @REFERENCES@
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109 ]]></help>
837fd4b0b3fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"
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110 <expand macro="citations"/>
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111 </tool>