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comparison racon.xml @ 8:e100a765370e draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
author bgruening
date Wed, 19 Oct 2022 16:12:55 +0000
parents d865b62f501c
children 936f0b5e7fcc
comparison
equal deleted inserted replaced
7:39bed8de8017 8:e100a765370e
1 <tool id="racon" name="Racon" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="racon" name="Racon" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>Consensus module for raw de novo DNA assembly of long uncorrected reads.</description> 2 <description>Consensus module for raw de novo DNA assembly of long uncorrected reads</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <version_command>racon --version</version_command> 7 <version_command>racon --version</version_command>
39 #else: 39 #else:
40 overlaps.paf 40 overlaps.paf
41 #end if 41 #end if
42 corrected_reads.$cext 42 corrected_reads.$cext
43 -t \${GALAXY_SLOTS:-4} 43 -t \${GALAXY_SLOTS:-4}
44 $u 44 $include_unpolished
45 $f 45 $fragment_correction
46 -w $w 46 -w $window_length
47 -q $q 47 -q $quality_threshold
48 -e $e 48 -e $error_threshold
49 -m $m 49 $no_trimming
50 -x $x 50 -m $match
51 -g $g 51 -x $mismatch
52 -g $gap
52 > racon_polished_consensus.fa 53 > racon_polished_consensus.fa
53 ]]></command> 54 ]]></command>
54 <inputs> 55 <inputs>
55 <param type="data" name="reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Sequences"/> 56 <param type="data" name="reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Sequences" help="input file in FASTA/FASTQ format (can be compressed with gzip) containing sequences used for correction"/>
56 <param type="data" name="overlaps" format="paf,sam,tabular" label="Overlaps"/> 57 <param type="data" name="overlaps" format="paf,sam,tabular" label="Overlaps" help="input file in MHAP/PAF/SAM format (can be compressed with gzip) containing overlaps between sequences and target sequences"/>
57 <param type="data" name="corrected_reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Target sequences"/> 58 <param type="data" name="corrected_reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Target sequences" help="Input file in FASTA/FASTQ format (can be compressed with gzip) containing sequences which will be corrected"/>
58 59 <param argument="--include-unpolished" type="boolean" truevalue="-u" falsevalue="" label="Include unpolished" help="Output unpolished target sequences" />
59 <param argument="-u" type="boolean" truevalue="-u" falsevalue="" label="output unpolished target sequences" /> 60 <param argument="--fragment-correction" type="boolean" truevalue="-f" falsevalue="" label="Fragment correction" help="Perform fragment correction instead of contig polishing. Note: overlaps file should contain dual/self overlaps" />
60 <param argument="-f" type="boolean" truevalue="-f" falsevalue="" label="perform fragment correction instead of contig polishing" /> 61 <param argument="--window-length" type="integer" value="500" label="Window length" help="Size of window on which POA is performed"/>
61 <param argument="-w" type="integer" value="500" label="Size of window on which POA is performed" /> 62 <param argument="--quality-threshold" type="float" min="0" value="10.0" label="Quality threshold" help="Threshold for average base quality of windows used in POA"/>
62 <param argument="-q" type="float" value="10.0" label="Threshold for average base quality of windows used in poa" /> 63 <param argument="--error-threshold" type="float" min="0" value="0.3" label="Error threshold" help="Maximum allowed error rate used for filtering overlaps" />
63 <param argument="-e" type="float" value="0.3" label="Maximum allowed error rate used for filtering overlaps" /> 64 <param argument="--no-trimming" type="boolean" truevalue="--no-trimming" falsevalue="" checked="false" label="No trimming" help="Disables consensus trimming at window ends" />
64 <param argument="-m" type="integer" value="5" label="Score for matching bases" /> 65 <param argument="--match" type="integer" value="3" label="Match score" help="Score for matching bases. Defalt: 3" />
65 <param argument="-x" type="integer" value="-4" label="Score for mismatching bases" /> 66 <param argument="--mismatch" type="integer" value="-5" label="Mismatch score" help="Score for mismatching bases. Default: -5" />
66 <param argument="-g" type="integer" value="-8" max="0" label="Gap penalty" /> 67 <param argument="--gap" type="integer" value="-4" max="0" label="Gap penalty" />
67
68 </inputs> 68 </inputs>
69 <outputs> 69 <outputs>
70 <data name="consensus" format="fasta" from_work_dir="racon_polished_consensus.fa" /> 70 <data name="consensus" format="fasta" from_work_dir="racon_polished_consensus.fa" label="${tool.name} on ${on_string}: consensus sequence"/>
71 </outputs> 71 </outputs>
72 <tests> 72 <tests>
73 <test> 73 <test expect_num_outputs="1">
74 <param name="reads" ftype="fasta" value="sample_reads.fasta"/> 74 <param name="reads" ftype="fasta" value="sample_reads.fasta"/>
75 <param name="overlaps" ftype="sam" value="sample_overlaps.sam"/> 75 <param name="overlaps" ftype="sam" value="sample_overlaps.sam"/>
76 <param name="corrected_reads" ftype="fasta" value="sample_layout.fasta"/> 76 <param name="corrected_reads" ftype="fasta" value="sample_layout.fasta"/>
77 <param name="u" value="true"/> 77 <param name="include_unpolished" value="true"/>
78 <param name="f" value="true"/> 78 <param name="fragment_correction" value="true"/>
79 <param name="w" value="800"/> 79 <param name="window_length" value="800"/>
80 <param name="e" value="0.2"/> 80 <param name="error_threshold" value="0.2"/>
81 <output name="consensus" ftype="fasta" file="consensus_result2.fasta"/> 81 <output name="consensus" ftype="fasta" file="consensus_result2.fasta"/>
82 </test> 82 </test>
83 <test> 83 <test expect_num_outputs="1">
84 <param name="reads" ftype="fasta" value="sample_reads.fasta"/> 84 <param name="reads" ftype="fasta" value="sample_reads.fasta"/>
85 <param name="overlaps" ftype="interval" value="sample_overlaps.paf"/> 85 <param name="overlaps" ftype="interval" value="sample_overlaps.paf"/>
86 <param name="corrected_reads" ftype="fasta" value="sample_layout.fasta"/> 86 <param name="corrected_reads" ftype="fasta" value="sample_layout.fasta"/>
87 <output name="consensus" ftype="fasta" file="consensus_result3.fasta"/> 87 <output name="consensus" ftype="fasta" file="consensus_result3.fasta"/>
88 </test>
89 <test expect_num_outputs="1">
90 <param name="reads" ftype="fasta" value="sample_reads.fasta"/>
91 <param name="overlaps" ftype="sam" value="sample_overlaps.sam"/>
92 <param name="corrected_reads" ftype="fasta" value="sample_layout.fasta"/>
93 <param name="include_unpolished" value="false"/>
94 <param name="fragment_correction" value="false"/>
95 <param name="quality_threshold" value="9.0"/>
96 <param name="no_trimming" value="true"/>
97 <param name="match" value="7"/>
98 <param name="mismatch" value="-4"/>
99 <param name="gap" value="-3"/>
100 <output name="consensus" ftype="fasta" file="consensus_result1.fasta"/>
88 </test> 101 </test>
89 </tests> 102 </tests>
90 <help><![CDATA[ 103 <help><![CDATA[
91 104
92 **What it does** 105 **What it does**