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comparison racon.xml @ 1:4df02149a270 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
author bgruening
date Thu, 19 Jul 2018 07:43:14 -0400
parents 51fd3136069d
children aa39b19ca11e
comparison
equal deleted inserted replaced
0:51fd3136069d 1:4df02149a270
1 <tool id="racon" name="Racon" version="1.3.1"> 1 <tool id="racon" name="Racon" version="1.3.1.1">
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>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '$reads' reads.${reads.ext} && 9 ln -s '$reads' reads.${reads.ext} &&
10 ln -s '$overlaps' overlaps.${overlaps.ext} && 10 #if $overlaps.ext == 'sam':
11 ln -s '$overlaps' overlaps.${overlaps.ext} &&
12 #else:
13 ln -s '$overlaps' overlaps.paf &&
14 #end if
11 ln -s '$corrected_reads' corrected_reads.${corrected_reads.ext} && 15 ln -s '$corrected_reads' corrected_reads.${corrected_reads.ext} &&
12 16
13 racon 17 racon
14 reads.${reads.ext} 18 reads.${reads.ext}
15 overlaps.${overlaps.ext} 19 #if $overlaps.ext == 'sam':
20 overlaps.${overlaps.ext}
21 #else:
22 overlaps.paf
23 #end if
16 corrected_reads.${corrected_reads.ext} 24 corrected_reads.${corrected_reads.ext}
17 -t \${GALAXY_SLOTS:-4} 25 -t \${GALAXY_SLOTS:-4}
18 $u 26 $u
19 $f 27 $f
20 -w $w 28 -w $w
25 -g $g 33 -g $g
26 > racon_polished_consensus.fa 34 > racon_polished_consensus.fa
27 ]]></command> 35 ]]></command>
28 <inputs> 36 <inputs>
29 <param type="data" name="reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Sequences"/> 37 <param type="data" name="reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Sequences"/>
30 <param type="data" name="overlaps" format="sam" label="Overlaps"/> 38 <param type="data" name="overlaps" format="sam,interval" label="Overlaps"/>
31 <param type="data" name="corrected_reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Target sequences"/> 39 <param type="data" name="corrected_reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Target sequences"/>
32 40
33 <param argument="-u" type="boolean" truevalue="-u" falsevalue="" label="output unpolished target sequences" /> 41 <param argument="-u" type="boolean" truevalue="-u" falsevalue="" label="output unpolished target sequences" />
34 <param argument="-f" type="boolean" truevalue="-f" falsevalue="" label="perform fragment correction instead of contig polishing" /> 42 <param argument="-f" type="boolean" truevalue="-f" falsevalue="" label="perform fragment correction instead of contig polishing" />
35 <param argument="-w" type="integer" value="500" label="Size of window on which POA is performed" /> 43 <param argument="-w" type="integer" value="500" label="Size of window on which POA is performed" />
52 <param name="f" value="true"/> 60 <param name="f" value="true"/>
53 <param name="w" value="800"/> 61 <param name="w" value="800"/>
54 <param name="e" value="0.2"/> 62 <param name="e" value="0.2"/>
55 <output name="consensus" ftype="fasta" file="consensus_result2.fasta"/> 63 <output name="consensus" ftype="fasta" file="consensus_result2.fasta"/>
56 </test> 64 </test>
65 <test>
66 <param name="reads" ftype="fasta" value="sample_reads.fasta"/>
67 <param name="overlaps" ftype="interval" value="sample_overlaps.paf"/>
68 <param name="corrected_reads" ftype="fasta" value="sample_layout.fasta"/>
69 <output name="consensus" ftype="fasta" file="consensus_result3.fasta"/>
70 </test>
57 </tests> 71 </tests>
58 <help><![CDATA[ 72 <help><![CDATA[
59 73
60 **What it does** 74 **What it does**
61 75