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comparison uvp.xml @ 6:869ab16717db draft

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"planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/uvp commit 2482e856a9414983c82d94c9f59ff8985574895e-dirty"
author dfornika
date Fri, 11 Oct 2019 20:48:39 -0400
parents d21fd5069821
children 679d120f8c09
comparison
equal deleted inserted replaced
5:d21fd5069821 6:869ab16717db
19 ln -s '${single_paired.input_sequences}' 'R1.fastq.gz' && 19 ln -s '${single_paired.input_sequences}' 'R1.fastq.gz' &&
20 #end if 20 #end if
21 uvp 21 uvp
22 --threads \${GALAXY_SLOTS:-1} 22 --threads \${GALAXY_SLOTS:-1}
23 #if $single_paired.single_paired_selector == 'yes' 23 #if $single_paired.single_paired_selector == 'yes'
24 -n '${single_paired.forward_input.element_identifier}' 24 -n 'sample'
25 -q 'R1.fastq.gz' 25 -q '${single_paired.forward_input}'
26 -q2 'R2.fastq.gz' 26 -q2 '${single_paired.reverse_input}'
27 #elif $single_paired.single_paired_selector == "collection": 27 #elif $single_paired.single_paired_selector == "collection":
28 -n '${single_paired.input_pair.forward.element_identifier}' 28 -n 'sample'
29 -q 'R1.fastq.gz' 29 -q '${single_paired.input_pair.forward}'
30 -q2 'R2.fastq.gz' 30 -q2 '${single_paired.input_pair.reverse}'
31 #else: 31 #else:
32 -n '${single_paired.input_sequences.element_identifier}' 32 -n 'sample'
33 -q 'R1.fastq.gz' 33 -q '${single_paired.input_sequences}'
34 #end if 34 #end if
35 --krakendb '${kraken_database.fields.path}' 35 --krakendb '${kraken_database.fields.path}'
36 -r '${reference}' 36 -r '${reference}'
37 ${annotate} 37 ${annotate}
38 ]]> 38 ]]>
62 </param> 62 </param>
63 <param name="reference" type="data" format="fasta" label="Reference Sequence" /> 63 <param name="reference" type="data" format="fasta" label="Reference Sequence" />
64 <param name="annotate" type="boolean" truevalue="--annotate" falsevalue="" /> 64 <param name="annotate" type="boolean" truevalue="--annotate" falsevalue="" />
65 </inputs> 65 </inputs>
66 <outputs> 66 <outputs>
67 <data name="lineage_report" label="Lineage Report" format="tabular" from_work_dir="Results/sample/sample.lineage_report.txt"/>
67 <data name="low_quals" label="Low-quality" format="tabular" from_work_dir="QC/low_quals.txt"/> 68 <data name="low_quals" label="Low-quality" format="tabular" from_work_dir="QC/low_quals.txt"/>
68 </outputs> 69 </outputs>
69 <tests> 70 <tests>
70 </tests> 71 </tests>
71 <help> 72 <help>