Mercurial > repos > iuc > spades_rnaviralspades

comparison rnaviralspades.xml @ 7:d5fb354f745d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
author iuc
date Tue, 23 Aug 2022 07:59:16 +0000
parents 48cf45a53456
children de1260f8a300
comparison
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6:48cf45a53456 7:d5fb354f745d
19 @PREPROCESS_SANGER_FILES@ 19 @PREPROCESS_SANGER_FILES@
20 20
21 @OMP_THREADS@ 21 @OMP_THREADS@
22 ## run 22 ## run
23 spades.py --rnaviral 23 spades.py --rnaviral
24 $operation_mode
24 -o 'output' 25 -o 'output'
25 @RESOURCES@ 26 @RESOURCES@
26 @INPUT_READS_MAIN@ 27 @INPUT_READS_MAIN@
27 #if $additional_reads.selector == 'true' 28 #if $additional_reads.selector == 'true'
28 @INPUT_READS_ADDITIONAL@ 29 @INPUT_READS_ADDITIONAL@
39 ## postprocessing 40 ## postprocessing
40 @STATS@ 41 @STATS@
41 @CORRECTED@ 42 @CORRECTED@
42 ]]></command> 43 ]]></command>
43 <inputs> 44 <inputs>
45 <expand macro="operation_mode" help="To run read error correction, reads should be in FASTQ format."/>
44 <expand macro="input_files_all" format="fastq,fasta,fastq.gz,fastqsanger.gz,fasta.gz" label="FASTQ RNA-seq file(s)"/> 46 <expand macro="input_files_all" format="fastq,fasta,fastq.gz,fastqsanger.gz,fasta.gz" label="FASTQ RNA-seq file(s)"/>
45 <expand macro="input_additional_files_all" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTQ RNA-seq file(s)"/> 47 <expand macro="input_additional_files_all" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTQ RNA-seq file(s)"/>
46 <section name="arf" title="Additional read files"> 48 <section name="arf" title="Additional read files">
47 <expand macro="sanger"/> 49 <expand macro="sanger"/>
48 <expand macro="nanopore_pacbio"/> 50 <expand macro="nanopore_pacbio"/>
142 <output name="out_cp"> 144 <output name="out_cp">
143 <assert_contents> 145 <assert_contents>
144 <has_n_lines n="0"/> 146 <has_n_lines n="0"/>
145 </assert_contents> 147 </assert_contents>
146 </output> 148 </output>
147 <output_collection name="out_cr" type="list" count="4"> 149 <output_collection name="out_cr" type="list" count="2">
148 <element name="ecoli_1K_1.fastq.gz.fastq0_0.cor"> 150 <element name="ecoli_1K_1.fastq.gz.fastq0_0">
149 <assert_contents> 151 <assert_contents>
150 <has_size value="34468" delta="2000"/> 152 <has_size value="34468" delta="2000"/>
151 </assert_contents> 153 </assert_contents>
152 </element> 154 </element>
153 <element name="ecoli_1K_2.fastq.gz.fastq0_0.cor"> 155 <element name="ecoli_1K_2.fastq.gz.fastq0_0">
154 <assert_contents> 156 <assert_contents>
155 <has_size value="34468" delta="2000"/> 157 <has_size value="34468" delta="2000"/>
156 </assert_contents> 158 </assert_contents>
157 </element> 159 </element>
158 </output_collection> 160 </output_collection>