Mercurial > repos > iuc > spades_metaplasmidspades
comparison metaplasmidspades.xml @ 7:e5a3b75a271f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
author | iuc |
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date | Tue, 23 Aug 2022 08:01:19 +0000 |
parents | 4a01e0d2892c |
children | 037f9927c4ff |
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6:4a01e0d2892c | 7:e5a3b75a271f |
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20 @PREPROCESS_ASSEMBLY_GRAPH_FILES@ | 20 @PREPROCESS_ASSEMBLY_GRAPH_FILES@ |
21 | 21 |
22 @OMP_THREADS@ | 22 @OMP_THREADS@ |
23 ## run | 23 ## run |
24 spades.py --meta --plasmid | 24 spades.py --meta --plasmid |
25 $operation_mode | |
25 -o 'output' | 26 -o 'output' |
26 @RESOURCES@ | 27 @RESOURCES@ |
27 @INPUT_READS_MAIN@ | 28 @INPUT_READS_MAIN@ |
28 #if $additional_reads.selector == 'true' | 29 #if $additional_reads.selector == 'true' |
29 @INPUT_READS_ADDITIONAL@ | 30 @INPUT_READS_ADDITIONAL@ |
40 ## postprocessing | 41 ## postprocessing |
41 @STATS@ | 42 @STATS@ |
42 @CORRECTED@ | 43 @CORRECTED@ |
43 ]]></command> | 44 ]]></command> |
44 <inputs> | 45 <inputs> |
46 <expand macro="operation_mode" help="To run read error correction, reads should be in FASTQ format."/> | |
45 <expand macro="input_files_paired" format="fastq, fastq.gz,fastqsanger.gz" label="FASTQ file(s)"/> | 47 <expand macro="input_files_paired" format="fastq, fastq.gz,fastqsanger.gz" label="FASTQ file(s)"/> |
46 <expand macro="input_additional_files_paired" format="fastq,fastq.gz,fastqsanger.gz" label="FASTQ file(s)"/> | 48 <expand macro="input_additional_files_paired" format="fastq,fastq.gz,fastqsanger.gz" label="FASTQ file(s)"/> |
47 <section name="arf" title="Additional read files"> | 49 <section name="arf" title="Additional read files"> |
48 <expand macro="nanopore_pacbio"/> | 50 <expand macro="nanopore_pacbio"/> |
49 <expand macro="sanger"/> | 51 <expand macro="sanger"/> |
125 <has_text_matching expression="#name	length	coverage"/> | 127 <has_text_matching expression="#name	length	coverage"/> |
126 <has_text_matching expression="NODE_1	9645	13.774865_cutoff_0_type_circular"/> | 128 <has_text_matching expression="NODE_1	9645	13.774865_cutoff_0_type_circular"/> |
127 </assert_contents> | 129 </assert_contents> |
128 </output> | 130 </output> |
129 <output_collection name="out_cr" type="list" count="3"> | 131 <output_collection name="out_cr" type="list" count="3"> |
130 <element name="pl1.fq.gz.fastq.00.0_0.cor"> | 132 <element name="pl1.fq.gz.fastq.00.0_0"> |
131 <assert_contents> | 133 <assert_contents> |
132 <has_size value="71752" delta="1000"/> | 134 <has_size value="71752" delta="1000"/> |
133 </assert_contents> | 135 </assert_contents> |
134 </element> | 136 </element> |
135 <element name="pl2.fq.gz.fastq.00.0_0.cor"> | 137 <element name="pl2.fq.gz.fastq.00.0_0"> |
136 <assert_contents> | 138 <assert_contents> |
137 <has_size value="71752" delta="1000"/> | 139 <has_size value="71752" delta="1000"/> |
138 </assert_contents> | 140 </assert_contents> |
139 </element> | 141 </element> |
140 <element name="pl_unpaired.00.0_0.cor"> | 142 <element name="pl_unpaired.00.0_0"> |
141 <assert_contents> | 143 <assert_contents> |
142 <has_size value="423" delta="100"/> | 144 <has_size value="423" delta="100"/> |
143 </assert_contents> | 145 </assert_contents> |
144 </element> | 146 </element> |
145 </output_collection> | 147 </output_collection> |
185 <param name="input2" value="pl2.fq.gz"/> | 187 <param name="input2" value="pl2.fq.gz"/> |
186 </conditional> | 188 </conditional> |
187 <param name="operation_mode" value="--only-error-correction"/> | 189 <param name="operation_mode" value="--only-error-correction"/> |
188 <param name="optional_output" value="cr,l"/> | 190 <param name="optional_output" value="cr,l"/> |
189 <output_collection name="out_cr" type="list" count="3"> | 191 <output_collection name="out_cr" type="list" count="3"> |
190 <element name="pl1.fq.gz.fastq.00.0_0.cor"> | 192 <element name="pl1.fq.gz.fastq.00.0_0"> |
191 <assert_contents> | 193 <assert_contents> |
192 <has_size value="71752" delta="1000"/> | 194 <has_size value="71752" delta="1000"/> |
193 </assert_contents> | 195 </assert_contents> |
194 </element> | 196 </element> |
195 <element name="pl2.fq.gz.fastq.00.0_0.cor"> | 197 <element name="pl2.fq.gz.fastq.00.0_0"> |
196 <assert_contents> | 198 <assert_contents> |
197 <has_size value="71752" delta="1000"/> | 199 <has_size value="71752" delta="1000"/> |
198 </assert_contents> | 200 </assert_contents> |
199 </element> | 201 </element> |
200 <element name="pl_unpaired.00.0_0.cor"> | 202 <element name="pl_unpaired.00.0_0"> |
201 <assert_contents> | 203 <assert_contents> |
202 <has_size value="423" delta="100"/> | 204 <has_size value="423" delta="100"/> |
203 </assert_contents> | 205 </assert_contents> |
204 </element> | 206 </element> |
205 </output_collection> | 207 </output_collection> |