Mercurial > repos > iuc > spades_metaplasmidspades

comparison metaplasmidspades.xml @ 7:e5a3b75a271f 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 08:01:19 +0000
parents 4a01e0d2892c
children 037f9927c4ff
comparison
equal deleted inserted replaced
6:4a01e0d2892c 7:e5a3b75a271f
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&#009;length&#009;coverage"/> 127 <has_text_matching expression="#name&#009;length&#009;coverage"/>
126 <has_text_matching expression="NODE_1&#009;9645&#009;13.774865_cutoff_0_type_circular"/> 128 <has_text_matching expression="NODE_1&#009;9645&#009;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>