Mercurial > repos > iuc > spades_metaviralspades

comparison metaviralspades.xml @ 11:6766a94ef559 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f1fde73752b1554bb17b027795b6b8fa9bfbe2c4
author iuc
date Wed, 12 Mar 2025 21:47:35 +0000
parents 5b26685e5d3b
children
comparison
equal deleted inserted replaced
10:ea83ac535a1f 11:6766a94ef559
41 @KMER@ 41 @KMER@
42 @PHREDOFFSET@ 42 @PHREDOFFSET@
43 @PIPELINE_OPTIONS@ 43 @PIPELINE_OPTIONS@
44 ## postprocessing 44 ## postprocessing
45 @STATS@ 45 @STATS@
46 @CORRECTED@
47 ]]></command> 46 ]]></command>
48 <inputs> 47 <inputs>
49 <expand macro="input_files_paired" format="fastq, fastq.gz,fastqsanger.gz" label="FASTQ file(s)"/> 48 <expand macro="input_files_paired" format="@FASTQ_INTYPES@" label="FASTQ file(s)"/>
50 <expand macro="input_additional_files_paired" format="fastq,fastq.gz,fastqsanger.gz" label="FASTQ file(s)"/> 49 <expand macro="input_additional_files_paired" format="@FASTQ_INTYPES@" label="FASTQ file(s)"/>
51 <section name="arf" title="Additional read files"> 50 <section name="arf" title="Additional read files">
52 <expand macro="nanopore_pacbio"/> 51 <expand macro="nanopore_pacbio"/>
53 <expand macro="sanger"/> 52 <expand macro="sanger"/>
54 <expand macro="contigs"/> 53 <expand macro="contigs"/>
55 <expand macro="assembly_graph"/> 54 <expand macro="assembly_graph"/>
86 --> 85 -->
87 86
88 <!-- #1 single, separate, fastq.gz, default parameters --> 87 <!-- #1 single, separate, fastq.gz, default parameters -->
89 <test expect_num_outputs="2"> 88 <test expect_num_outputs="2">
90 <conditional name="singlePaired"> 89 <conditional name="singlePaired">
91 <param name="sPaired" value="paired"/> 90 <param name="sPaired" value="paired_collection"/>
92 <param name="input1" value="pl1.fq.gz"/> 91 <param name="input">
93 <param name="input2" value="pl2.fq.gz"/> 92 <collection type="list:paired">
93 <element name="pl">
94 <collection type="paired">
95 <element name="forward" value="pl1.fq.gz" ftype="fastqsanger.gz"/>
96 <element name="reverse" value="pl2.fq.gz" ftype="fastqsanger.gz"/>
97 </collection>
98 </element>
99 </collection>
100 </param>
94 </conditional> 101 </conditional>
95 <output name="out_cn"> 102 <output name="out_cn">
96 <assert_contents> 103 <assert_contents>
97 <has_n_lines n="163"/> 104 <has_n_lines n="163"/>
98 <has_text_matching expression=">NODE\_1\_length\_9689\_cov\_.+"/> 105 <has_text_matching expression=">NODE\_1\_length\_9689\_cov\_.+"/>
106 </output> 113 </output>
107 </test> 114 </test>
108 <!-- #2 single, separate, fastq, custom parameters --> 115 <!-- #2 single, separate, fastq, custom parameters -->
109 <test expect_num_outputs="6"> 116 <test expect_num_outputs="6">
110 <conditional name="singlePaired"> 117 <conditional name="singlePaired">
111 <param name="sPaired" value="paired"/> 118 <param name="sPaired" value="paired_collection"/>
112 <param name="input1" value="pl1.fq.gz"/> 119 <param name="input">
113 <param name="input2" value="pl2.fq.gz"/> 120 <collection type="list:paired">
121 <element name="pl">
122 <collection type="paired">
123 <element name="forward" value="pl1.fq.gz" ftype="fastqsanger.gz"/>
124 <element name="reverse" value="pl2.fq.gz" ftype="fastqsanger.gz"/>
125 </collection>
126 </element>
127 </collection>
128 </param>
114 </conditional> 129 </conditional>
115 <conditional name="kmer_cond"> 130 <conditional name="kmer_cond">
116 <param name="kmer_sel" value="manual"/> 131 <param name="kmer_sel" value="manual"/>
117 <param name="manual" value="33"/> 132 <param name="manual" value="33"/>
118 </conditional> 133 </conditional>
130 <has_text_matching expression="#name&#009;length&#009;coverage"/> 145 <has_text_matching expression="#name&#009;length&#009;coverage"/>
131 <has_text_matching expression="NODE_1&#009;9645&#009;13.774865_cutoff_0_type_circular"/> 146 <has_text_matching expression="NODE_1&#009;9645&#009;13.774865_cutoff_0_type_circular"/>
132 </assert_contents> 147 </assert_contents>
133 </output> 148 </output>
134 <output_collection name="out_cr" type="list" count="3"> 149 <output_collection name="out_cr" type="list" count="3">
135 <element name="pl1.fq.gz.fastq.00.0_0"> 150 <element name="pl1.fastq00.0_0">
136 <assert_contents> 151 <assert_contents>
137 <has_size value="71752" delta="1000"/> 152 <has_size value="71752" delta="1000"/>
138 </assert_contents> 153 </assert_contents>
139 </element> 154 </element>
140 <element name="pl2.fq.gz.fastq.00.0_0"> 155 <element name="pl2.fastq00.0_0">
141 <assert_contents> 156 <assert_contents>
142 <has_size value="71752" delta="1000"/> 157 <has_size value="71752" delta="1000"/>
143 </assert_contents> 158 </assert_contents>
144 </element> 159 </element>
145 <element name="pl_unpaired.00.0_0"> 160 <element name="pl_unpaired00.0_0">
146 <assert_contents> 161 <assert_contents>
147 <has_size value="423" delta="100"/> 162 <has_size value="423" delta="100"/>
148 </assert_contents> 163 </assert_contents>
149 </element> 164 </element>
150 </output_collection> 165 </output_collection>
161 <has_text_matching expression="NODE_1&#009;9645&#009;13.774865_cutoff_0_type_circular"/> 176 <has_text_matching expression="NODE_1&#009;9645&#009;13.774865_cutoff_0_type_circular"/>
162 </assert_contents> 177 </assert_contents>
163 </output> 178 </output>
164 <output name="out_l"> 179 <output name="out_l">
165 <assert_contents> 180 <assert_contents>
166 <has_text_matching expression="Thank you for using SPAdes!"/> 181 <has_text_matching expression="Thank you for using metaviralSPAdes!"/>
167 </assert_contents> 182 </assert_contents>
168 </output> 183 </output>
169 </test> 184 </test>
170 <!-- #3 --> 185 <!-- #3 -->
171 <test expect_num_outputs="1"> 186 <test expect_num_outputs="1">
172 <conditional name="singlePaired"> 187 <conditional name="singlePaired">
173 <param name="sPaired" value="paired"/> 188 <param name="sPaired" value="paired_collection"/>
174 <param name="input1" value="pl1.fq.gz"/> 189 <param name="input">
175 <param name="input2" value="pl2.fq.gz"/> 190 <collection type="list:paired">
191 <element name="pl">
192 <collection type="paired">
193 <element name="forward" value="pl1.fq.gz" ftype="fastqsanger.gz"/>
194 <element name="reverse" value="pl2.fq.gz" ftype="fastqsanger.gz"/>
195 </collection>
196 </element>
197 </collection>
198 </param>
176 </conditional> 199 </conditional>
177 <param name="operation_mode" value="--only-assembler"/> 200 <param name="operation_mode" value="--only-assembler"/>
178 <param name="optional_output" value="l"/> 201 <param name="optional_output" value="l"/>
179 <output name="out_l"> 202 <output name="out_l">
180 <assert_contents> 203 <assert_contents>
181 <has_text_matching expression="Thank you for using SPAdes!"/> 204 <has_text_matching expression="Thank you for using metaviralSPAdes!"/>
182 </assert_contents> 205 </assert_contents>
183 </output> 206 </output>
184 </test> 207 </test>
185 <!-- #4, only corrected reads are created as an output --> 208 <!-- #4, only corrected reads are created as an output -->
186 <test expect_num_outputs="2"> 209 <test expect_num_outputs="2">
187 <conditional name="singlePaired"> 210 <conditional name="singlePaired">
188 <param name="sPaired" value="paired"/> 211 <param name="sPaired" value="paired_collection"/>
189 <param name="input1" value="pl1.fq.gz"/> 212 <param name="input">
190 <param name="input2" value="pl2.fq.gz"/> 213 <collection type="list:paired">
214 <element name="pl">
215 <collection type="paired">
216 <element name="forward" value="pl1.fq.gz" ftype="fastqsanger.gz"/>
217 <element name="reverse" value="pl2.fq.gz" ftype="fastqsanger.gz"/>
218 </collection>
219 </element>
220 </collection>
221 </param>
191 </conditional> 222 </conditional>
192 <param name="operation_mode" value="--only-error-correction"/> 223 <param name="operation_mode" value="--only-error-correction"/>
193 <param name="optional_output" value="cr,l"/> 224 <param name="optional_output" value="cr,l"/>
194 <output_collection name="out_cr" type="list" count="3"> 225 <output_collection name="out_cr" type="list" count="3">
195 <element name="pl1.fq.gz.fastq.00.0_0"> 226 <element name="pl1.fastq00.0_0">
196 <assert_contents> 227 <assert_contents>
197 <has_size value="71752" delta="1000"/> 228 <has_size value="71752" delta="1000"/>
198 </assert_contents> 229 </assert_contents>
199 </element> 230 </element>
200 <element name="pl2.fq.gz.fastq.00.0_0"> 231 <element name="pl2.fastq00.0_0">
201 <assert_contents> 232 <assert_contents>
202 <has_size value="71752" delta="1000"/> 233 <has_size value="71752" delta="1000"/>
203 </assert_contents> 234 </assert_contents>
204 </element> 235 </element>
205 <element name="pl_unpaired.00.0_0"> 236 <element name="pl_unpaired00.0_0">
206 <assert_contents> 237 <assert_contents>
207 <has_size value="423" delta="100"/> 238 <has_size value="423" delta="100"/>
208 </assert_contents> 239 </assert_contents>
209 </element> 240 </element>
210 </output_collection> 241 </output_collection>
211 <output name="out_l"> 242 <output name="out_l">
212 <assert_contents> 243 <assert_contents>
213 <has_text_matching expression="Thank you for using SPAdes!"/> 244 <has_text_matching expression="Thank you for using metaviralSPAdes!"/>
214 </assert_contents> 245 </assert_contents>
215 </output> 246 </output>
216 </test> 247 </test>
217 </tests> 248 </tests>
218 <help><![CDATA[ 249 <help><![CDATA[