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comparison kma_map.xml @ 3:0e8330535ea0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 8c23e6a057edc7697f51ccabba16fb4fdabbab71
author iuc
date Wed, 23 Jul 2025 12:20:33 +0000
parents 98099e4da1fd
children 8fbd98f37c10
comparison
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2:98099e4da1fd 3:0e8330535ea0
8 </requirements> 8 </requirements>
9 <version_command>kma -v</version_command> 9 <version_command>kma -v</version_command>
10 <command detect_errors="exit_code"> 10 <command detect_errors="exit_code">
11 <![CDATA[ 11 <![CDATA[
12 kma 12 kma
13 -t \${GALAXY_SLOTS:-1} 13 -t "\${GALAXY_SLOTS:-1}"
14 -t_db '${kma_index.fields.path}' 14 -t_db '${kma_index.fields.path}'
15 #if $single_paired.single_paired_selector == 'paired' 15 #if $single_paired.single_paired_selector == "paired_collection":
16 -ipe '${single_paired.forward_input}' '${single_paired.reverse_input}'
17 #elif $single_paired.single_paired_selector == "paired_collection":
18 -ipe '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}' 16 -ipe '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}'
19 #else: 17 #else:
20 -i '${single_paired.input_sequences}' 18 -i '${single_paired.input_sequences}'
21 #end if 19 #end if
22 #if str($settings.advanced) == "advanced" 20 #if str($settings.advanced) == "advanced"
74 </command> 72 </command>
75 <inputs> 73 <inputs>
76 <conditional name="single_paired"> 74 <conditional name="single_paired">
77 <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired"> 75 <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
78 <option value="paired_collection">Paired collection</option> 76 <option value="paired_collection">Paired collection</option>
79 <option value="paired">Paired-end data</option>
80 <option selected="True" value="single">Single-end data</option> 77 <option selected="True" value="single">Single-end data</option>
81 </param> 78 </param>
82 <when value="paired_collection"> 79 <when value="paired_collection">
83 <param argument="-ipe" format="@INTYPES@" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" /> 80 <param argument="-ipe" format="@INTYPES@" name="input_pair" type="data_collection" collection_type="paired" label="Paired reads" help="FASTQ datasets" />
84 </when>
85 <when value="paired">
86 <param argument="-ipe" format="@INTYPES@" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/>
87 <param argument="-ipe" format="@INTYPES@" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/>
88 </when> 81 </when>
89 <when value="single"> 82 <when value="single">
90 <param argument="-i" format="@INTYPES@" label="Input sequences" name="input_sequences" type="data" help="FASTQ datasets"/> 83 <param argument="-i" format="@INTYPES@" label="Input sequences" name="input_sequences" type="data" help="FASTQ datasets"/>
91 </when> 84 </when>
92 </conditional> 85 </conditional>
136 <filter>settings['matrix']</filter> 129 <filter>settings['matrix']</filter>
137 </data> 130 </data>
138 </outputs> 131 </outputs>
139 <tests> 132 <tests>
140 <test expect_num_outputs="4"> 133 <test expect_num_outputs="4">
141 <param name="single_paired_selector" value="single"/> 134 <conditional name="single_paired">
142 <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/> 135 <param name="single_paired_selector" value="single"/>
143 <param name="advanced" value="advanced"/> 136 <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/>
144 <param name="kmer_size" value="8"/> 137 </conditional>
138 <conditional name="settings">
139 <param name="advanced" value="advanced"/>
140 <param name="kmer_size" value="8"/>
141 </conditional>
145 <param name="kma_index" value="test_index"/> 142 <param name="kma_index" value="test_index"/>
146 <output name="result_overview" ftype="tabular"> 143 <output name="result_overview" ftype="tabular">
147 <assert_contents> 144 <assert_contents>
148 <has_n_lines n="3"/> 145 <has_n_lines n="3"/>
149 <has_n_columns n="11"/> 146 <has_n_columns n="11"/>
172 <has_text text="b0842_1"/> 169 <has_text text="b0842_1"/>
173 </assert_contents> 170 </assert_contents>
174 </output> 171 </output>
175 </test> 172 </test>
176 <test expect_num_outputs="5"> 173 <test expect_num_outputs="5">
177 <param name="single_paired_selector" value="single"/> 174 <conditional name="single_paired">
178 <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/> 175 <param name="single_paired_selector" value="single"/>
179 <param name="advanced" value="advanced"/> 176 <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/>
180 <param name="kmer_size" value="8"/> 177 </conditional>
181 <param name="matrix" value="true"/> 178 <conditional name="settings">
179 <param name="advanced" value="advanced"/>
180 <param name="kmer_size" value="8"/>
181 <param name="matrix" value="true"/>
182 </conditional>
182 <param name="kma_index" value="test_index"/> 183 <param name="kma_index" value="test_index"/>
183 <output name="assembly_matrix" ftype="tabular"> 184 <output name="assembly_matrix" ftype="tabular">
184 <assert_contents> 185 <assert_contents>
185 <has_n_lines n="2553"/> 186 <has_n_lines n="2551"/>
186 <has_n_columns n="7" comment="#"/> 187 <has_n_columns n="7" comment="#"/>
187 <has_line_matching expression="^A&#009;.*"/> 188 <has_line_matching expression="^A&#009;.*"/>
188 <has_line_matching expression="^T&#009;.*"/> 189 <has_line_matching expression="^T&#009;.*"/>
189 <has_line_matching expression="^C&#009;.*"/> 190 <has_line_matching expression="^C&#009;.*"/>
190 <has_line_matching expression="^G&#009;.*"/> 191 <has_line_matching expression="^G&#009;.*"/>
192 </assert_contents>
193 </output>
194 </test>
195 <test expect_num_outputs="4">
196 <conditional name="single_paired">
197 <param name="single_paired_selector" value="paired_collection"/>
198 <param name="input_pair">
199 <collection type="paired">
200 <element name="forward" value="ERR884056_ecoli_b0842.mapped_R1.fastq.gz"/>
201 <element name="reverse" value="ERR884056_ecoli_b0842.mapped_R1.fastq.gz"/>
202 </collection>
203 </param>
204 </conditional>
205 <conditional name="settings">
206 <param name="advanced" value="advanced"/>
207 <param name="kmer_size" value="8"/>
208 </conditional>
209 <param name="kma_index" value="test_index"/>
210 <output name="result_overview" ftype="tabular">
211 <assert_contents>
212 <has_n_lines n="4"/>
213 <has_n_columns n="11"/>
214 <has_text text="#Template"/>
215 <has_text text="b0842_1"/>
216 </assert_contents>
217 </output>
218 <output name="consensus_alignment" ftype="txt">
219 <assert_contents>
220 <has_n_lines n="255"/>
221 <has_text text="b0842_1"/>
222 <has_text text="query" n="63"/>
223 <has_text text="template" n="63"/>
224 </assert_contents>
225 </output>
226 <output name="consensus_sequences" ftype="fasta">
227 <assert_contents>
228 <has_line_matching expression="^>.*" n="3"/>
229 <has_line_matching expression="^>b0842_1"/>
230 </assert_contents>
231 </output>
232 <output name="read_mapping" ftype="tabular">
233 <assert_contents>
234 <has_n_lines n="1012"/>
235 <has_n_columns n="7"/>
236 <has_text text="b0842_1"/>
191 </assert_contents> 237 </assert_contents>
192 </output> 238 </output>
193 </test> 239 </test>
194 </tests> 240 </tests>
195 <help><![CDATA[ 241 <help><![CDATA[