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comparison kma_map.xml @ 2:3cd89604dffd draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma commit f040316174672d9e3ce53b1873ab07cff1128940
author iuc
date Mon, 15 Dec 2025 21:59:27 +0000
parents 4b3fca68379b
children
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1:4b3fca68379b 2:3cd89604dffd
1 <tool id="kma_map" name="Map with KMA" version="@TOOL_VERSION@+galaxy1"> 1 <tool id="kma_map" name="Map with KMA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
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>
105 <when value="advanced"> 98 <when value="advanced">
106 <param argument="-k" name="kmer_size" type="integer" min="4" value="16" max="32" label="Kmer Size" /> 99 <param argument="-k" name="kmer_size" type="integer" min="4" value="16" max="32" label="Kmer Size" />
107 <param argument="-p" name="p_value" type="float" min="0.0" value="0.05" max="1.0" label="p-value"/> 100 <param argument="-p" name="p_value" type="float" min="0.0" value="0.05" max="1.0" label="p-value"/>
108 <param argument="-ex_mode" name="exhaustive_mode" type="boolean" truevalue="-ex_mode" falsevalue="" label="Exhaustive Mode" /> 101 <param argument="-ex_mode" name="exhaustive_mode" type="boolean" truevalue="-ex_mode" falsevalue="" label="Exhaustive Mode" />
109 <param argument="-deCon" name="decontaminate" type="boolean" truevalue="-deCon" falsevalue="" label="Decontaminate" /> 102 <param argument="-deCon" name="decontaminate" type="boolean" truevalue="-deCon" falsevalue="" label="Decontaminate" />
110 <param argument="-dense" name="dense" type="boolean" truevalue="-dense" falsevalue="" label="Do not allow insertions in assembly" /> 103 <param argument="-dense" type="boolean" truevalue="-dense" falsevalue="" label="Do not allow insertions in assembly" />
111 <param argument="-ref_fsa" name="ref_fsa" type="boolean" truevalue="-ref_fsa" falsevalue="" label="Consensus sequence has 'n' instead of gaps" /> 104 <param argument="-ref_fsa" type="boolean" truevalue="-ref_fsa" falsevalue="" label="Consensus sequence has 'n' instead of gaps" />
112 <param argument="-matrix" name="matrix" type="boolean" truevalue="-matrix" falsevalue="" label="Output assembly matrix" /> 105 <param argument="-matrix" type="boolean" truevalue="-matrix" falsevalue="" label="Output assembly matrix" />
113 <param argument="-a" name="all_best_mappings" type="boolean" truevalue="-a" falsevalue="" label="Print all best mappings" /> 106 <param argument="-a" name="all_best_mappings" type="boolean" truevalue="-a" falsevalue="" label="Print all best mappings" />
114 <param argument="-mp" name="minimum_phred_score" type="integer" min="0" value="20" max="60" label="Minimum phred score" /> 107 <param argument="-mp" name="minimum_phred_score" type="integer" min="0" value="20" max="60" label="Minimum phred score" />
115 <param argument="-5p" name="cut_5_prime" type="integer" min="0" value="0" max="64" label="Cut a constant number of nucleotides from the 5 prime" /> 108 <param argument="-5p" name="cut_5_prime" type="integer" min="0" value="0" max="64" label="Cut a constant number of nucleotides from the 5 prime" />
116 <param argument="-Sparse" name="only_count_kmers" type="boolean" truevalue="-Sparse" falsevalue="" label="Only count kmers" /> 109 <param argument="-Sparse" name="only_count_kmers" type="boolean" truevalue="-Sparse" falsevalue="" label="Only count kmers" />
117 <param argument="-ID" name="min_id" type="float" min="0.0" value="1.0" max="100.0" label="Minimum percent identity"/> 110 <param argument="-ID" name="min_id" type="float" min="0.0" value="1.0" max="100.0" label="Minimum percent identity"/>
118 <param argument="-1t1" name="force_end_to_end" type="boolean" truevalue="-1t1" falsevalue="" label="Force end to end mapping" /> 111 <param argument="-1t1" name="force_end_to_end" type="boolean" truevalue="-1t1" falsevalue="" label="Force end to end mapping" />
119 <param argument="-bcd" name="base_call_depth" type="integer" min="1" value="1" max="1000" label="Minimum depth at base" /> 112 <param argument="-bcd" name="base_call_depth" type="integer" min="1" value="1" max="1000" label="Minimum depth at base" />
120 <param argument="-mq" name="minimum_mapping_quality" type="integer" min="0" value="0" max="100" label="Minimum mapping quality" /> 113 <param argument="-mq" name="minimum_mapping_quality" type="integer" min="0" value="0" max="100" label="Minimum mapping quality" />
121 <param argument="-reward" name="reward" type="integer" min="1" value="1" max="100" label="Score for match" /> 114 <param argument="-reward" type="integer" min="1" value="1" max="100" label="Score for match" />
122 <param argument="-penalty" name="penalty" type="integer" min="-100" value="-2" max="0" label="Penalty for mismatch" /> 115 <param argument="-penalty" type="integer" min="-100" value="-2" max="0" label="Penalty for mismatch" />
123 <param argument="-gapopen " name="gapopen" type="integer" min="-100" value="-3" max="0" label="Penalty for gap opening" /> 116 <param argument="-gapopen" type="integer" min="-100" value="-3" max="0" label="Penalty for gap opening" />
124 <param argument="-gapextend" name="gapextend" type="integer" min="-100" value="-1" max="0" label="Penalty for gap extension" /> 117 <param argument="-gapextend" type="integer" min="-100" value="-1" max="0" label="Penalty for gap extension" />
125 <param argument="-per" name="pairing_reward" type="integer" min="1" value="7" max="100" label="Reward for pairing reads" /> 118 <param argument="-per" name="pairing_reward" type="integer" min="1" value="7" max="100" label="Reward for pairing reads" />
126 <param argument="-cge" name="set_cge_penalties_and_rewards" type="boolean" truevalue="-cge" falsevalue="" label="Set CGE penalties and rewards" /> 119 <param argument="-cge" name="set_cge_penalties_and_rewards" type="boolean" truevalue="-cge" falsevalue="" label="Set CGE penalties and rewards" />
127 </when> 120 </when>
128 </conditional> 121 </conditional>
129 </inputs> 122 </inputs>
130 <outputs> 123 <outputs>
131 <data name="result_overview" label="Result overview" format="tabular" from_work_dir="output.res" /> 124 <data name="result_overview" label="${tool.name} on ${on_string}: Result overview" format="tabular" from_work_dir="output.res" />
132 <data name="consensus_alignment" label="Consensus alignment" format="fasta" from_work_dir="output.aln" /> 125 <data name="consensus_alignment" label="${tool.name} on ${on_string}: Consensus alignment" format="txt" from_work_dir="output.aln" />
133 <data name="consensus_sequences" label="Consensus sequences" format="fasta" from_work_dir="output.fsa" /> 126 <data name="consensus_sequences" label="${tool.name} on ${on_string}: Consensus sequences" format="fasta" from_work_dir="output.fsa" />
134 <data name="read_mapping" label="Read mapping info" format="tabular" from_work_dir="output.frag" /> 127 <data name="read_mapping" label="${tool.name} on ${on_string}: Read mapping info" format="tabular" from_work_dir="output.frag" />
135 <data name="assembly_matrix" label="Assembly matrix" format="txt" from_work_dir="output.mat"> 128 <data name="assembly_matrix" label="${tool.name} on ${on_string}: Assembly matrix" format="tabular" from_work_dir="output.mat">
136 <filter>settings['matrix']</filter> 129 <filter>settings['matrix']</filter>
137 </data> 130 </data>
138 </outputs> 131 </outputs>
139 <tests> 132 <tests>
140 <test> 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" file="ERR884056.res" ftype="tabular"/> 143 <output name="result_overview" ftype="tabular">
147 <output name="consensus_alignment" file="ERR884056.aln" ftype="fasta"/> 144 <assert_contents>
148 <output name="consensus_sequences" file="ERR884056.fsa" ftype="fasta"/> 145 <has_n_lines n="3"/>
149 <output name="read_mapping" file="ERR884056.frag" ftype="tabular"/> 146 <has_n_columns n="11"/>
147 <has_text text="#Template"/>
148 <has_text text="b0842_1"/>
149 </assert_contents>
150 </output>
151 <output name="consensus_alignment" ftype="txt">
152 <assert_contents>
153 <has_n_lines n="170"/>
154 <has_text text="b0842_1"/>
155 <has_text text="query" n="42"/>
156 <has_text text="template" n="42"/>
157 </assert_contents>
158 </output>
159 <output name="consensus_sequences" ftype="fasta">
160 <assert_contents>
161 <has_line_matching expression="^>.*" n="2"/>
162 <has_line_matching expression="^>b0842_1"/>
163 </assert_contents>
164 </output>
165 <output name="read_mapping" ftype="tabular">
166 <assert_contents>
167 <has_n_lines n="513"/>
168 <has_n_columns n="7"/>
169 <has_text text="b0842_1"/>
170 </assert_contents>
171 </output>
150 </test> 172 </test>
151 <test> 173 <test expect_num_outputs="5">
152 <param name="single_paired_selector" value="single"/> 174 <conditional name="single_paired">
153 <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/> 175 <param name="single_paired_selector" value="single"/>
154 <param name="advanced" value="advanced"/> 176 <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/>
155 <param name="kmer_size" value="8"/> 177 </conditional>
156 <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>
157 <param name="kma_index" value="test_index"/> 183 <param name="kma_index" value="test_index"/>
158 <output name="assembly_matrix" file="ERR884056.mat" ftype="txt"/> 184 <output name="assembly_matrix" ftype="tabular">
185 <assert_contents>
186 <has_n_lines n="2578"/>
187 <has_n_columns n="7" comment="#"/>
188 <has_line_matching expression="^A&#009;.*"/>
189 <has_line_matching expression="^T&#009;.*"/>
190 <has_line_matching expression="^C&#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="1048"/>
235 <has_n_columns n="7"/>
236 <has_text text="b0842_1"/>
237 </assert_contents>
238 </output>
159 </test> 239 </test>
160 </tests> 240 </tests>
161 <help> 241 <help><![CDATA[
162 <![CDATA[
163 242
164 When the mapping is done KMA will produce the following files: 243 When the mapping is done KMA will produce the following files:
165 244
166 *.res A result overview giving the most common statistics for each mapped template. 245 * .res A result overview giving the most common statistics for each mapped template.
167 *.fsa The consensus sequences drawn from the alignments. 246 * .fsa The consensus sequences drawn from the alignments.
168 *.aln The consensus alignment of the reads against their template. 247 * .aln The consensus alignment of the reads against their template.
169 *.frag Mapping information on each mapped read, columns are: 248 * .frag Mapping information on each mapped read, columns are:
170 1. read 249 1. read
171 2. number of equally well mapping templates 250 2. number of equally well mapping templates
172 3. mapping score 251 3. mapping score
173 4. start position 252 4. start position
174 5. end position (w.r.t. template) 253 5. end position (w.r.t. template)
175 6. the choosen template. 254 6. the choosen template.
176 *.mat Base counts on each position in each template, (only if “-matrix” is enabled)
177 255
178 ]]> 256 * .mat Base counts on each position in each template, (only if `-matrix` is enabled)
179 </help> 257 ]]></help>
180 <expand macro="citations" /> 258 <expand macro="citations" />
181 </tool> 259 </tool>