Mercurial > repos > iuc > kma

comparison kma_map.xml @ 2:98099e4da1fd draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 812bb0a31f030096bf1b0836f64e76b820c8e2c2
author iuc
date Fri, 14 Jun 2024 21:15:44 +0000
parents 95ab864b281a
children
comparison
equal deleted inserted replaced
1:95ab864b281a 2:98099e4da1fd
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@+galaxy0" profile="23.0">
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>
105 <when value="advanced"> 105 <when value="advanced">
106 <param argument="-k" name="kmer_size" type="integer" min="4" value="16" max="32" label="Kmer Size" /> 106 <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"/> 107 <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" /> 108 <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" /> 109 <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" /> 110 <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" /> 111 <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" /> 112 <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" /> 113 <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" /> 114 <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" /> 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" />
116 <param argument="-Sparse" name="only_count_kmers" type="boolean" truevalue="-Sparse" falsevalue="" label="Only count kmers" /> 116 <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"/> 117 <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" /> 118 <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" /> 119 <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" /> 120 <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" /> 121 <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" /> 122 <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" /> 123 <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" /> 124 <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" /> 125 <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" /> 126 <param argument="-cge" name="set_cge_penalties_and_rewards" type="boolean" truevalue="-cge" falsevalue="" label="Set CGE penalties and rewards" />
127 </when> 127 </when>
128 </conditional> 128 </conditional>
129 </inputs> 129 </inputs>
130 <outputs> 130 <outputs>
131 <data name="result_overview" label="Result overview" format="tabular" from_work_dir="output.res" /> 131 <data name="result_overview" label="${tool.name} on ${on_string}: Result overview" format="tabular" from_work_dir="output.res" />
132 <data name="consensus_alignment" label="Consensus alignment" format="fasta" from_work_dir="output.aln" /> 132 <data name="consensus_alignment" label="${tool.name} on ${on_string}: Consensus alignment" format="txt" from_work_dir="output.aln" />
133 <data name="consensus_sequences" label="Consensus sequences" format="fasta" from_work_dir="output.fsa" /> 133 <data name="consensus_sequences" label="${tool.name} on ${on_string}: Consensus sequences" format="fasta" from_work_dir="output.fsa" />
134 <data name="read_mapping" label="Read mapping info" format="tabular" from_work_dir="output.frag" /> 134 <data name="read_mapping" label="${tool.name} on ${on_string}: Read mapping info" format="tabular" from_work_dir="output.frag" />
135 <data name="assembly_matrix" label="Assembly matrix" format="txt" from_work_dir="output.mat"> 135 <data name="assembly_matrix" label="${tool.name} on ${on_string}: Assembly matrix" format="tabular" from_work_dir="output.mat">
136 <filter>settings['matrix']</filter> 136 <filter>settings['matrix']</filter>
137 </data> 137 </data>
138 </outputs> 138 </outputs>
139 <tests> 139 <tests>
140 <test> 140 <test expect_num_outputs="4">
141 <param name="single_paired_selector" value="single"/> 141 <param name="single_paired_selector" value="single"/>
142 <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/> 142 <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/>
143 <param name="advanced" value="advanced"/> 143 <param name="advanced" value="advanced"/>
144 <param name="kmer_size" value="8"/> 144 <param name="kmer_size" value="8"/>
145 <param name="kma_index" value="test_index"/> 145 <param name="kma_index" value="test_index"/>
146 <output name="result_overview" file="ERR884056.res" ftype="tabular"/> 146 <output name="result_overview" ftype="tabular">
147 <output name="consensus_alignment" file="ERR884056.aln" ftype="fasta"/> 147 <assert_contents>
148 <output name="consensus_sequences" file="ERR884056.fsa" ftype="fasta"/> 148 <has_n_lines n="3"/>
149 <output name="read_mapping" file="ERR884056.frag" ftype="tabular"/> 149 <has_n_columns n="11"/>
150 <has_text text="#Template"/>
151 <has_text text="b0842_1"/>
152 </assert_contents>
153 </output>
154 <output name="consensus_alignment" ftype="txt">
155 <assert_contents>
156 <has_n_lines n="170"/>
157 <has_text text="b0842_1"/>
158 <has_text text="query" n="42"/>
159 <has_text text="template" n="42"/>
160 </assert_contents>
161 </output>
162 <output name="consensus_sequences" ftype="fasta">
163 <assert_contents>
164 <has_line_matching expression="^>.*" n="2"/>
165 <has_line_matching expression="^>b0842_1"/>
166 </assert_contents>
167 </output>
168 <output name="read_mapping" ftype="tabular">
169 <assert_contents>
170 <has_n_lines n="492"/>
171 <has_n_columns n="7"/>
172 <has_text text="b0842_1"/>
173 </assert_contents>
174 </output>
150 </test> 175 </test>
151 <test> 176 <test expect_num_outputs="5">
152 <param name="single_paired_selector" value="single"/> 177 <param name="single_paired_selector" value="single"/>
153 <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/> 178 <param name="input_sequences" value="ERR884056_ecoli_b0842.mapped_R1.fastq" ftype="fastq"/>
154 <param name="advanced" value="advanced"/> 179 <param name="advanced" value="advanced"/>
155 <param name="kmer_size" value="8"/> 180 <param name="kmer_size" value="8"/>
156 <param name="matrix" value="true"/> 181 <param name="matrix" value="true"/>
157 <param name="kma_index" value="test_index"/> 182 <param name="kma_index" value="test_index"/>
158 <output name="assembly_matrix" file="ERR884056.mat" ftype="txt"/> 183 <output name="assembly_matrix" ftype="tabular">
184 <assert_contents>
185 <has_n_lines n="2553"/>
186 <has_n_columns n="7" comment="#"/>
187 <has_line_matching expression="^A&#009;.*"/>
188 <has_line_matching expression="^T&#009;.*"/>
189 <has_line_matching expression="^C&#009;.*"/>
190 <has_line_matching expression="^G&#009;.*"/>
191 </assert_contents>
192 </output>
159 </test> 193 </test>
160 </tests> 194 </tests>
161 <help> 195 <help><![CDATA[
162 <![CDATA[
163 196
164 When the mapping is done KMA will produce the following files: 197 When the mapping is done KMA will produce the following files:
165 198
166 *.res A result overview giving the most common statistics for each mapped template. 199 * .res A result overview giving the most common statistics for each mapped template.
167 *.fsa The consensus sequences drawn from the alignments. 200 * .fsa The consensus sequences drawn from the alignments.
168 *.aln The consensus alignment of the reads against their template. 201 * .aln The consensus alignment of the reads against their template.
169 *.frag Mapping information on each mapped read, columns are: 202 * .frag Mapping information on each mapped read, columns are:
170 1. read 203 1. read
171 2. number of equally well mapping templates 204 2. number of equally well mapping templates
172 3. mapping score 205 3. mapping score
173 4. start position 206 4. start position
174 5. end position (w.r.t. template) 207 5. end position (w.r.t. template)
175 6. the choosen template. 208 6. the choosen template.
176 *.mat Base counts on each position in each template, (only if “-matrix” is enabled)
177 209
178 ]]> 210 * .mat Base counts on each position in each template, (only if `-matrix` is enabled)
179 </help> 211 ]]></help>
180 <expand macro="citations" /> 212 <expand macro="citations" />
181 </tool> 213 </tool>