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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199
author galaxyp
date Sat, 11 May 2024 16:46:46 +0000
parents 7a5ff5359b13
children
comparison
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4:7a5ff5359b13 5:d6dcd3173bdf
1 <tool id="metanovo" name="MetaNovo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09"> 1 <tool id="metanovo" name="MetaNovo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">
2 <description> 2 <description>
3 Produce targeted databases for mass spectrometry analysis. 3 Produce targeted databases for mass spectrometry analysis.
4 </description> 4 </description>
5 <requirements>
6 <requirement type="package" version="@TOOL_VERSION@">metanovo</requirement>
7 </requirements>
8 <macros> 5 <macros>
9 <token name="@TOOL_VERSION@">1.9.4</token> 6 <token name="@TOOL_VERSION@">1.9.4</token>
10 <token name="@VERSION_SUFFIX@">4</token> 7 <token name="@VERSION_SUFFIX@">4</token>
11 <token name="@SUBSTITUTION_RX@">[^\w\-\.]</token> 8 <token name="@SUBSTITUTION_RX@">[^\w\-\.]</token>
12 <import>macros_modifications.xml</import> 9 <import>macros_modifications.xml</import>
13 </macros> 10 </macros>
11 <xrefs>
12 <xref type="bio.tools">metanovo</xref>
13 </xrefs>
14 <requirements>
15 <requirement type="package" version="@TOOL_VERSION@">metanovo</requirement>
16 </requirements>
14 <command> 17 <command>
15 <![CDATA[ 18 <![CDATA[
16 #import re 19 #import re
17 #set $mgf_dir = 'mgf_files' 20 #set $mgf_dir = 'mgf_files'
18 #set $fasta_dir = 'fasta_file' 21 #set $fasta_dir = 'fasta_file'
150 153
151 <section name="processing_control" expanded="False" title="Processing Control"> 154 <section name="processing_control" expanded="False" title="Processing Control">
152 <param name="CHUNKSIZE" label="Size to split fasta for parallel processing" value="100000" type="integer" optional="true"/> 155 <param name="CHUNKSIZE" label="Size to split fasta for parallel processing" value="100000" type="integer" optional="true"/>
153 </section> 156 </section>
154 <section name="metanovo_parameters" expanded="False" title="MetaNovo Parameters"> 157 <section name="metanovo_parameters" expanded="False" title="MetaNovo Parameters">
155 <param name="mn_specificity" argument="-mn_specificity" label="Enzyme Specificity" type="select"> 158 <param argument="-mn_specificity" label="Enzyme Specificity" type="select">
156 <option selected="true" value="specific">specific</option> 159 <option selected="true" value="specific">specific</option>
157 <option value="semi-specific">semi-specific</option> 160 <option value="semi-specific">semi-specific</option>
158 <option value="unspecific">unspecific</option> 161 <option value="unspecific">unspecific</option>
159 </param> 162 </param>
160 <param name="mn_enzymes" argument="-mn_enzymes" label="Enzyme Rule" type="select"> 163 <param argument="-mn_enzymes" label="Enzyme Rule" type="select">
161 <option value="Trypsin">Trypsin</option> 164 <option value="Trypsin">Trypsin</option>
162 <option selected="true" value="Trypsin, no P rule">Trypsin, no P rule</option> 165 <option selected="true" value="Trypsin, no P rule">Trypsin, no P rule</option>
163 <option value="Whole protein">Whole protein</option> 166 <option value="Whole protein">Whole protein</option>
164 </param> 167 </param>
165 <param name="mn_max_missed_cleavages" argument="-mn_max_missed_cleavages" label="Number of enzymatic missed cleavages" value="2" type="integer" optional="true"/> 168 <param argument="-mn_max_missed_cleavages" label="Number of enzymatic missed cleavages" value="2" type="integer" optional="true"/>
166 </section> 169 </section>
167 <section name="spectrum_matching_parameters" expanded="False" title="Spectrum Matching Parameters"> 170 <section name="spectrum_matching_parameters" expanded="False" title="Spectrum Matching Parameters">
168 <param name="prec_tol" argument="-prec_tol" label="Precursor ion mass tolerance" value="10.0" type="float" optional="true"/> 171 <param argument="-prec_tol" label="Precursor ion mass tolerance" value="10.0" type="float" optional="true"/>
169 <param name="prec_ppm" argument="-prec_ppm" label="Precursor ion tolerance unit" type="select"> 172 <param argument="-prec_ppm" label="Precursor ion tolerance unit" type="select">
170 <option value="0">Da</option> 173 <option value="0">Da</option>
171 <option selected="true" value="1">ppm</option> 174 <option selected="true" value="1">ppm</option>
172 </param> 175 </param>
173 <param name="frag_tol" argument="-frag_tol" label="Fragment ion mass tolerance" value="0.05" type="float" optional="true"/> 176 <param argument="-frag_tol" label="Fragment ion mass tolerance" value="0.05" type="float" optional="true"/>
174 <param name="frag_ppm" argument="-frag_ppm" label="Fragment ion tolerance unit" type="select"> 177 <param argument="-frag_ppm" label="Fragment ion tolerance unit" type="select">
175 <option selected="true" value="0">Da</option> 178 <option selected="true" value="0">Da</option>
176 <option value="1">ppm</option> 179 <option value="1">ppm</option>
177 </param> 180 </param>
178 <param name="digestion" argument="-digestion" label="Digestion" type="select"> 181 <param argument="-digestion" label="Digestion" type="select">
179 <option selected="true" value="0">Enzyme</option> 182 <option selected="true" value="0">Enzyme</option>
180 <option value="1">Unspecific</option> 183 <option value="1">Unspecific</option>
181 <option value="2">Whole Protein</option> 184 <option value="2">Whole Protein</option>
182 </param> 185 </param>
183 <param name="enzyme" argument="-enzyme" label="Enzyme" type="select" multiple="true"> 186 <param argument="-enzyme" label="Enzyme" type="select" multiple="true">
184 <option value="Trypsin">Trypsin</option> 187 <option value="Trypsin">Trypsin</option>
185 <option selected="true" value="Trypsin (no P rule)">Trypsin (no P rule)</option> 188 <option selected="true" value="Trypsin (no P rule)">Trypsin (no P rule)</option>
186 <option value="Arg-C">Arg-C</option> 189 <option value="Arg-C">Arg-C</option>
187 <option value="Arg-C (no P rule)">Arg-C (no P rule)</option> 190 <option value="Arg-C (no P rule)">Arg-C (no P rule)</option>
188 <option value="Arg-N">Arg-N</option> 191 <option value="Arg-N">Arg-N</option>
197 <option value="Pepsin A">Pepsin A</option> 200 <option value="Pepsin A">Pepsin A</option>
198 <option value="CNBr">CNBr</option> 201 <option value="CNBr">CNBr</option>
199 <option value="Thermolysin">Thermolysin</option> 202 <option value="Thermolysin">Thermolysin</option>
200 <option value="LysargiNase">LysargiNase</option> 203 <option value="LysargiNase">LysargiNase</option>
201 </param> 204 </param>
202 <param name="specificity" argument="-specificity" label="Specificity" type="select"> 205 <param argument="-specificity" label="Specificity" type="select">
203 <option selected="true" value="0">Specific</option> 206 <option selected="true" value="0">Specific</option>
204 <option value="1">Semi-Specific</option> 207 <option value="1">Semi-Specific</option>
205 <option value="2">N-term Specific</option> 208 <option value="2">N-term Specific</option>
206 <option value="3">C-term Specific</option> 209 <option value="3">C-term Specific</option>
207 </param> 210 </param>
208 <param name="mc" argument="-mc" label="Number of allowed missed cleavages" value="2" type="text" optional="true" help="If more than one enzyme was used, please provide the missed cleavages for every enzyme in the same order, with a comma separated list, e.g. &quot;2, 1&quot;."/> 211 <param argument="-mc" label="Number of allowed missed cleavages" value="2" type="text" optional="true" help="If more than one enzyme was used, please provide the missed cleavages for every enzyme in the same order, with a comma separated list, e.g. &quot;2, 1&quot;."/>
209 <param name="fixed_mods" argument="-fixed_mods" label="Fixed modifications as comma separated list" type="select" multiple="true"> 212 <param argument="-fixed_mods" label="Fixed modifications as comma separated list" type="select" multiple="true">
210 <expand macro="fixed_modifications"/> 213 <expand macro="fixed_modifications"/>
211 </param> 214 </param>
212 <param name="variable_mods" argument="-variable_mods" label="Variable modifications as comma separated list" type="select" multiple="true"> 215 <param argument="-variable_mods" label="Variable modifications as comma separated list" type="select" multiple="true">
213 <expand macro="variable_modifications"/> 216 <expand macro="variable_modifications"/>
214 </param> 217 </param>
215 <param name="min_charge" argument="-min_charge" label="Minimal charge to search for" value="2" type="integer" optional="true"/> 218 <param argument="-min_charge" label="Minimal charge to search for" value="2" type="integer" optional="true"/>
216 <param name="max_charge" argument="-max_charge" label="Maximal charge to search for" value="4" type="integer" optional="true"/> 219 <param argument="-max_charge" label="Maximal charge to search for" value="4" type="integer" optional="true"/>
217 <param name="fi" argument="-fi" label="Type of forward ion searched" value="b" type="text" optional="true"/> 220 <param argument="-fi" label="Type of forward ion searched" value="b" type="text" optional="true"/>
218 <param name="ri" argument="-ri" label="Type of rewind ion searched" value="y" type="text" optional="true"/> 221 <param argument="-ri" label="Type of rewind ion searched" value="y" type="text" optional="true"/>
219 <param name="min_isotope" argument="-min_isotope" label="Minimum precursor isotope" value="0" type="integer" optional="true"/> 222 <param argument="-min_isotope" label="Minimum precursor isotope" value="0" type="integer" optional="true"/>
220 <param name="max_isotope" argument="-max_isotope" label="Maximum precursor isotope" value="1" type="integer" optional="true"/> 223 <param argument="-max_isotope" label="Maximum precursor isotope" value="1" type="integer" optional="true"/>
221 </section> 224 </section>
222 <section name="spectrum_annotation" expanded="False" title="Spectrum Annotation"> 225 <section name="spectrum_annotation" expanded="False" title="Spectrum Annotation">
223 <param name="annotation_level" argument="-annotation_level" label="The intensity threshold to consider for annotation" value="0.75" type="float" optional="true" help="Using percentiles, 0.75 means that the 25% most intense peaks will be annotated."/> 226 <param argument="-annotation_level" label="The intensity threshold to consider for annotation" value="0.75" type="float" optional="true" help="Using percentiles, 0.75 means that the 25% most intense peaks will be annotated."/>
224 <param name="annotation_high_resolution" argument="-annotation_high_resolution" label="If true the most accurate peak will be selected within the m/z tolerance." truevalue="1" falsevalue="0" type="boolean" checked="true"/> 227 <param argument="-annotation_high_resolution" label="If true the most accurate peak will be selected within the m/z tolerance." truevalue="1" falsevalue="0" type="boolean" checked="true"/>
225 </section> 228 </section>
226 <section name="sequence_matching" expanded="False" title="Sequence Matching"> 229 <section name="sequence_matching" expanded="False" title="Sequence Matching">
227 <param name="sequence_index_type" argument="-sequence_index_type" label="sequence_index_type (deprecated)" value="0" type="integer" optional="true"/> 230 <param argument="-sequence_index_type" label="sequence_index_type (deprecated)" value="0" type="integer" optional="true"/>
228 <param name="sequence_matching_type" argument="-sequence_matching_type" label="The peptide to protein sequence matching type" type="select"> 231 <param argument="-sequence_matching_type" label="The peptide to protein sequence matching type" type="select">
229 <option value="0">Character Sequence</option> 232 <option value="0">Character Sequence</option>
230 <option value="1">Amino Acids</option> 233 <option value="1">Amino Acids</option>
231 <option selected="true" value="2">Indistinguishable Amino Acids</option> 234 <option selected="true" value="2">Indistinguishable Amino Acids</option>
232 </param> 235 </param>
233 <param name="sequence_matching_x" argument="-sequence_matching_x" label="The maximal share of Xs in a sequence, 0.25 means 25% of X's" value="0.25" type="float" optional="true"/> 236 <param argument="-sequence_matching_x" label="The maximal share of Xs in a sequence, 0.25 means 25% of X's" value="0.25" type="float" optional="true"/>
234 </section> 237 </section>
235 <section name="import_filters" expanded="False" title="Import Filters"> 238 <section name="import_filters" expanded="False" title="Import Filters">
236 <param name="import_peptide_length_min" argument="-import_peptide_length_min" label="The minimal peptide length to consider when importing identification files" value="8" type="integer" optional="true"/> 239 <param argument="-import_peptide_length_min" label="The minimal peptide length to consider when importing identification files" value="8" type="integer" optional="true"/>
237 <param name="import_peptide_length_max" argument="-import_peptide_length_max" label="The maximal peptide length to consider when importing identification files" value="30" type="integer" optional="true"/> 240 <param argument="-import_peptide_length_max" label="The maximal peptide length to consider when importing identification files" value="30" type="integer" optional="true"/>
238 <param name="import_precursor_mz_ppm" argument="-import_precurosor_mz_ppm [sic]" label="Maximal precursor ion deviation unit" type="select"> 241 <param argument="-import_precursor_mz_ppm" label="Maximal precursor ion deviation unit" type="select">
239 <option selected="true" value="0">Da</option> 242 <option selected="true" value="0">Da</option>
240 <option value="1">ppm</option> 243 <option value="1">ppm</option>
241 </param> 244 </param>
242 <param name="exclude_unknown_ptms" argument="-exclude_unknown_ptms" label="Peptides presenting unrecognized PTMs will be excluded" truevalue="1" falsevalue="0" type="boolean" checked="true"/> 245 <param argument="-exclude_unknown_ptms" label="Peptides presenting unrecognized PTMs will be excluded" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
243 </section> 246 </section>
244 <section name="ptm_localization" expanded="False" title="PTM Localization"> 247 <section name="ptm_localization" expanded="False" title="PTM Localization">
245 <param name="ptm_score" argument="-ptm_score" label="The PTM probabilistic score to use for modification localization" type="select"> 248 <param argument="-ptm_score" label="The PTM probabilistic score to use for modification localization" type="select">
246 <option value="0">A-score</option> 249 <option value="0">A-score</option>
247 <option selected="true" value="1">PhosphoRS</option> 250 <option selected="true" value="1">PhosphoRS</option>
248 <option value="2">None</option> 251 <option value="2">None</option>
249 </param> 252 </param>
250 <param name="score_neutral_losses" argument="-score_neutral_losses" label="Include neutral losses in spectrum annotation of the PTM score" truevalue="1" falsevalue="0" type="boolean" checked="false"/> 253 <param argument="-score_neutral_losses" label="Include neutral losses in spectrum annotation of the PTM score" truevalue="1" falsevalue="0" type="boolean" checked="false"/>
251 <param name="ptm_sequence_matching_type" argument="-ptm_sequence_matching_type" label="The modification to peptide sequence matching type" type="select"> 254 <param argument="-ptm_sequence_matching_type" label="The modification to peptide sequence matching type" type="select">
252 <option value="0">Character Sequence</option> 255 <option value="0">Character Sequence</option>
253 <option selected="true" value="1">Amino Acids</option> 256 <option selected="true" value="1">Amino Acids</option>
254 <option value="2">Indistinguishable Amino Acids</option> 257 <option value="2">Indistinguishable Amino Acids</option>
255 </param> 258 </param>
256 <param name="ptm_alignment" argument="-ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" truevalue="1" falsevalue="0" type="boolean" checked="true"/> 259 <param argument="-ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
257 </section> 260 </section>
258 <section name="gene_annotation" expanded="False" title="Gene Annotation"> 261 <section name="gene_annotation" expanded="False" title="Gene Annotation">
259 <param name="useGeneMapping" argument="-useGeneMapping" label="Use and save gene mappings along with the project" truevalue="1" falsevalue="0" type="boolean" checked="true" help="UniProt databases only"/> 262 <param argument="-useGeneMapping" label="Use and save gene mappings along with the project" truevalue="1" falsevalue="0" type="boolean" checked="true" help="UniProt databases only"/>
260 <param name="updateGeneMapping" argument="-updateGeneMapping" label="Update gene mappings automatically from Ensembl" truevalue="1" falsevalue="0" type="boolean" checked="true" help="UniProt databases only"/> 263 <param argument="-updateGeneMapping" label="Update gene mappings automatically from Ensembl" truevalue="1" falsevalue="0" type="boolean" checked="true" help="UniProt databases only"/>
261 </section> 264 </section>
262 <section name="protein_inference" expanded="False" title="Protein Inference"> 265 <section name="protein_inference" expanded="False" title="Protein Inference">
263 <param name="simplify_groups" argument="-simplify_groups" label="Simplify protein groups" truevalue="1" falsevalue="0" type="boolean" checked="true"/> 266 <param argument="-simplify_groups" label="Simplify protein groups" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
264 <param name="simplify_score" argument="-simplify_score" label="Simplify protein groups based on the PeptideShaker target/decoy score" truevalue="1" falsevalue="0" type="boolean" checked="true"/> 267 <param argument="-simplify_score" label="Simplify protein groups based on the PeptideShaker target/decoy score" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
265 <param name="simplify_enzymaticity" argument="-simplify_enzymaticity" label="Simplify protein groups based on the peptide enzymaticity" truevalue="1" falsevalue="0" type="boolean" checked="true"/> 268 <param argument="-simplify_enzymaticity" label="Simplify protein groups based on the peptide enzymaticity" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
266 <param name="simplify_evidence" argument="-simplify_evidence" label="Simplify protein groups based on the UniProt protein evidence" truevalue="1" falsevalue="0" type="boolean" checked="true"/> 269 <param argument="-simplify_evidence" label="Simplify protein groups based on the UniProt protein evidence" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
267 <param name="simplify_uncharacterized" argument="-simplify_uncharacterized" label="Simplify protein groups based on the protein characterization" truevalue="1" falsevalue="0" type="boolean" checked="true"/> 270 <param argument="-simplify_uncharacterized" label="Simplify protein groups based on the protein characterization" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
268 </section> 271 </section>
269 <section name="validation_levels" expanded="False" title="Validation Levels"> 272 <section name="validation_levels" expanded="False" title="Validation Levels">
270 <param name="psm_fdr" argument="-psm_fdr" label="FDR at the PSM level in percent" value="1" type="integer" optional="true"/> 273 <param argument="-psm_fdr" label="FDR at the PSM level in percent" value="1" type="integer" optional="true"/>
271 <param name="peptide_fdr" argument="-peptide_fdr" label="FDR at the peptide level in percent" value="1" type="integer" optional="true"/> 274 <param argument="-peptide_fdr" label="FDR at the peptide level in percent" value="1" type="integer" optional="true"/>
272 <param name="protein_fdr" argument="-protein_fdr" label="FDR at the protein level in percent" value="1" type="integer" optional="true"/> 275 <param argument="-protein_fdr" label="FDR at the protein level in percent" value="1" type="integer" optional="true"/>
273 <param name="group_psms" argument="-group_psms" label="Group PSMs by charge for scoring and validation" truevalue="1" falsevalue="0" type="boolean" checked="true"/> 276 <param argument="-group_psms" label="Group PSMs by charge for scoring and validation" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
274 <param name="group_peptides" argument="-group_peptides" label="Group peptides by modification status for scoring and validation" truevalue="1" falsevalue="0" type="boolean" checked="true"/> 277 <param argument="-group_peptides" label="Group peptides by modification status for scoring and validation" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
275 <param name="merge_subgroups" argument="-group_peptides" label="Merge small PSM and peptide groups for scoring and validation" truevalue="1" falsevalue="0" type="boolean" checked="true"/> 278 <param argument="-merge_subgroups" label="Merge small PSM and peptide groups for scoring and validation" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
276 </section> 279 </section>
277 <section name="fraction_analysis" expanded="False" title="Fraction Analysis"> 280 <section name="fraction_analysis" expanded="False" title="Fraction Analysis">
278 <param name="protein_fraction_mw_confidence" argument="-protein_fraction_mw_confidence" label="Minimum confidence required for a protein in the fraction MW plot" value="95.0" type="float" optional="true"/> 281 <param argument="-protein_fraction_mw_confidence" label="Minimum confidence required for a protein in the fraction MW plot" value="95.0" type="float" optional="true"/>
279 </section> 282 </section>
280 <section name="directag" expanded="False" title="DirecTag"> 283 <section name="directag" expanded="False" title="DirecTag">
281 <param name="directag_tic_cutoff" argument="-directag_tic_cutoff" label="TIC cutoff in percent" value="85" type="integer" optional="true"/> 284 <param argument="-directag_tic_cutoff" label="TIC cutoff in percent" value="85" type="integer" optional="true"/>
282 <param name="directag_max_peak_count" argument="-directag_max_peak_count" label="Max peak count" value="400" type="integer" optional="true"/> 285 <param argument="-directag_max_peak_count" label="Max peak count" value="400" type="integer" optional="true"/>
283 <param name="directag_intensity_classes" argument="-directag_intensity_classes" label="Number of intensity classes" value="3" type="integer" optional="true"/> 286 <param argument="-directag_intensity_classes" label="Number of intensity classes" value="3" type="integer" optional="true"/>
284 <param name="directag_adjust_precursor" argument="-directag_adjust_precursor" label="Adjust precursor" truevalue="1" falsevalue="0" type="boolean" checked="false"/> 287 <param argument="-directag_adjust_precursor" label="Adjust precursor" truevalue="1" falsevalue="0" type="boolean" checked="false"/>
285 <param name="directag_min_adjustment" argument="-directag_min_adjustment" label="Minimum precursor adjustment" value="-2.5" type="float" optional="true"/> 288 <param argument="-directag_min_adjustment" label="Minimum precursor adjustment" value="-2.5" type="float" optional="true"/>
286 <param name="directag_max_adjustment" argument="-directag_max_adjustment" label="Maximum precursor adjustment" value="2.5" type="float" optional="true"/> 289 <param argument="-directag_max_adjustment" label="Maximum precursor adjustment" value="2.5" type="float" optional="true"/>
287 <param name="directag_adjustment_step" argument="-directag_adjustment_step" label="Precursor adjustment step" value="0.1" type="float" optional="true"/> 290 <param argument="-directag_adjustment_step" label="Precursor adjustment step" value="0.1" type="float" optional="true"/>
288 <param name="directag_charge_states" argument="-directag_charge_states" label="Number of charge states considered" value="3" type="integer" optional="true"/> 291 <param argument="-directag_charge_states" label="Number of charge states considered" value="3" type="integer" optional="true"/>
289 <param name="directag_ms_charge_state" argument="-directag_ms_charge_state" label="Use charge state from M spectrum" truevalue="1" falsevalue="0" type="boolean" checked="false"/> 292 <param argument="-directag_ms_charge_state" label="Use charge state from M spectrum" truevalue="1" falsevalue="0" type="boolean" checked="false"/>
290 <param name="directag_duplicate_spectra" argument="-directag_duplicate_spectra" label="Duplicate spectra per charge" truevalue="1" falsevalue="0" type="boolean" checked="true"/> 293 <param argument="-directag_duplicate_spectra" label="Duplicate spectra per charge" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
291 <param name="directag_deisotoping" argument="-directag_deisotoping" label="Deisotoping mode" type="select"> 294 <param argument="-directag_deisotoping" label="Deisotoping mode" type="select">
292 <option selected="true" value="0">No deisotoping</option> 295 <option selected="true" value="0">No deisotoping</option>
293 <option value="1">Precursor only</option> 296 <option value="1">Precursor only</option>
294 <option value="2">Precursor and candidate</option> 297 <option value="2">Precursor and candidate</option>
295 </param> 298 </param>
296 <param name="directag_isotope_tolerance" argument="-directag_isotope_tolerance" label="Isotope mz tolerance" value="0.25" type="float" optional="true"/> 299 <param argument="-directag_isotope_tolerance" label="Isotope mz tolerance" value="0.25" type="float" optional="true"/>
297 <param name="directag_complement_tolerance" argument="-directag_complement_tolerance" label="Complement mz tolerance" value="0.5" type="float" optional="true"/> 300 <param argument="-directag_complement_tolerance" label="Complement mz tolerance" value="0.5" type="float" optional="true"/>
298 <param name="directag_tag_length" argument="-directag_tag_length" label="Tag length" value="4" type="integer" optional="true"/> 301 <param argument="-directag_tag_length" label="Tag length" value="4" type="integer" optional="true"/>
299 <param name="directag_max_var_mods" argument="-directag_max_var_mods" label="Maximum variable modifications per sequence" value="2" type="integer" optional="true"/> 302 <param argument="-directag_max_var_mods" label="Maximum variable modifications per sequence" value="2" type="integer" optional="true"/>
300 <param name="directag_max_tag_count" argument="-directag_max_tag_count" label="Maximum tag count" value="5" type="integer" optional="true"/> 303 <param argument="-directag_max_tag_count" label="Maximum tag count" value="5" type="integer" optional="true"/>
301 <param name="directag_intensity_weight" argument="-directag_intensity_weight" label="Intensity score weight" value="1.0" type="float" optional="true"/> 304 <param argument="-directag_intensity_weight" label="Intensity score weight" value="1.0" type="float" optional="true"/>
302 <param name="directag_fidelity_weight" argument="-directag_fidelity_weight" label="Fidelity score weight" value="1.0" type="float" optional="true"/> 305 <param argument="-directag_fidelity_weight" label="Fidelity score weight" value="1.0" type="float" optional="true"/>
303 <param name="directag_complement_weight" argument="-directag_complement_weight" label="Complement score weight" value="1.0" type="float" optional="true"/> 306 <param argument="-directag_complement_weight" label="Complement score weight" value="1.0" type="float" optional="true"/>
304 </section> 307 </section>
305 </inputs> 308 </inputs>
306 <outputs> 309 <outputs>
307 <data name="output_fasta" format="fasta" from_work_dir="metanovo/metanovo.fasta" label="${tool.name} on ${on_string}: FASTA"/> 310 <data name="output_fasta" format="fasta" from_work_dir="metanovo/metanovo.fasta" label="${tool.name} on ${on_string}: FASTA"/>
308 <data name="output_csv" format="csv" from_work_dir="metanovo/metanovo.csv" label="${tool.name} on ${on_string}: CSV"/> 311 <data name="output_csv" format="csv" from_work_dir="metanovo/metanovo.csv" label="${tool.name} on ${on_string}: CSV"/>