Mercurial > repos > galaxyp > openms_percolatoradapter
comparison PercolatorAdapter.xml @ 6:147aaac03456 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author | galaxyp |
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date | Tue, 13 Oct 2020 20:29:32 +0000 |
parents | e7881a82b56d |
children | 016964c597f5 |
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5:dbfb6bb95754 | 6:147aaac03456 |
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30 #end if | 30 #end if |
31 mkdir out && | 31 mkdir out && |
32 #if "out_pin_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | 32 #if "out_pin_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
33 mkdir out_pin && | 33 mkdir out_pin && |
34 #end if | 34 #end if |
35 #if "out_pout_target_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
36 mkdir out_pout_target && | |
37 #end if | |
38 #if "out_pout_decoy_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
39 mkdir out_pout_decoy && | |
40 #end if | |
41 #if "out_pout_target_proteins_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
42 mkdir out_pout_target_proteins && | |
43 #end if | |
44 #if "out_pout_decoy_proteins_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
45 mkdir out_pout_decoy_proteins && | |
46 #end if | |
35 #if "weights_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | 47 #if "weights_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
36 mkdir weights && | 48 mkdir weights && |
37 #end if | 49 #end if |
38 #if $adv_opts_cond.adv_opts_selector=='advanced': | 50 #if $adv_opts_cond.adv_opts_selector=='advanced': |
39 #if $adv_opts_cond.init_weights: | 51 #if $adv_opts_cond.init_weights: |
68 'out/output.${out_type}' | 80 'out/output.${out_type}' |
69 #if "out_pin_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | 81 #if "out_pin_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
70 -out_pin | 82 -out_pin |
71 'out_pin/output.${gxy2omsext("tabular")}' | 83 'out_pin/output.${gxy2omsext("tabular")}' |
72 #end if | 84 #end if |
85 #if "out_pout_target_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
86 -out_pout_target | |
87 'out_pout_target/output.${gxy2omsext("tabular")}' | |
88 #end if | |
89 #if "out_pout_decoy_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
90 -out_pout_decoy | |
91 'out_pout_decoy/output.${gxy2omsext("tabular")}' | |
92 #end if | |
93 #if "out_pout_target_proteins_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
94 -out_pout_target_proteins | |
95 'out_pout_target_proteins/output.${gxy2omsext("tabular")}' | |
96 #end if | |
97 #if "out_pout_decoy_proteins_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
98 -out_pout_decoy_proteins | |
99 'out_pout_decoy_proteins/output.${gxy2omsext("tabular")}' | |
100 #end if | |
73 #if "weights_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | 101 #if "weights_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
74 -weights | 102 -weights |
75 'weights/output.${gxy2omsext("txt")}' | 103 'weights/output.${gxy2omsext("tabular")}' |
76 #end if | 104 #end if |
77 #if $adv_opts_cond.adv_opts_selector=='advanced': | 105 #if $adv_opts_cond.adv_opts_selector=='advanced': |
78 #if $adv_opts_cond.init_weights: | 106 #if $adv_opts_cond.init_weights: |
79 -init-weights | 107 -init_weights |
80 'adv_opts_cond.init_weights/${re.sub("[^\w\-_]", "_", $adv_opts_cond.init_weights.element_identifier)}.$gxy2omsext($adv_opts_cond.init_weights.ext)' | 108 'adv_opts_cond.init_weights/${re.sub("[^\w\-_]", "_", $adv_opts_cond.init_weights.element_identifier)}.$gxy2omsext($adv_opts_cond.init_weights.ext)' |
81 #end if | 109 #end if |
82 #if $adv_opts_cond.fasta: | 110 #if $adv_opts_cond.fasta: |
83 -fasta | 111 -fasta |
84 'adv_opts_cond.fasta/${re.sub("[^\w\-_]", "_", $adv_opts_cond.fasta.element_identifier)}.$gxy2omsext($adv_opts_cond.fasta.ext)' | 112 'adv_opts_cond.fasta/${re.sub("[^\w\-_]", "_", $adv_opts_cond.fasta.element_identifier)}.$gxy2omsext($adv_opts_cond.fasta.ext)' |
91 ## Postprocessing | 119 ## Postprocessing |
92 && mv 'out/output.${out_type}' '$out' | 120 && mv 'out/output.${out_type}' '$out' |
93 #if "out_pin_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | 121 #if "out_pin_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
94 && mv 'out_pin/output.${gxy2omsext("tabular")}' '$out_pin' | 122 && mv 'out_pin/output.${gxy2omsext("tabular")}' '$out_pin' |
95 #end if | 123 #end if |
124 #if "out_pout_target_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
125 && mv 'out_pout_target/output.${gxy2omsext("tabular")}' '$out_pout_target' | |
126 #end if | |
127 #if "out_pout_decoy_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
128 && mv 'out_pout_decoy/output.${gxy2omsext("tabular")}' '$out_pout_decoy' | |
129 #end if | |
130 #if "out_pout_target_proteins_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
131 && mv 'out_pout_target_proteins/output.${gxy2omsext("tabular")}' '$out_pout_target_proteins' | |
132 #end if | |
133 #if "out_pout_decoy_proteins_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
134 && mv 'out_pout_decoy_proteins/output.${gxy2omsext("tabular")}' '$out_pout_decoy_proteins' | |
135 #end if | |
96 #if "weights_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | 136 #if "weights_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
97 && mv 'weights/output.${gxy2omsext("txt")}' '$weights' | 137 && mv 'weights/output.${gxy2omsext("tabular")}' '$weights' |
98 #end if | 138 #end if |
99 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS | 139 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
100 && mv '@EXECUTABLE@.ctd' '$ctd_out' | 140 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
101 #end if]]></command> | 141 #end if]]></command> |
102 <configfiles> | 142 <configfiles> |
127 <option value="glu-c">glu-c</option> | 167 <option value="glu-c">glu-c</option> |
128 <option value="trypsin" selected="true">trypsin</option> | 168 <option value="trypsin" selected="true">trypsin</option> |
129 <option value="trypsinp">trypsinp</option> | 169 <option value="trypsinp">trypsinp</option> |
130 <expand macro="list_string_san"/> | 170 <expand macro="list_string_san"/> |
131 </param> | 171 </param> |
132 <param name="peptide_level_fdrs" argument="-peptide-level-fdrs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculate peptide-level FDRs instead of PSM-level FDRs" help=""/> | 172 <param name="peptide_level_fdrs" argument="-peptide_level_fdrs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculate peptide-level FDRs instead of PSM-level FDRs" help=""/> |
133 <param name="protein_level_fdrs" argument="-protein-level-fdrs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the picked protein-level FDR to infer protein probabilities" help="Use the -fasta option and -decoy-pattern to set the Fasta file and decoy pattern"/> | 173 <param name="protein_level_fdrs" argument="-protein_level_fdrs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the picked protein-level FDR to infer protein probabilities" help="Use the -fasta option and -decoy_pattern to set the Fasta file and decoy pattern"/> |
134 <param name="osw_level" argument="-osw_level" type="text" optional="true" value="ms2" label="OSW: Either "ms1", "ms2" or "transition"; the data level selected for scoring" help=""> | 174 <param name="osw_level" argument="-osw_level" type="text" optional="true" value="ms2" label="OSW: Either "ms1", "ms2" or "transition"; the data level selected for scoring" help=""> |
135 <expand macro="list_string_san"/> | 175 <expand macro="list_string_san"/> |
136 </param> | 176 </param> |
137 <param name="score_type" argument="-score_type" display="radio" type="select" optional="false" label="Type of the peptide main score" help=""> | 177 <param name="score_type" argument="-score_type" display="radio" type="select" optional="false" label="Type of the peptide main score" help=""> |
138 <option value="q-value" selected="true">q-value</option> | 178 <option value="q-value" selected="true">q-value</option> |
139 <option value="pep">pep</option> | 179 <option value="pep">pep</option> |
140 <option value="svm">svm</option> | 180 <option value="svm">svm</option> |
141 <expand macro="list_string_san"/> | 181 <expand macro="list_string_san"/> |
142 </param> | 182 </param> |
143 <expand macro="adv_opts_macro"> | 183 <expand macro="adv_opts_macro"> |
144 <param name="generic_feature_set" argument="-generic-feature-set" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use only generic" help="(i.e. not search engine specific) features. Generating search engine specific features for common search engines by PSMFeatureExtractor will typically boost the identification rate significantly"/> | 184 <param name="generic_feature_set" argument="-generic_feature_set" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use only generic" help="(i.e. not search engine specific) features. Generating search engine specific features for common search engines by PSMFeatureExtractor will typically boost the identification rate significantly"/> |
145 <param name="subset_max_train" argument="-subset-max-train" type="integer" optional="true" value="0" label="Only train an SVM on a subset of <x> PSMs, and use the resulting score vector to evaluate the other PSMs" help="Recommended when analyzing huge numbers (>1 million) of PSMs. When set to 0, all PSMs are used for training as normal"/> | 185 <param name="subset_max_train" argument="-subset_max_train" type="integer" optional="true" value="0" label="Only train an SVM on a subset of <x> PSMs, and use the resulting score vector to evaluate the other PSMs" help="Recommended when analyzing huge numbers (>1 million) of PSMs. When set to 0, all PSMs are used for training as normal"/> |
146 <param name="cpos" argument="-cpos" type="float" optional="true" value="0.0" label="Cpos, penalty for mistakes made on positive examples" help="Set by cross validation if not specified"/> | 186 <param name="cpos" argument="-cpos" type="float" optional="true" value="0.0" label="Cpos, penalty for mistakes made on positive examples" help="Set by cross validation if not specified"/> |
147 <param name="cneg" argument="-cneg" type="float" optional="true" value="0.0" label="Cneg, penalty for mistakes made on negative examples" help="Set by cross validation if not specified"/> | 187 <param name="cneg" argument="-cneg" type="float" optional="true" value="0.0" label="Cneg, penalty for mistakes made on negative examples" help="Set by cross validation if not specified"/> |
148 <param name="testFDR" argument="-testFDR" type="float" optional="true" value="0.01" label="False discovery rate threshold for evaluating best cross validation result and the reported end result" help=""/> | 188 <param name="testFDR" argument="-testFDR" type="float" optional="true" value="0.01" label="False discovery rate threshold for evaluating best cross validation result and the reported end result" help=""/> |
149 <param name="trainFDR" argument="-trainFDR" type="float" optional="true" value="0.01" label="False discovery rate threshold to define positive examples in training" help="Set to testFDR if 0"/> | 189 <param name="trainFDR" argument="-trainFDR" type="float" optional="true" value="0.01" label="False discovery rate threshold to define positive examples in training" help="Set to testFDR if 0"/> |
150 <param name="maxiter" argument="-maxiter" type="integer" optional="true" value="10" label="Maximal number of iterations" help=""/> | 190 <param name="maxiter" argument="-maxiter" type="integer" optional="true" value="10" label="Maximal number of iterations" help=""/> |
151 <param name="quick_validation" argument="-quick-validation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Quicker execution by reduced internal cross-validation" help=""/> | 191 <param name="nested_xval_bins" argument="-nested_xval_bins" type="integer" optional="true" value="1" label="Number of nested cross-validation bins in the 3 splits" help=""/> |
152 <param name="init_weights" argument="-init-weights" type="data" format="txt" optional="true" label="Read initial weights to the given file" help=" select txt data sets(s)"/> | 192 <param name="quick_validation" argument="-quick_validation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Quicker execution by reduced internal cross-validation" help=""/> |
153 <param name="default_direction" argument="-default-direction" type="text" optional="true" value="" label="The most informative feature given as the feature name, can be negated to indicate that a lower value is bette" help=""> | 193 <param name="init_weights" argument="-init_weights" type="data" format="tabular" optional="true" label="Read initial weights to the given file" help=" select tabular data sets(s)"/> |
194 <param name="static" argument="-static" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use static model (requires init-weights parameter to be set)" help=""/> | |
195 <param name="default_direction" argument="-default_direction" type="text" optional="true" value="" label="The most informative feature given as the feature name, can be negated to indicate that a lower value is bette" help=""> | |
154 <expand macro="list_string_san"/> | 196 <expand macro="list_string_san"/> |
155 </param> | 197 </param> |
156 <param name="verbose" argument="-verbose" type="integer" optional="true" value="2" label="Set verbosity of output: 0=no processing info, 5=all" help=""/> | 198 <param name="verbose" argument="-verbose" type="integer" optional="true" value="2" label="Set verbosity of output: 0=no processing info, 5=all" help=""/> |
157 <param name="unitnorm" argument="-unitnorm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use unit normalization [0-1] instead of standard deviation normalization" help=""/> | 199 <param name="unitnorm" argument="-unitnorm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use unit normalization [0-1] instead of standard deviation normalization" help=""/> |
158 <param name="test_each_iteration" argument="-test-each-iteration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Measure performance on test set each iteration" help=""/> | 200 <param name="test_each_iteration" argument="-test_each_iteration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Measure performance on test set each iteration" help=""/> |
159 <param name="override" argument="-override" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Override error check and do not fall back on default score vector in case of suspect score vecto" help=""/> | 201 <param name="override" argument="-override" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Override error check and do not fall back on default score vector in case of suspect score vecto" help=""/> |
160 <param name="seed" argument="-seed" type="integer" optional="true" value="1" label="Setting seed of the random number generato" help=""/> | 202 <param name="seed" argument="-seed" type="integer" optional="true" value="1" label="Setting seed of the random number generato" help=""/> |
161 <param name="doc" argument="-doc" type="integer" optional="true" value="0" label="Include description of correct features" help=""/> | 203 <param name="doc" argument="-doc" type="integer" optional="true" value="0" label="Include description of correct features" help=""/> |
162 <param name="klammer" argument="-klammer" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Retention time features calculated as in Klammer et al" help="Only available if -doc is set"/> | 204 <param name="klammer" argument="-klammer" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Retention time features calculated as in Klammer et al" help="Only available if -doc is set"/> |
163 <param name="fasta" argument="-fasta" type="data" format="fasta" optional="true" label="Provide the fasta file as the argument to this flag, which will be used for protein grouping based on an in-silico digest (only valid if option -protein-level-fdrs is active)" help=" select fasta data sets(s)"/> | 205 <param name="fasta" argument="-fasta" type="data" format="fasta" optional="true" label="Provide the fasta file as the argument to this flag, which will be used for protein grouping based on an in-silico digest (only valid if option -protein_level_fdrs is active)" help=" select fasta data sets(s)"/> |
164 <param name="decoy_pattern" argument="-decoy-pattern" type="text" optional="true" value="random" label="Define the text pattern to identify the decoy proteins and/or PSMs, set this up if the label that identifies the decoys in the database is not the default (Only valid if option -protein-level-fdrs is active)" help=""> | 206 <param name="decoy_pattern" argument="-decoy_pattern" type="text" optional="true" value="random" label="Define the text pattern to identify the decoy proteins and/or PSMs, set this up if the label that identifies the decoys in the database is not the default (Only valid if option -protein_level_fdrs is active)" help=""> |
165 <expand macro="list_string_san"/> | 207 <expand macro="list_string_san"/> |
166 </param> | 208 </param> |
167 <param name="post_processing_tdc" argument="-post-processing-tdc" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use target-decoy competition to assign q-values and PEPs" help=""/> | 209 <param name="post_processing_tdc" argument="-post_processing_tdc" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use target-decoy competition to assign q-values and PEPs" help=""/> |
168 <param name="train_best_positive" argument="-train-best-positive" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enforce that, for each spectrum, at most one PSM is included in the positive set during each training iteration" help="If the user only provides one PSM per spectrum, this filter will have no effect"/> | 210 <param name="train_best_positive" argument="-train_best_positive" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enforce that, for each spectrum, at most one PSM is included in the positive set during each training iteration" help="If the user only provides one PSM per spectrum, this filter will have no effect"/> |
169 <param name="ipf_max_peakgroup_pep" argument="-ipf_max_peakgroup_pep" type="float" optional="true" value="0.7" label="OSW/IPF: Assess transitions only for candidate peak groups until maximum posterior error probability" help=""/> | 211 <param name="ipf_max_peakgroup_pep" argument="-ipf_max_peakgroup_pep" type="float" optional="true" value="0.7" label="OSW/IPF: Assess transitions only for candidate peak groups until maximum posterior error probability" help=""/> |
170 <param name="ipf_max_transition_isotope_overlap" argument="-ipf_max_transition_isotope_overlap" type="float" optional="true" value="0.5" label="OSW/IPF: Maximum isotope overlap to consider transitions in IPF" help=""/> | 212 <param name="ipf_max_transition_isotope_overlap" argument="-ipf_max_transition_isotope_overlap" type="float" optional="true" value="0.5" label="OSW/IPF: Maximum isotope overlap to consider transitions in IPF" help=""/> |
171 <param name="ipf_min_transition_sn" argument="-ipf_min_transition_sn" type="float" optional="true" value="0.0" label="OSW/IPF: Minimum log signal-to-noise level to consider transitions in IPF" help="Set -1 to disable this filter"/> | 213 <param name="ipf_min_transition_sn" argument="-ipf_min_transition_sn" type="float" optional="true" value="0.0" label="OSW/IPF: Minimum log signal-to-noise level to consider transitions in IPF" help="Set -1 to disable this filter"/> |
172 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> | 214 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
173 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 215 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
174 <expand macro="list_string_san"/> | 216 <expand macro="list_string_san"/> |
175 </param> | 217 </param> |
176 </expand> | 218 </expand> |
177 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> | 219 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
178 <option value="out_pin_FLAG">out_pin (Enables the test mode (needed for internal use only))</option> | 220 <option value="out_pin_FLAG">out_pin (Write pin file (e.g., for debugging))</option> |
179 <option value="weights_FLAG">weights (Enables the test mode (needed for internal use only))</option> | 221 <option value="out_pout_target_FLAG">out_pout_target (Write pout file (e.g., for debugging))</option> |
222 <option value="out_pout_decoy_FLAG">out_pout_decoy (Write pout file (e.g., for debugging))</option> | |
223 <option value="out_pout_target_proteins_FLAG">out_pout_target_proteins (Write pout file (e.g., for debugging))</option> | |
224 <option value="out_pout_decoy_proteins_FLAG">out_pout_decoy_proteins (Write pout file (e.g., for debugging))</option> | |
225 <option value="weights_FLAG">weights (Output final weights to the given file)</option> | |
180 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 226 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
181 </param> | 227 </param> |
182 </inputs> | 228 </inputs> |
183 <outputs> | 229 <outputs> |
184 <data name="out" label="${tool.name} on ${on_string}: out"> | 230 <data name="out" label="${tool.name} on ${on_string}: out"> |
189 </change_format> | 235 </change_format> |
190 </data> | 236 </data> |
191 <data name="out_pin" label="${tool.name} on ${on_string}: out_pin" format="tabular"> | 237 <data name="out_pin" label="${tool.name} on ${on_string}: out_pin" format="tabular"> |
192 <filter>OPTIONAL_OUTPUTS is not None and "out_pin_FLAG" in OPTIONAL_OUTPUTS</filter> | 238 <filter>OPTIONAL_OUTPUTS is not None and "out_pin_FLAG" in OPTIONAL_OUTPUTS</filter> |
193 </data> | 239 </data> |
194 <data name="weights" label="${tool.name} on ${on_string}: weights" format="txt"> | 240 <data name="out_pout_target" label="${tool.name} on ${on_string}: out_pout_target" format="tabular"> |
241 <filter>OPTIONAL_OUTPUTS is not None and "out_pout_target_FLAG" in OPTIONAL_OUTPUTS</filter> | |
242 </data> | |
243 <data name="out_pout_decoy" label="${tool.name} on ${on_string}: out_pout_decoy" format="tabular"> | |
244 <filter>OPTIONAL_OUTPUTS is not None and "out_pout_decoy_FLAG" in OPTIONAL_OUTPUTS</filter> | |
245 </data> | |
246 <data name="out_pout_target_proteins" label="${tool.name} on ${on_string}: out_pout_target_proteins" format="tabular"> | |
247 <filter>OPTIONAL_OUTPUTS is not None and "out_pout_target_proteins_FLAG" in OPTIONAL_OUTPUTS</filter> | |
248 </data> | |
249 <data name="out_pout_decoy_proteins" label="${tool.name} on ${on_string}: out_pout_decoy_proteins" format="tabular"> | |
250 <filter>OPTIONAL_OUTPUTS is not None and "out_pout_decoy_proteins_FLAG" in OPTIONAL_OUTPUTS</filter> | |
251 </data> | |
252 <data name="weights" label="${tool.name} on ${on_string}: weights" format="tabular"> | |
195 <filter>OPTIONAL_OUTPUTS is not None and "weights_FLAG" in OPTIONAL_OUTPUTS</filter> | 253 <filter>OPTIONAL_OUTPUTS is not None and "weights_FLAG" in OPTIONAL_OUTPUTS</filter> |
196 </data> | 254 </data> |
197 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 255 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
198 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 256 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
199 </data> | 257 </data> |
203 <expand macro="manutest_PercolatorAdapter"/> | 261 <expand macro="manutest_PercolatorAdapter"/> |
204 </tests> | 262 </tests> |
205 <help><![CDATA[Facilitate input to Percolator and reintegrate. | 263 <help><![CDATA[Facilitate input to Percolator and reintegrate. |
206 | 264 |
207 | 265 |
208 For more information, visit http://www.openms.de/documentation/TOPP_PercolatorAdapter.html]]></help> | 266 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_PercolatorAdapter.html]]></help> |
209 <expand macro="references"/> | 267 <expand macro="references"/> |
210 </tool> | 268 </tool> |