Mercurial > repos > galaxyp > openms_staticmodification
comparison macros_discarded_auto.xml @ 0:3087dee547e7 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 19:15:05 +0000 |
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| children |
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| -1:000000000000 | 0:3087dee547e7 |
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| 1 | |
| 2 <xml name="manutest_OpenSwathFileSplitter"> | |
| 3 <test expect_num_outputs="2"> | |
| 4 <conditional name="adv_opts_cond"> | |
| 5 <param name="adv_opts_selector" value="advanced"/> | |
| 6 <param name="force" value="false"/> | |
| 7 <param name="test" value="true"/> | |
| 8 </conditional> | |
| 9 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> | |
| 10 <output_collection name="outputDirectory" count=""/> | |
| 11 <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/> | |
| 12 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_qc_FLAG"/> | |
| 13 <output name="ctd_out" ftype="xml"> | |
| 14 <assert_contents> | |
| 15 <is_valid_xml/> | |
| 16 </assert_contents> | |
| 17 </output> | |
| 18 </test></xml> | |
| 19 <xml name="manutest_IDRipper"> | |
| 20 <test expect_num_outputs="1"> | |
| 21 <conditional name="adv_opts_cond"> | |
| 22 <param name="adv_opts_selector" value="advanced"/> | |
| 23 <param name="force" value="false"/> | |
| 24 <param name="test" value="true"/> | |
| 25 </conditional> | |
| 26 <param name="in" value="IDRipper_1_input.idXML"/> | |
| 27 <output_collection name="out_path" count=""/> | |
| 28 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 29 <output name="ctd_out" ftype="xml"> | |
| 30 <assert_contents> | |
| 31 <is_valid_xml/> | |
| 32 </assert_contents> | |
| 33 </output> | |
| 34 </test><test expect_num_outputs="1"> | |
| 35 <conditional name="adv_opts_cond"> | |
| 36 <param name="adv_opts_selector" value="advanced"/> | |
| 37 <param name="force" value="false"/> | |
| 38 <param name="test" value="true"/> | |
| 39 </conditional> | |
| 40 <param name="in" value="IDRipper_2_input.idXML"/> | |
| 41 <output_collection name="out_path" count=""/> | |
| 42 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 43 <output name="ctd_out" ftype="xml"> | |
| 44 <assert_contents> | |
| 45 <is_valid_xml/> | |
| 46 </assert_contents> | |
| 47 </output> | |
| 48 </test><test expect_num_outputs="1"> | |
| 49 <conditional name="adv_opts_cond"> | |
| 50 <param name="adv_opts_selector" value="advanced"/> | |
| 51 <param name="force" value="false"/> | |
| 52 <param name="test" value="true"/> | |
| 53 </conditional> | |
| 54 <param name="in" value="IDRipper_3_output.idXML"/> | |
| 55 <output_collection name="out_path" count=""/> | |
| 56 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 57 <output name="ctd_out" ftype="xml"> | |
| 58 <assert_contents> | |
| 59 <is_valid_xml/> | |
| 60 </assert_contents> | |
| 61 </output> | |
| 62 </test></xml> | |
| 63 <xml name="manutest_MzMLSplitter"> | |
| 64 <test expect_num_outputs="1"> | |
| 65 <conditional name="adv_opts_cond"> | |
| 66 <param name="adv_opts_selector" value="advanced"/> | |
| 67 <param name="force" value="false"/> | |
| 68 <param name="test" value="true"/> | |
| 69 </conditional> | |
| 70 <param name="in" value="FileFilter_1_input.mzML"/> | |
| 71 <output_collection name="out" count=""/> | |
| 72 <param name="parts" value="2"/> | |
| 73 <param name="size" value="0"/> | |
| 74 <param name="unit" value="MB"/> | |
| 75 <param name="no_chrom" value="false"/> | |
| 76 <param name="no_spec" value="false"/> | |
| 77 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 78 <output name="ctd_out" ftype="xml"> | |
| 79 <assert_contents> | |
| 80 <is_valid_xml/> | |
| 81 </assert_contents> | |
| 82 </output> | |
| 83 </test><test expect_num_outputs="1"> | |
| 84 <conditional name="adv_opts_cond"> | |
| 85 <param name="adv_opts_selector" value="advanced"/> | |
| 86 <param name="force" value="false"/> | |
| 87 <param name="test" value="true"/> | |
| 88 </conditional> | |
| 89 <param name="in" value="FileFilter_1_input.mzML"/> | |
| 90 <output_collection name="out" count=""/> | |
| 91 <param name="parts" value="1"/> | |
| 92 <param name="size" value="40"/> | |
| 93 <param name="unit" value="KB"/> | |
| 94 <param name="no_chrom" value="false"/> | |
| 95 <param name="no_spec" value="false"/> | |
| 96 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 97 <output name="ctd_out" ftype="xml"> | |
| 98 <assert_contents> | |
| 99 <is_valid_xml/> | |
| 100 </assert_contents> | |
| 101 </output> | |
| 102 </test></xml> | |
| 103 <xml name="manutest_MSFraggerAdapter"> | |
| 104 <test expect_num_outputs="3"> | |
| 105 <conditional name="adv_opts_cond"> | |
| 106 <param name="adv_opts_selector" value="advanced"/> | |
| 107 <param name="force" value="false"/> | |
| 108 <param name="test" value="true"/> | |
| 109 </conditional> | |
| 110 <param name="java_heapmemory" value="2600"/> | |
| 111 <param name="in" value="spectra.mzML"/> | |
| 112 <output name="out" file="MSFraggerAdapter_7_out_tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 113 <output name="opt_out" file="MSFraggerAdapter_7_opt_out_tmp.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> | |
| 114 <param name="database" value="proteins.fasta"/> | |
| 115 <section name="tolerance"> | |
| 116 <param name="precursor_mass_tolerance" value="20.0"/> | |
| 117 <param name="precursor_mass_unit" value="ppm"/> | |
| 118 <param name="precursor_true_tolerance" value="0.0"/> | |
| 119 <param name="precursor_true_unit" value="ppm"/> | |
| 120 <param name="fragment_mass_tolerance" value="20.0"/> | |
| 121 <param name="fragment_mass_unit" value="ppm"/> | |
| 122 <param name="isotope_error" value="0"/> | |
| 123 </section> | |
| 124 <section name="digest"> | |
| 125 <param name="search_enzyme_name" value="Trypsin"/> | |
| 126 <param name="search_enzyme_cutafter" value="KR"/> | |
| 127 <param name="search_enzyme_nocutbefore" value="P"/> | |
| 128 <param name="num_enzyme_termini" value="semi"/> | |
| 129 <param name="allowed_missed_cleavage" value="2"/> | |
| 130 <param name="min_length" value="7"/> | |
| 131 <param name="max_length" value="64"/> | |
| 132 <param name="mass_range_min" value="500.0"/> | |
| 133 <param name="mass_range_max" value="5000.0"/> | |
| 134 </section> | |
| 135 <section name="varmod"> | |
| 136 <param name="clip_nterm_m" value="false"/> | |
| 137 <param name="masses" value=""/> | |
| 138 <param name="syntaxes" value=""/> | |
| 139 <param name="enable_common" value="true"/> | |
| 140 <param name="not_allow_multiple_variable_mods_on_residue" value="false"/> | |
| 141 <param name="max_variable_mods_per_mod" value="2"/> | |
| 142 <param name="max_variable_mods_combinations" value="5000"/> | |
| 143 </section> | |
| 144 <section name="spectrum"> | |
| 145 <param name="minimum_peaks" value="10"/> | |
| 146 <param name="use_topn_peaks" value="50"/> | |
| 147 <param name="minimum_ratio" value="0.0"/> | |
| 148 <param name="clear_mz_range_min" value="0.0"/> | |
| 149 <param name="clear_mz_range_max" value="0.0"/> | |
| 150 <param name="max_fragment_charge" value="2"/> | |
| 151 <param name="override_charge" value="false"/> | |
| 152 <param name="precursor_charge_min" value="1"/> | |
| 153 <param name="precursor_charge_max" value="4"/> | |
| 154 </section> | |
| 155 <section name="search"> | |
| 156 <param name="track_zero_topn" value="0"/> | |
| 157 <param name="zero_bin_accept_expect" value="0.0"/> | |
| 158 <param name="zero_bin_mult_expect" value="1.0"/> | |
| 159 <param name="add_topn_complementary" value="0"/> | |
| 160 <param name="min_fragments_modeling" value="3"/> | |
| 161 <param name="min_matched_fragments" value="4"/> | |
| 162 <param name="output_report_topn" value="1"/> | |
| 163 <param name="output_max_expect" value="50.0"/> | |
| 164 </section> | |
| 165 <section name="statmod"> | |
| 166 <param name="add_cterm_peptide" value="0.0"/> | |
| 167 <param name="add_nterm_peptide" value="0.0"/> | |
| 168 <param name="add_cterm_protein" value="0.0"/> | |
| 169 <param name="add_nterm_protein" value="0.0"/> | |
| 170 <param name="add_G_glycine" value="0.0"/> | |
| 171 <param name="add_A_alanine" value="0.0"/> | |
| 172 <param name="add_S_serine" value="0.0"/> | |
| 173 <param name="add_P_proline" value="0.0"/> | |
| 174 <param name="add_V_valine" value="0.0"/> | |
| 175 <param name="add_T_threonine" value="0.0"/> | |
| 176 <param name="add_C_cysteine" value="57.021464"/> | |
| 177 <param name="add_L_leucine" value="0.0"/> | |
| 178 <param name="add_I_isoleucine" value="0.0"/> | |
| 179 <param name="add_N_asparagine" value="0.0"/> | |
| 180 <param name="add_D_aspartic_acid" value="0.0"/> | |
| 181 <param name="add_Q_glutamine" value="0.0"/> | |
| 182 <param name="add_K_lysine" value="0.0"/> | |
| 183 <param name="add_E_glutamic_acid" value="0.0"/> | |
| 184 <param name="add_M_methionine" value="0.0"/> | |
| 185 <param name="add_H_histidine" value="0.0"/> | |
| 186 <param name="add_F_phenylalanine" value="0.0"/> | |
| 187 <param name="add_R_arginine" value="0.0"/> | |
| 188 <param name="add_Y_tyrosine" value="0.0"/> | |
| 189 <param name="add_W_tryptophan" value="0.0"/> | |
| 190 </section> | |
| 191 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,opt_out_FLAG"/> | |
| 192 <output name="ctd_out" ftype="xml"> | |
| 193 <assert_contents> | |
| 194 <is_valid_xml/> | |
| 195 </assert_contents> | |
| 196 </output> | |
| 197 </test><test expect_num_outputs="2"> | |
| 198 <conditional name="adv_opts_cond"> | |
| 199 <param name="adv_opts_selector" value="advanced"/> | |
| 200 <param name="force" value="false"/> | |
| 201 <param name="test" value="true"/> | |
| 202 </conditional> | |
| 203 <param name="java_heapmemory" value="2600"/> | |
| 204 <param name="in" value="spectra_comet.mzML"/> | |
| 205 <output name="out" file="MSFraggerAdapter_8_out_tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 206 <param name="database" value="proteins.fasta"/> | |
| 207 <section name="tolerance"> | |
| 208 <param name="precursor_mass_tolerance" value="20.0"/> | |
| 209 <param name="precursor_mass_unit" value="ppm"/> | |
| 210 <param name="precursor_true_tolerance" value="0.0"/> | |
| 211 <param name="precursor_true_unit" value="ppm"/> | |
| 212 <param name="fragment_mass_tolerance" value="20.0"/> | |
| 213 <param name="fragment_mass_unit" value="ppm"/> | |
| 214 <param name="isotope_error" value="0"/> | |
| 215 </section> | |
| 216 <section name="digest"> | |
| 217 <param name="search_enzyme_name" value="Trypsin"/> | |
| 218 <param name="search_enzyme_cutafter" value="KR"/> | |
| 219 <param name="search_enzyme_nocutbefore" value="P"/> | |
| 220 <param name="num_enzyme_termini" value="semi"/> | |
| 221 <param name="allowed_missed_cleavage" value="2"/> | |
| 222 <param name="min_length" value="7"/> | |
| 223 <param name="max_length" value="64"/> | |
| 224 <param name="mass_range_min" value="500.0"/> | |
| 225 <param name="mass_range_max" value="5000.0"/> | |
| 226 </section> | |
| 227 <section name="varmod"> | |
| 228 <param name="clip_nterm_m" value="false"/> | |
| 229 <param name="masses" value=""/> | |
| 230 <param name="syntaxes" value=""/> | |
| 231 <param name="enable_common" value="true"/> | |
| 232 <param name="not_allow_multiple_variable_mods_on_residue" value="false"/> | |
| 233 <param name="max_variable_mods_per_mod" value="2"/> | |
| 234 <param name="max_variable_mods_combinations" value="5000"/> | |
| 235 </section> | |
| 236 <section name="spectrum"> | |
| 237 <param name="minimum_peaks" value="10"/> | |
| 238 <param name="use_topn_peaks" value="50"/> | |
| 239 <param name="minimum_ratio" value="0.0"/> | |
| 240 <param name="clear_mz_range_min" value="0.0"/> | |
| 241 <param name="clear_mz_range_max" value="0.0"/> | |
| 242 <param name="max_fragment_charge" value="2"/> | |
| 243 <param name="override_charge" value="false"/> | |
| 244 <param name="precursor_charge_min" value="1"/> | |
| 245 <param name="precursor_charge_max" value="4"/> | |
| 246 </section> | |
| 247 <section name="search"> | |
| 248 <param name="track_zero_topn" value="0"/> | |
| 249 <param name="zero_bin_accept_expect" value="0.0"/> | |
| 250 <param name="zero_bin_mult_expect" value="1.0"/> | |
| 251 <param name="add_topn_complementary" value="0"/> | |
| 252 <param name="min_fragments_modeling" value="3"/> | |
| 253 <param name="min_matched_fragments" value="4"/> | |
| 254 <param name="output_report_topn" value="1"/> | |
| 255 <param name="output_max_expect" value="50.0"/> | |
| 256 </section> | |
| 257 <section name="statmod"> | |
| 258 <param name="add_cterm_peptide" value="0.0"/> | |
| 259 <param name="add_nterm_peptide" value="0.0"/> | |
| 260 <param name="add_cterm_protein" value="0.0"/> | |
| 261 <param name="add_nterm_protein" value="0.0"/> | |
| 262 <param name="add_G_glycine" value="0.0"/> | |
| 263 <param name="add_A_alanine" value="0.0"/> | |
| 264 <param name="add_S_serine" value="0.0"/> | |
| 265 <param name="add_P_proline" value="0.0"/> | |
| 266 <param name="add_V_valine" value="0.0"/> | |
| 267 <param name="add_T_threonine" value="0.0"/> | |
| 268 <param name="add_C_cysteine" value="57.021464"/> | |
| 269 <param name="add_L_leucine" value="0.0"/> | |
| 270 <param name="add_I_isoleucine" value="0.0"/> | |
| 271 <param name="add_N_asparagine" value="0.0"/> | |
| 272 <param name="add_D_aspartic_acid" value="0.0"/> | |
| 273 <param name="add_Q_glutamine" value="0.0"/> | |
| 274 <param name="add_K_lysine" value="0.0"/> | |
| 275 <param name="add_E_glutamic_acid" value="0.0"/> | |
| 276 <param name="add_M_methionine" value="0.0"/> | |
| 277 <param name="add_H_histidine" value="0.0"/> | |
| 278 <param name="add_F_phenylalanine" value="0.0"/> | |
| 279 <param name="add_R_arginine" value="0.0"/> | |
| 280 <param name="add_Y_tyrosine" value="0.0"/> | |
| 281 <param name="add_W_tryptophan" value="0.0"/> | |
| 282 </section> | |
| 283 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 284 <output name="ctd_out" ftype="xml"> | |
| 285 <assert_contents> | |
| 286 <is_valid_xml/> | |
| 287 </assert_contents> | |
| 288 </output> | |
| 289 </test></xml> | |
| 290 <xml name="manutest_MaRaClusterAdapter"> | |
| 291 <test expect_num_outputs="2"> | |
| 292 <conditional name="adv_opts_cond"> | |
| 293 <param name="adv_opts_selector" value="advanced"/> | |
| 294 <param name="verbose" value="2"/> | |
| 295 <param name="precursor_tolerance" value="20.0"/> | |
| 296 <param name="precursor_tolerance_units" value="ppm"/> | |
| 297 <param name="force" value="false"/> | |
| 298 <param name="test" value="true"/> | |
| 299 </conditional> | |
| 300 <param name="in" value="MaRaClusterAdapter_1_in_1.mzML,MaRaClusterAdapter_1_in_2.mzML"/> | |
| 301 <param name="id_in" value="MaRaClusterAdapter_1_in_3.idXML"/> | |
| 302 <output name="out" file="MaRaClusterAdapter_2_out_1.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 303 <param name="pcut" value="-10.0"/> | |
| 304 <param name="min_cluster_size" value="1"/> | |
| 305 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> | |
| 306 <output name="ctd_out" ftype="xml"> | |
| 307 <assert_contents> | |
| 308 <is_valid_xml/> | |
| 309 </assert_contents> | |
| 310 </output> | |
| 311 </test></xml> | |
| 312 <xml name="manutest_NovorAdapter"> | |
| 313 <test expect_num_outputs="2"> | |
| 314 <conditional name="adv_opts_cond"> | |
| 315 <param name="adv_opts_selector" value="advanced"/> | |
| 316 <param name="force" value="false"/> | |
| 317 <param name="test" value="true"/> | |
| 318 </conditional> | |
| 319 <param name="in" value="NovorAdapter_in.mzML"/> | |
| 320 <output name="out" file="NovorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> | |
| 321 <param name="enzyme" value="Trypsin"/> | |
| 322 <param name="fragmentation" value="CID"/> | |
| 323 <param name="massAnalyzer" value="Trap"/> | |
| 324 <param name="fragment_mass_tolerance" value="0.5"/> | |
| 325 <param name="precursor_mass_tolerance" value="15.0"/> | |
| 326 <param name="precursor_error_units" value="ppm"/> | |
| 327 <param name="variable_modifications" value="Acetyl (K)"/> | |
| 328 <param name="fixed_modifications" value="Carbamidomethyl (C)"/> | |
| 329 <param name="forbiddenResidues" value="I"/> | |
| 330 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 331 <output name="ctd_out" ftype="xml"> | |
| 332 <assert_contents> | |
| 333 <is_valid_xml/> | |
| 334 </assert_contents> | |
| 335 </output> | |
| 336 </test></xml> | |
| 337 <xml name="manutest_SpectraSTSearchAdapter"> | |
| 338 <test expect_num_outputs="2"> | |
| 339 <conditional name="adv_opts_cond"> | |
| 340 <param name="adv_opts_selector" value="advanced"/> | |
| 341 <param name="use_isotopically_averaged_mass" value="false"/> | |
| 342 <param name="use_all_charge_states" value="false"/> | |
| 343 <param name="force" value="false"/> | |
| 344 <param name="test" value="true"/> | |
| 345 </conditional> | |
| 346 <param name="spectra_files" value="SpectrastAdapter_1_hack.mzML"/> | |
| 347 <param name="output_files_type" value="pep.xml"/> | |
| 348 <output_collection name="output_files" count="1"/> | |
| 349 <param name="library_file" value="testLib.splib" ftype="splib"/> | |
| 350 <param name="sequence_database_type" value="AA"/> | |
| 351 <param name="precursor_mz_tolerance" value="3.0"/> | |
| 352 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 353 <output name="ctd_out" ftype="xml"> | |
| 354 <assert_contents> | |
| 355 <is_valid_xml/> | |
| 356 </assert_contents> | |
| 357 </output> | |
| 358 </test><test expect_num_outputs="2"> | |
| 359 <conditional name="adv_opts_cond"> | |
| 360 <param name="adv_opts_selector" value="advanced"/> | |
| 361 <param name="use_isotopically_averaged_mass" value="false"/> | |
| 362 <param name="use_all_charge_states" value="false"/> | |
| 363 <param name="force" value="false"/> | |
| 364 <param name="test" value="true"/> | |
| 365 </conditional> | |
| 366 <param name="spectra_files" value="SpectrastAdapter_1_hack.mzML"/> | |
| 367 <param name="output_files_type" value="tsv"/> | |
| 368 <output_collection name="output_files" count="1"/> | |
| 369 <param name="library_file" value="testLib.splib" ftype="splib"/> | |
| 370 <param name="sequence_database_type" value="AA"/> | |
| 371 <param name="precursor_mz_tolerance" value="3.0"/> | |
| 372 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
| 373 <output name="ctd_out" ftype="xml"> | |
| 374 <assert_contents> | |
| 375 <is_valid_xml/> | |
| 376 </assert_contents> | |
| 377 </output> | |
| 378 </test></xml> |