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comparison FileFilter.xml @ 7:fce0d752c6c5 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
author galaxyp
date Mon, 12 Feb 2018 12:52:41 -0500
parents 59adb20eb08a
children 348aec6301b1
comparison
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6:1209627f53d9 7:fce0d752c6c5
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [File Handling]--> 3 <!--Proposed Tool Section: [File Handling]-->
4 <tool id="FileFilter" name="FileFilter" version="2.2.0"> 4 <tool id="FileFilter" name="FileFilter" version="2.3.0">
5 <description>Extracts or manipulates portions of data from peak, feature or consensus-feature files.</description> 5 <description>Extracts or manipulates portions of data from peak, feature or consensus-feature files.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FileFilter</token> 7 <token name="@EXECUTABLE@">FileFilter</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
371 </valid> 371 </valid>
372 </sanitizer> 372 </sanitizer>
373 </param> 373 </param>
374 <param name="param_sort" display="radio" type="boolean" truevalue="-sort" falsevalue="" checked="false" optional="True" label="Sorts the output according to RT and m/z" help="(-sort) "/> 374 <param name="param_sort" display="radio" type="boolean" truevalue="-sort" falsevalue="" checked="false" optional="True" label="Sorts the output according to RT and m/z" help="(-sort) "/>
375 <param name="param_peak_options_sn" type="float" value="0.0" label="Write peaks with S/N &gt; 'sn' values only" help="(-sn) "/> 375 <param name="param_peak_options_sn" type="float" value="0.0" label="Write peaks with S/N &gt; 'sn' values only" help="(-sn) "/>
376 <repeat name="rep_param_peak_options_rm_pc_charge" min="0" max="1" title="param_peak_options_rm_pc_charge"> 376 <repeat name="rep_param_peak_options_rm_pc_charge" min="0" title="param_peak_options_rm_pc_charge">
377 <param name="param_peak_options_rm_pc_charge" type="text" size="30" value="0" label="Remove MS(2) spectra with these precursor charges" help="(-rm_pc_charge) All spectra without precursor are kept!"> 377 <param name="param_peak_options_rm_pc_charge" type="text" size="30" value="0" label="Remove MS(2) spectra with these precursor charges" help="(-rm_pc_charge) All spectra without precursor are kept!">
378 <sanitizer> 378 <sanitizer>
379 <valid initial="string.printable"> 379 <valid initial="string.printable">
380 <remove value="'"/> 380 <remove value="'"/>
381 <remove value="&quot;"/> 381 <remove value="&quot;"/>
389 <remove value="'"/> 389 <remove value="'"/>
390 <remove value="&quot;"/> 390 <remove value="&quot;"/>
391 </valid> 391 </valid>
392 </sanitizer> 392 </sanitizer>
393 </param> 393 </param>
394 <repeat name="rep_param_peak_options_pc_mz_list" min="0" max="1" title="param_peak_options_pc_mz_list"> 394 <repeat name="rep_param_peak_options_pc_mz_list" min="0" title="param_peak_options_pc_mz_list">
395 <param name="param_peak_options_pc_mz_list" type="text" size="30" value="0" label="List of m/z values" help="(-pc_mz_list) If a precursor window covers ANY of these values, the corresponding MS/MS spectrum will be kept"> 395 <param name="param_peak_options_pc_mz_list" type="text" size="30" value="0" label="List of m/z values" help="(-pc_mz_list) If a precursor window covers ANY of these values, the corresponding MS/MS spectrum will be kept">
396 <sanitizer> 396 <sanitizer>
397 <valid initial="string.printable"> 397 <valid initial="string.printable">
398 <remove value="'"/> 398 <remove value="'"/>
399 <remove value="&quot;"/> 399 <remove value="&quot;"/>
452 <option value="Precursor">Precursor</option> 452 <option value="Precursor">Precursor</option>
453 <option value="EnhancedMultiplyCharged">EnhancedMultiplyCharged</option> 453 <option value="EnhancedMultiplyCharged">EnhancedMultiplyCharged</option>
454 <option value="TimeDelayedFragmentation">TimeDelayedFragmentation</option> 454 <option value="TimeDelayedFragmentation">TimeDelayedFragmentation</option>
455 <option value="ElectromagneticRadiation">ElectromagneticRadiation</option> 455 <option value="ElectromagneticRadiation">ElectromagneticRadiation</option>
456 <option value="Emission">Emission</option> 456 <option value="Emission">Emission</option>
457 <option value="Absorbtion">Absorbtion</option> 457 <option value="Absorption">Absorption</option>
458 </param> 458 </param>
459 <param name="param_spectra_remove_activation" type="select" optional="True" label="Remove MSn scans where any of its precursors features a certain activation method" help="(-remove_activation) "> 459 <param name="param_spectra_remove_activation" type="select" optional="True" label="Remove MSn scans where any of its precursors features a certain activation method" help="(-remove_activation) ">
460 <option value="Collision-induced dissociation">Collision-induced dissociation</option> 460 <option value="Collision-induced dissociation">Collision-induced dissociation</option>
461 <option value="Post-source decay">Post-source decay</option> 461 <option value="Post-source decay">Post-source decay</option>
462 <option value="Plasma desorption">Plasma desorption</option> 462 <option value="Plasma desorption">Plasma desorption</option>
501 <option value="Precursor">Precursor</option> 501 <option value="Precursor">Precursor</option>
502 <option value="EnhancedMultiplyCharged">EnhancedMultiplyCharged</option> 502 <option value="EnhancedMultiplyCharged">EnhancedMultiplyCharged</option>
503 <option value="TimeDelayedFragmentation">TimeDelayedFragmentation</option> 503 <option value="TimeDelayedFragmentation">TimeDelayedFragmentation</option>
504 <option value="ElectromagneticRadiation">ElectromagneticRadiation</option> 504 <option value="ElectromagneticRadiation">ElectromagneticRadiation</option>
505 <option value="Emission">Emission</option> 505 <option value="Emission">Emission</option>
506 <option value="Absorbtion">Absorbtion</option> 506 <option value="Absorption">Absorption</option>
507 </param> 507 </param>
508 <param name="param_spectra_select_activation" type="select" optional="True" label="Retain MSn scans where any of its precursors features a certain activation method" help="(-select_activation) "> 508 <param name="param_spectra_select_activation" type="select" optional="True" label="Retain MSn scans where any of its precursors features a certain activation method" help="(-select_activation) ">
509 <option value="Collision-induced dissociation">Collision-induced dissociation</option> 509 <option value="Collision-induced dissociation">Collision-induced dissociation</option>
510 <option value="Post-source decay">Post-source decay</option> 510 <option value="Post-source decay">Post-source decay</option>
511 <option value="Plasma desorption">Plasma desorption</option> 511 <option value="Plasma desorption">Plasma desorption</option>
547 <remove value="'"/> 547 <remove value="'"/>
548 <remove value="&quot;"/> 548 <remove value="&quot;"/>
549 </valid> 549 </valid>
550 </sanitizer> 550 </sanitizer>
551 </param> 551 </param>
552 <repeat name="rep_param_consensus_map" min="0" max="1" title="param_consensus_map"> 552 <repeat name="rep_param_consensus_map" min="0" title="param_consensus_map">
553 <param name="param_consensus_map" type="text" size="30" value="0" label="Maps to be extracted from a consensus" help="(-map) "> 553 <param name="param_consensus_map" type="text" size="30" value="0" label="Maps to be extracted from a consensus" help="(-map) ">
554 <sanitizer> 554 <sanitizer>
555 <valid initial="string.printable"> 555 <valid initial="string.printable">
556 <remove value="'"/> 556 <remove value="'"/>
557 <remove value="&quot;"/> 557 <remove value="&quot;"/>
563 <param name="param_consensus_blackorwhitelist_blacklist" display="radio" type="select" optional="False" value="true" label="True: remove matched MS2" help="(-blacklist) False: retain matched MS2 spectra. Other levels are kept"> 563 <param name="param_consensus_blackorwhitelist_blacklist" display="radio" type="select" optional="False" value="true" label="True: remove matched MS2" help="(-blacklist) False: retain matched MS2 spectra. Other levels are kept">
564 <option value="false">false</option> 564 <option value="false">false</option>
565 <option value="true" selected="true">true</option> 565 <option value="true" selected="true">true</option>
566 </param> 566 </param>
567 <param name="param_consensus_blackorwhitelist_file" type="data" format="consensusxml" optional="True" label="Input file containing consensus features whose corresponding MS2 spectra should be removed from the mzML file! &lt;br&gt;Matching tolerances are taken from 'consensus:blackorwhitelist:rt' and 'consensus:blackorwhitelist:mz' options" help="(-file) &lt;br&gt;If consensus:blackorwhitelist:maps is specified, only these will be used. &lt;br&gt;"/> 567 <param name="param_consensus_blackorwhitelist_file" type="data" format="consensusxml" optional="True" label="Input file containing consensus features whose corresponding MS2 spectra should be removed from the mzML file! &lt;br&gt;Matching tolerances are taken from 'consensus:blackorwhitelist:rt' and 'consensus:blackorwhitelist:mz' options" help="(-file) &lt;br&gt;If consensus:blackorwhitelist:maps is specified, only these will be used. &lt;br&gt;"/>
568 <repeat name="rep_param_consensus_blackorwhitelist_maps" min="0" max="1" title="param_consensus_blackorwhitelist_maps"> 568 <repeat name="rep_param_consensus_blackorwhitelist_maps" min="0" title="param_consensus_blackorwhitelist_maps">
569 <param name="param_consensus_blackorwhitelist_maps" type="text" size="30" value="0" label="Maps used for black/white list filtering" help="(-maps) "> 569 <param name="param_consensus_blackorwhitelist_maps" type="text" size="30" value="0" label="Maps used for black/white list filtering" help="(-maps) ">
570 <sanitizer> 570 <sanitizer>
571 <valid initial="string.printable"> 571 <valid initial="string.printable">
572 <remove value="'"/> 572 <remove value="'"/>
573 <remove value="&quot;"/> 573 <remove value="&quot;"/>
592 <remove value="'"/> 592 <remove value="'"/>
593 <remove value="&quot;"/> 593 <remove value="&quot;"/>
594 </valid> 594 </valid>
595 </sanitizer> 595 </sanitizer>
596 </param> 596 </param>
597 <repeat name="rep_param_f_and_c_remove_meta" min="0" max="1" title="param_f_and_c_remove_meta"> 597 <repeat name="rep_param_f_and_c_remove_meta" min="0" title="param_f_and_c_remove_meta">
598 <param name="param_f_and_c_remove_meta" type="text" size="30" label="Expects a 3-tuple (=3 entries in the list), i.e" help="(-remove_meta) &lt;name&gt; 'lt|eq|gt' &lt;value&gt;; the first is the name of meta value, followed by the comparison operator (equal, less or greater) and the value to compare to. All comparisons are done after converting the given value to the corresponding data value type of the meta value (for lists, this simply compares length, not content!)!"> 598 <param name="param_f_and_c_remove_meta" type="text" size="30" label="Expects a 3-tuple (=3 entries in the list), i.e" help="(-remove_meta) &lt;name&gt; 'lt|eq|gt' &lt;value&gt;; the first is the name of meta value, followed by the comparison operator (equal, less or greater) and the value to compare to. All comparisons are done after converting the given value to the corresponding data value type of the meta value (for lists, this simply compares length, not content!)!">
599 <sanitizer> 599 <sanitizer>
600 <valid initial="string.printable"> 600 <valid initial="string.printable">
601 <remove value="'"/> 601 <remove value="'"/>
602 <remove value="&quot;"/> 602 <remove value="&quot;"/>
603 </valid> 603 </valid>
604 </sanitizer> 604 </sanitizer>
605 </param> 605 </param>
606 </repeat> 606 </repeat>
607 <param name="param_id_keep_best_score_id" display="radio" type="boolean" truevalue="-id:keep_best_score_id" falsevalue="" checked="false" optional="True" label="in case of multiple peptide identifications, keep only the id with best score" help="(-keep_best_score_id) "/> 607 <param name="param_id_keep_best_score_id" display="radio" type="boolean" truevalue="-id:keep_best_score_id" falsevalue="" checked="false" optional="True" label="in case of multiple peptide identifications, keep only the id with best score" help="(-keep_best_score_id) "/>
608 <repeat name="rep_param_id_sequences_whitelist" min="0" max="1" title="param_id_sequences_whitelist"> 608 <repeat name="rep_param_id_sequences_whitelist" min="0" title="param_id_sequences_whitelist">
609 <param name="param_id_sequences_whitelist" type="text" size="30" label="keep only features with white listed sequences," help="(-sequences_whitelist) e.g. LYSNLVER or the modification (Oxidation)"> 609 <param name="param_id_sequences_whitelist" type="text" size="30" label="keep only features with white listed sequences," help="(-sequences_whitelist) e.g. LYSNLVER or the modification (Oxidation)">
610 <sanitizer> 610 <sanitizer>
611 <valid initial="string.printable"> 611 <valid initial="string.printable">
612 <remove value="'"/> 612 <remove value="'"/>
613 <remove value="&quot;"/> 613 <remove value="&quot;"/>
614 </valid> 614 </valid>
615 </sanitizer> 615 </sanitizer>
616 </param> 616 </param>
617 </repeat> 617 </repeat>
618 <repeat name="rep_param_id_accessions_whitelist" min="0" max="1" title="param_id_accessions_whitelist"> 618 <repeat name="rep_param_id_accessions_whitelist" min="0" title="param_id_accessions_whitelist">
619 <param name="param_id_accessions_whitelist" type="text" size="30" label="keep only features with white listed accessions," help="(-accessions_whitelist) e.g. sp|P02662|CASA1_BOVIN"> 619 <param name="param_id_accessions_whitelist" type="text" size="30" label="keep only features with white listed accessions," help="(-accessions_whitelist) e.g. sp|P02662|CASA1_BOVIN">
620 <sanitizer> 620 <sanitizer>
621 <valid initial="string.printable"> 621 <valid initial="string.printable">
622 <remove value="'"/> 622 <remove value="'"/>
623 <remove value="&quot;"/> 623 <remove value="&quot;"/>