Mercurial > repos > galaxyp > peptideshaker
comparison searchgui.xml @ 41:3634c90301af draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit dea56622eb32b82c87dc87567dc89db3a787033d
| author | galaxyp |
|---|---|
| date | Sat, 28 Oct 2017 04:16:50 -0400 |
| parents | a72c48001f7c |
| children | 9e20c34298e3 |
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| 40:a72c48001f7c | 41:3634c90301af |
|---|---|
| 1 <tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@"> | 1 <tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.1"> |
| 2 <description> | 2 <description> |
| 3 Perform protein identification using various search engines and prepare results for input to Peptide Shaker | 3 Perform protein identification using various search engines and prepare results for input to Peptide Shaker |
| 4 </description> | 4 </description> |
| 5 <macros> | 5 <macros> |
| 6 <import>macros.xml</import> | 6 <import>macros.xml</import> |
| 535 label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="false" /> | 535 label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="false" /> |
| 536 <param name="xtandem_output_sequences" help="Controls output of sequence information" | 536 <param name="xtandem_output_sequences" help="Controls output of sequence information" |
| 537 label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" /> | 537 label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" /> |
| 538 <param name="xtandem_output_spectra" help="Controls output of spectrum information" | 538 <param name="xtandem_output_spectra" help="Controls output of spectrum information" |
| 539 label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" /> | 539 label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" /> |
| 540 <!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="text" help="Path to a spectrum data file for use by skyline." --> | 540 <!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="txt" help="Path to a spectrum data file for use by skyline." --> |
| 541 | 541 |
| 542 <conditional name="xtandem_refine"><!-- -xtandem_refine --> | 542 <conditional name="xtandem_refine"><!-- -xtandem_refine --> |
| 543 <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement"> | 543 <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement"> |
| 544 <option value="no" selected="True">Don't refine</option> | 544 <option value="no" selected="True">Don't refine</option> |
| 545 <option value="yes" >Use refinement</option> | 545 <option value="yes" >Use refinement</option> |
| 674 label="MSGF: Search Decoys" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/> | 674 label="MSGF: Search Decoys" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/> |
| 675 <param name="msgf_min_pep_length" type="integer" value="6" | 675 <param name="msgf_min_pep_length" type="integer" value="6" |
| 676 label="MSGF: Minimum Peptide Length" help="Minimum length for a peptide to be considered"/> | 676 label="MSGF: Minimum Peptide Length" help="Minimum length for a peptide to be considered"/> |
| 677 <param name="msgf_max_pep_length" type="integer" value="30" | 677 <param name="msgf_max_pep_length" type="integer" value="30" |
| 678 label="MSGF: Maximum Peptide Length" help="Maximum length for a peptide to be considered"/> | 678 label="MSGF: Maximum Peptide Length" help="Maximum length for a peptide to be considered"/> |
| 679 <param name="msgf_termini" type="select" format="text" | 679 <param name="msgf_termini" type="select" format="txt" |
| 680 label="MSGF: Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2"> | 680 label="MSGF: Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2"> |
| 681 <option value="0">0 (ie non-specific cleavage)</option> | 681 <option value="0">0 (ie non-specific cleavage)</option> |
| 682 <option value="1">1 (ie semi-tryptic cleavage)</option> | 682 <option value="1">1 (ie semi-tryptic cleavage)</option> |
| 683 <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option> | 683 <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option> |
| 684 </param> | 684 </param> |