Mercurial > repos > galaxyp > openms_openswathdiaprescoring
comparison OpenSwathDIAPreScoring.xml @ 0:b1af731ae341 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
| author | galaxyp |
|---|---|
| date | Wed, 01 Mar 2017 12:59:14 -0500 |
| parents | |
| children | 932066012f7b |
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| -1:000000000000 | 0:b1af731ae341 |
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| 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.--> | |
| 3 <!--Proposed Tool Section: [Targeted Experiments]--> | |
| 4 <tool id="OpenSwathDIAPreScoring" name="OpenSwathDIAPreScoring" version="2.1.0"> | |
| 5 <description>Scoring spectra using the DIA scores.</description> | |
| 6 <macros> | |
| 7 <token name="@EXECUTABLE@">OpenSwathDIAPreScoring</token> | |
| 8 <import>macros.xml</import> | |
| 9 </macros> | |
| 10 <expand macro="references"/> | |
| 11 <expand macro="stdio"/> | |
| 12 <expand macro="requirements"/> | |
| 13 <command>OpenSwathDIAPreScoring | |
| 14 | |
| 15 #if $param_tr: | |
| 16 -tr $param_tr | |
| 17 #end if | |
| 18 #if $param_out: | |
| 19 -out $param_out | |
| 20 #end if | |
| 21 -swath_files | |
| 22 #for token in $param_swath_files: | |
| 23 $token | |
| 24 #end for | |
| 25 #if $param_min_upper_edge_dist: | |
| 26 -min_upper_edge_dist $param_min_upper_edge_dist | |
| 27 #end if | |
| 28 #if $adv_opts.adv_opts_selector=='advanced': | |
| 29 #if $adv_opts.param_force: | |
| 30 -force | |
| 31 #end if | |
| 32 #end if | |
| 33 </command> | |
| 34 <inputs> | |
| 35 <param name="param_tr" type="data" format="traml" optional="False" label="transition file" help="(-tr) "/> | |
| 36 <param name="param_swath_files" type="data" format="mzml" multiple="true" optional="True" size="30" label="Swath files that were used to extract the transitions" help="(-swath_files) If present, SWATH specific scoring will be applied"> | |
| 37 <sanitizer> | |
| 38 <valid initial="string.printable"> | |
| 39 <remove value="'"/> | |
| 40 <remove value="""/> | |
| 41 </valid> | |
| 42 </sanitizer> | |
| 43 </param> | |
| 44 <param name="param_min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help="(-min_upper_edge_dist) "/> | |
| 45 <expand macro="advanced_options"> | |
| 46 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | |
| 47 </expand> | |
| 48 </inputs> | |
| 49 <outputs> | |
| 50 <data name="param_out" format="tabular"/> | |
| 51 </outputs> | |
| 52 <help>Scoring spectra using the DIA scores. | |
| 53 | |
| 54 | |
| 55 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/TOPP_OpenSwathDIAPreScoring.html</help> | |
| 56 </tool> |