Mercurial > repos > galaxyp > openms_externalcalibration
comparison ExternalCalibration.xml @ 0:40cb91bfc04b draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
| author | galaxyp |
|---|---|
| date | Wed, 01 Mar 2017 10:13:30 -0500 |
| parents | |
| children | ce346d7073cb |
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| -1:000000000000 | 0:40cb91bfc04b |
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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: [Signal processing and preprocessing]--> | |
| 4 <tool id="ExternalCalibration" name="ExternalCalibration" version="2.1.0"> | |
| 5 <description>Applies an external mass recalibration.</description> | |
| 6 <macros> | |
| 7 <token name="@EXECUTABLE@">ExternalCalibration</token> | |
| 8 <import>macros.xml</import> | |
| 9 </macros> | |
| 10 <expand macro="references"/> | |
| 11 <expand macro="stdio"/> | |
| 12 <expand macro="requirements"/> | |
| 13 <command>ExternalCalibration | |
| 14 | |
| 15 #if $param_in: | |
| 16 -in $param_in | |
| 17 #end if | |
| 18 #if $param_out: | |
| 19 -out $param_out | |
| 20 #end if | |
| 21 #if $param_offset: | |
| 22 -offset $param_offset | |
| 23 #end if | |
| 24 #if $param_slope: | |
| 25 -slope $param_slope | |
| 26 #end if | |
| 27 #if $param_power: | |
| 28 -power $param_power | |
| 29 #end if | |
| 30 | |
| 31 #if $rep_param_ms_level: | |
| 32 -ms_level | |
| 33 #for token in $rep_param_ms_level: | |
| 34 #if " " in str(token): | |
| 35 "$token.param_ms_level" | |
| 36 #else | |
| 37 $token.param_ms_level | |
| 38 #end if | |
| 39 #end for | |
| 40 #end if | |
| 41 #if $adv_opts.adv_opts_selector=='advanced': | |
| 42 #if $adv_opts.param_force: | |
| 43 -force | |
| 44 #end if | |
| 45 #end if | |
| 46 </command> | |
| 47 <inputs> | |
| 48 <param name="param_in" type="data" format="mzml" optional="False" label="Input peak file" help="(-in) "/> | |
| 49 <param name="param_offset" type="float" value="0.0" label="Mass offset in ppm" help="(-offset) "/> | |
| 50 <param name="param_slope" type="float" value="0.0" label="Slope (dependent on m/z)" help="(-slope) "/> | |
| 51 <param name="param_power" type="float" value="0.0" label="Power (dependent on m/z)" help="(-power) "/> | |
| 52 <repeat name="rep_param_ms_level" min="0" max="1" title="param_ms_level"> | |
| 53 <param name="param_ms_level" type="text" size="30" value="1 2 3" label="Target MS levels to apply the transformation onto" help="(-ms_level) Scans with other levels remain unchanged"> | |
| 54 <sanitizer> | |
| 55 <valid initial="string.printable"> | |
| 56 <remove value="'"/> | |
| 57 <remove value="""/> | |
| 58 </valid> | |
| 59 </sanitizer> | |
| 60 </param> | |
| 61 </repeat> | |
| 62 <expand macro="advanced_options"> | |
| 63 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | |
| 64 </expand> | |
| 65 </inputs> | |
| 66 <outputs> | |
| 67 <data name="param_out" format="mzml"/> | |
| 68 </outputs> | |
| 69 <help>Applies an external mass recalibration. | |
| 70 | |
| 71 | |
| 72 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ExternalCalibration.html</help> | |
| 73 </tool> |