Mercurial > repos > galaxyp > openms_featurelinkerlabeled
comparison FeatureLinkerLabeled.xml @ 0:2fe5ef9f1760 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
| author | galaxyp |
|---|---|
| date | Wed, 01 Mar 2017 12:45:07 -0500 |
| parents | |
| children | 77f29f5244d9 |
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| -1:000000000000 | 0:2fe5ef9f1760 |
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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: [Map Alignment]--> | |
| 4 <tool id="FeatureLinkerLabeled" name="FeatureLinkerLabeled" version="2.1.0"> | |
| 5 <description>Groups corresponding isotope-labeled features in a feature map.</description> | |
| 6 <macros> | |
| 7 <token name="@EXECUTABLE@">FeatureLinkerLabeled</token> | |
| 8 <import>macros.xml</import> | |
| 9 </macros> | |
| 10 <expand macro="references"/> | |
| 11 <expand macro="stdio"/> | |
| 12 <expand macro="requirements"/> | |
| 13 <command>FeatureLinkerLabeled | |
| 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_algorithm_rt_estimate: | |
| 22 -algorithm:rt_estimate $param_algorithm_rt_estimate | |
| 23 #end if | |
| 24 #if $param_algorithm_rt_pair_dist: | |
| 25 -algorithm:rt_pair_dist $param_algorithm_rt_pair_dist | |
| 26 #end if | |
| 27 #if $param_algorithm_rt_dev_low: | |
| 28 -algorithm:rt_dev_low $param_algorithm_rt_dev_low | |
| 29 #end if | |
| 30 #if $param_algorithm_rt_dev_high: | |
| 31 -algorithm:rt_dev_high $param_algorithm_rt_dev_high | |
| 32 #end if | |
| 33 | |
| 34 #if $rep_param_algorithm_mz_pair_dists: | |
| 35 -algorithm:mz_pair_dists | |
| 36 #for token in $rep_param_algorithm_mz_pair_dists: | |
| 37 #if " " in str(token): | |
| 38 "$token.param_algorithm_mz_pair_dists" | |
| 39 #else | |
| 40 $token.param_algorithm_mz_pair_dists | |
| 41 #end if | |
| 42 #end for | |
| 43 #end if | |
| 44 #if $param_algorithm_mz_dev: | |
| 45 -algorithm:mz_dev $param_algorithm_mz_dev | |
| 46 #end if | |
| 47 #if $adv_opts.adv_opts_selector=='advanced': | |
| 48 #if $adv_opts.param_force: | |
| 49 -force | |
| 50 #end if | |
| 51 #if $adv_opts.param_algorithm_mrm: | |
| 52 -algorithm:mrm | |
| 53 #end if | |
| 54 #end if | |
| 55 </command> | |
| 56 <inputs> | |
| 57 <param name="param_in" type="data" format="featurexml" optional="False" label="Input file" help="(-in) "/> | |
| 58 <param name="param_algorithm_rt_estimate" display="radio" type="select" optional="False" value="true" label="If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance" help="(-rt_estimate) Note that this works only datasets with a significant amount of pairs! If 'false' the parameters 'rt_pair_dist', 'rt_dev_low' and 'rt_dev_high' define the optimal distance"> | |
| 59 <option value="true" selected="true">true</option> | |
| 60 <option value="false">false</option> | |
| 61 </param> | |
| 62 <param name="param_algorithm_rt_pair_dist" type="float" value="-20.0" label="optimal pair distance in RT [sec] from light to heavy feature" help="(-rt_pair_dist) "/> | |
| 63 <param name="param_algorithm_rt_dev_low" type="float" min="0.0" optional="True" value="15.0" label="maximum allowed deviation below optimal retention time distance" help="(-rt_dev_low) "/> | |
| 64 <param name="param_algorithm_rt_dev_high" type="float" min="0.0" optional="True" value="15.0" label="maximum allowed deviation above optimal retention time distance" help="(-rt_dev_high) "/> | |
| 65 <repeat name="rep_param_algorithm_mz_pair_dists" min="0" max="1" title="param_algorithm_mz_pair_dists"> | |
| 66 <param name="param_algorithm_mz_pair_dists" type="text" size="30" value="4.0" label="optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3, ." help="(-mz_pair_dists) by division through charge)"> | |
| 67 <sanitizer> | |
| 68 <valid initial="string.printable"> | |
| 69 <remove value="'"/> | |
| 70 <remove value="""/> | |
| 71 </valid> | |
| 72 </sanitizer> | |
| 73 </param> | |
| 74 </repeat> | |
| 75 <param name="param_algorithm_mz_dev" type="float" min="0.0" optional="True" value="0.05" label="maximum allowed deviation from optimal m/z distance" help="(-mz_dev) "/> | |
| 76 <expand macro="advanced_options"> | |
| 77 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | |
| 78 <param name="param_algorithm_mrm" display="radio" type="boolean" truevalue="-algorithm:mrm" falsevalue="" checked="false" optional="True" label="this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account)" help="(-mrm) "/> | |
| 79 </expand> | |
| 80 </inputs> | |
| 81 <outputs> | |
| 82 <data name="param_out" format="consensusxml"/> | |
| 83 </outputs> | |
| 84 <help>Groups corresponding isotope-labeled features in a feature map. | |
| 85 | |
| 86 | |
| 87 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureLinkerLabeled.html</help> | |
| 88 </tool> |