Mercurial > repos > galaxyp > openms_baselinefilter

annotate BaselineFilter.xml @ 11:f5946590b034 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 08:05:09 -0400
parents 50e62ab930b2
children 2c6de76669fe
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
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4 <tool id="BaselineFilter" name="BaselineFilter" version="2.3.0">
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5 <description>Removes the baseline from profile spectra using a top-hat filter.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">BaselineFilter</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command detect_errors="aggressive"><![CDATA[BaselineFilter
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 #if $param_struc_elem_length:
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22 -struc_elem_length $param_struc_elem_length
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23 #end if
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24 #if $param_struc_elem_unit:
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25 -struc_elem_unit
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26 #if " " in str($param_struc_elem_unit):
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27 "$param_struc_elem_unit"
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28 #else
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29 $param_struc_elem_unit
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30 #end if
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31 #end if
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32 #if $param_method:
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33 -method
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34 #if " " in str($param_method):
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35 "$param_method"
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36 #else
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37 $param_method
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38 #end if
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39 #end if
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40 #if $adv_opts.adv_opts_selector=='advanced':
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41 #if $adv_opts.param_force:
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42 -force
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43 #end if
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44 #end if
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45 ]]></command>
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46 <inputs>
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47 <param name="param_in" type="data" format="mzml" optional="False" label="input raw data file" help="(-in) "/>
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48 <param name="param_struc_elem_length" type="float" value="3.0" label="Length of the structuring element (should be wider than maximal peak width - see documentation)" help="(-struc_elem_length) "/>
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49 <param name="param_struc_elem_unit" display="radio" type="select" optional="False" value="Thomson" label="Unit of 'struc_elem_length' paramete" help="(-struc_elem_unit) ">
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50 <option value="Thomson" selected="true">Thomson</option>
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51 <option value="DataPoints">DataPoints</option>
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52 </param>
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53 <param name="param_method" type="select" optional="False" value="tophat" label="The name of the morphological filter to be applied" help="(-method) If you are unsure, use the default">
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54 <option value="identity">identity</option>
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55 <option value="erosion">erosion</option>
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56 <option value="dilation">dilation</option>
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57 <option value="opening">opening</option>
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58 <option value="closing">closing</option>
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59 <option value="gradient">gradient</option>
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60 <option value="tophat" selected="true">tophat</option>
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61 <option value="bothat">bothat</option>
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62 <option value="erosion_simple">erosion_simple</option>
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63 <option value="dilation_simple">dilation_simple</option>
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64 </param>
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65 <expand macro="advanced_options">
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66 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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67 </expand>
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68 </inputs>
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69 <outputs>
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70 <data name="param_out" format="mzml"/>
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71 </outputs>
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72 <help>Removes the baseline from profile spectra using a top-hat filter.
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73
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74
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75 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_BaselineFilter.html</help>
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76 </tool>