Mercurial > repos > galaxyp > openms_baselinefilter

annotate BaselineFilter.xml @ 13:2c6de76669fe draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 27 Aug 2020 19:36:32 -0400
parents f5946590b034
children 1936361a3dbb
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4768c361b11f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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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 <import>macros_autotest.xml</import>
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10 <import>macros_test.xml</import>
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11 </macros>
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12 <expand macro="requirements"/>
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13 <expand macro="stdio"/>
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14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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15 @EXT_FOO@
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16 #import re
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18 ## Preprocessing
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19 mkdir in &&
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20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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21 mkdir out &&
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23 ## Main program call
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24
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25 set -o pipefail &&
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26 @EXECUTABLE@ -write_ctd ./ &&
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27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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29 -in
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30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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31 -out
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32 'out/output.${gxy2omsext("mzml")}'
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34 ## Postprocessing
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35 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
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36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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38 #end if]]></command>
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39 <configfiles>
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40 <inputs name="args_json" data_style="paths"/>
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41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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42 </configfiles>
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43 <inputs>
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44 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input raw data file" help=" select mzml data sets(s)"/>
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45 <param name="struc_elem_length" argument="-struc_elem_length" type="float" optional="true" value="3.0" label="Length of the structuring element (should be wider than maximal peak width - see documentation)" help=""/>
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46 <param name="struc_elem_unit" argument="-struc_elem_unit" display="radio" type="select" optional="false" label="Unit of 'struc_elem_length' paramete" help="">
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47 <option value="Thomson" selected="true">Thomson</option>
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48 <option value="DataPoints">DataPoints</option>
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49 <expand macro="list_string_san"/>
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50 </param>
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51 <param name="method" argument="-method" type="select" optional="false" label="The name of the morphological filter to be applied" help="If you are unsure, use the default">
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52 <option value="identity">identity</option>
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53 <option value="erosion">erosion</option>
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54 <option value="dilation">dilation</option>
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55 <option value="opening">opening</option>
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56 <option value="closing">closing</option>
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57 <option value="gradient">gradient</option>
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58 <option value="tophat" selected="true">tophat</option>
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59 <option value="bothat">bothat</option>
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60 <option value="erosion_simple">erosion_simple</option>
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61 <option value="dilation_simple">dilation_simple</option>
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62 <expand macro="list_string_san"/>
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63 </param>
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64 <expand macro="adv_opts_macro">
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65 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
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66 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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67 <expand macro="list_string_san"/>
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68 </param>
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69 </expand>
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70 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
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71 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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72 </param>
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73 </inputs>
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74 <outputs>
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75 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
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76 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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77 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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78 </data>
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79 </outputs>
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80 <tests>
2c6de76669fe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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81 <expand macro="autotest_BaselineFilter"/>
2c6de76669fe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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82 <expand macro="manutest_BaselineFilter"/>
2c6de76669fe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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83 </tests>
2c6de76669fe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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84 <help><![CDATA[Removes the baseline from profile spectra using a top-hat filter.
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4768c361b11f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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85
4768c361b11f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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86
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2c6de76669fe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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87 For more information, visit http://www.openms.de/documentation/TOPP_BaselineFilter.html]]></help>
2c6de76669fe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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88 <expand macro="references"/>
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4768c361b11f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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89 </tool>