Mercurial > repos > galaxyp > openms_spectrafilterparentpeakmower

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:30:08 +0000
parents 5694ec584f4c
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b16ae1f4e2ed planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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1 <!--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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2 <!--Proposed Tool Section: [Spectrum processing: peak smoothing / normalization]-->
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3 <tool id="SpectraFilterParentPeakMower" name="SpectraFilterParentPeakMower" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Applies thresholdfilter to peak spectra</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">SpectraFilterParentPeakMower</token>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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12 @EXT_FOO@
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13 #import re
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15 ## Preprocessing
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16 mkdir in &&
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17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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18 mkdir out &&
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20 ## Main program call
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22 set -o pipefail &&
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23 @EXECUTABLE@ -write_ctd ./ &&
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24 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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25 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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26 -in
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27 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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28 -out
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29 'out/output.${gxy2omsext("mzml")}'
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30
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31 ## Postprocessing
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32 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
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33 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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34 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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35 #end if]]></command>
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36 <configfiles>
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37 <inputs name="args_json" data_style="paths"/>
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38 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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39 </configfiles>
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40 <inputs>
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41 <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
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42 <section name="algorithm" title="Algorithm parameter subsection" help="" expanded="false">
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43 <param name="window_size" argument="-algorithm:window_size" type="float" value="2.0" label="The size of the m/z window where the peaks are removed, +/- window_size" help=""/>
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44 <param name="default_charge" argument="-algorithm:default_charge" type="integer" value="2" label="If the precursor has no charge set, the default charge is assumed" help=""/>
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45 <param name="clean_all_charge_states" argument="-algorithm:clean_all_charge_states" type="integer" value="1" label="Set to 1 if precursor ions of all possible charge states should be removed" help=""/>
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46 <param name="consider_NH3_loss" argument="-algorithm:consider_NH3_loss" type="integer" value="1" label="Whether NH3 loss peaks from the precursor should be removed" help=""/>
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47 <param name="consider_H2O_loss" argument="-algorithm:consider_H2O_loss" type="integer" value="1" label="Whether H2O loss peaks from the precursor should be removed" help=""/>
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48 <param name="reduce_by_factor" argument="-algorithm:reduce_by_factor" type="integer" value="0" label="Reduce the intensities of the precursor and related ions by a given factor (set 'set_to_zero' to 0)" help=""/>
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49 <param name="factor" argument="-algorithm:factor" type="float" value="1000.0" label="Factor which is used to reduce the intensities if 'reduce_by_factor' is selected" help=""/>
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50 <param name="set_to_zero" argument="-algorithm:set_to_zero" type="integer" value="1" label="Reduce the intensities of the precursor and related ions to zero" help=""/>
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51 </section>
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52 <expand macro="adv_opts_macro">
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53 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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54 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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55 <expand macro="list_string_san" name="test"/>
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56 </param>
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57 </expand>
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58 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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59 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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60 </param>
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61 </inputs>
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62 <outputs>
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63 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
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64 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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65 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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66 </data>
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67 </outputs>
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68 <tests>
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69 <test expect_num_outputs="1">
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70 <!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
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71 <param name="adv_opts|test" value="true"/>
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72 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
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73 <output name="out" value="SpectraFilterParentPeakMower.mzML" compare="sim_size"/>
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74 </test>
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75 </tests>
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76 <help><![CDATA[Applies thresholdfilter to peak spectra.
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2199afa87e7d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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79 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpectraFilterParentPeakMower.html]]></help>
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e60558a87656 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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80 <expand macro="references"/>
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509659eeec69 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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81 </tool>