Mercurial > repos > galaxyp > openms_featurelinkerunlabeled

annotate FeatureLinkerUnlabeled.xml @ 13:a6e006df7659 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:38:32 +0000
parents 6b88274392ce
children b46263c3ee99
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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: [Map Alignment]-->
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4 <tool id="FeatureLinkerUnlabeled" name="FeatureLinkerUnlabeled" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Groups corresponding features from multiple maps.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FeatureLinkerUnlabeled</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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17
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18 ## Preprocessing
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19 mkdir in &&
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20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
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21 mkdir out &&
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22 #if $design:
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23 mkdir design &&
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24 ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
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25 #end if
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27 ## Main program call
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29 set -o pipefail &&
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30 @EXECUTABLE@ -write_ctd ./ &&
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31 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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32 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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33 -in
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34 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
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35 -out
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36 'out/output.${gxy2omsext("consensusxml")}'
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37 #if $design:
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38 -design
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39 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)'
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40 #end if
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42 ## Postprocessing
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43 && mv 'out/output.${gxy2omsext("consensusxml")}' '$out'
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44 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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45 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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46 #end if]]></command>
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47 <configfiles>
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48 <inputs name="args_json" data_style="paths"/>
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49 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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50 </configfiles>
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51 <inputs>
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52 <param name="in" argument="-in" type="data" format="consensusxml,featurexml" multiple="true" optional="false" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
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53 <param name="design" argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/>
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54 <param name="keep_subelements" argument="-keep_subelements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" help=""/>
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55 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
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56 <param name="second_nearest_gap" argument="-algorithm:second_nearest_gap" type="float" optional="true" min="1.0" value="2.0" label="Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself" help=""/>
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57 <param name="use_identifications" argument="-algorithm:use_identifications" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered)" help=""/>
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58 <param name="ignore_charge" argument="-algorithm:ignore_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" help=""/>
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59 <param name="ignore_adduct" argument="-algorithm:ignore_adduct" type="boolean" truevalue="true" falsevalue="false" checked="true" label="true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts" help=""/>
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60 <section name="distance_RT" title="Distance component based on RT differences" help="" expanded="false">
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61 <param name="max_difference" argument="-algorithm:distance_RT:max_difference" type="float" optional="true" min="0.0" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help=""/>
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62 <param name="exponent" argument="-algorithm:distance_RT:exponent" type="float" optional="true" min="0.0" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
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63 <param name="weight" argument="-algorithm:distance_RT:weight" type="float" optional="true" min="0.0" value="1.0" label="Final RT distances are weighted by this facto" help=""/>
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64 </section>
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65 <section name="distance_MZ" title="Distance component based on m/z differences" help="" expanded="false">
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66 <param name="max_difference" argument="-algorithm:distance_MZ:max_difference" type="float" optional="true" min="0.0" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help=""/>
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67 <param name="unit" argument="-algorithm:distance_MZ:unit" display="radio" type="select" optional="false" label="Unit of the 'max_difference' paramete" help="">
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68 <option value="Da" selected="true">Da</option>
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69 <option value="ppm">ppm</option>
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70 <expand macro="list_string_san"/>
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71 </param>
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72 <param name="exponent" argument="-algorithm:distance_MZ:exponent" type="float" optional="true" min="0.0" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
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73 <param name="weight" argument="-algorithm:distance_MZ:weight" type="float" optional="true" min="0.0" value="1.0" label="Final m/z distances are weighted by this facto" help=""/>
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74 </section>
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75 <section name="distance_intensity" title="Distance component based on differences in relative intensity (usually relative to highest peak in the whole data set)" help="" expanded="false">
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76 <param name="exponent" argument="-algorithm:distance_intensity:exponent" type="float" optional="true" min="0.0" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
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77 <param name="weight" argument="-algorithm:distance_intensity:weight" type="float" optional="true" min="0.0" value="0.0" label="Final intensity distances are weighted by this facto" help=""/>
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78 <param name="log_transform" argument="-algorithm:distance_intensity:log_transform" display="radio" type="select" optional="false" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
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79 <option value="enabled">enabled</option>
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80 <option value="disabled" selected="true">disabled</option>
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81 <expand macro="list_string_san"/>
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82 </param>
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83 </section>
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84 </section>
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85 <expand macro="adv_opts_macro">
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86 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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87 <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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88 <expand macro="list_string_san"/>
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89 </param>
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90 </expand>
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91 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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92 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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93 </param>
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94 </inputs>
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95 <outputs>
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96 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/>
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97 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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98 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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99 </data>
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100 </outputs>
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101 <tests>
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102 <expand macro="autotest_FeatureLinkerUnlabeled"/>
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103 <expand macro="manutest_FeatureLinkerUnlabeled"/>
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104 </tests>
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105 <help><![CDATA[Groups corresponding features from multiple maps.
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106
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107
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108 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FeatureLinkerUnlabeled.html]]></help>
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109 <expand macro="references"/>
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110 </tool>