Mercurial > repos > galaxyp > openms_featurelinkerlabeled

annotate FeatureLinkerLabeled.xml @ 15:d9ebdc2e55fe draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:09:37 +0000
parents a33857ab19d0
children 90a5563d9a69
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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="FeatureLinkerLabeled" name="FeatureLinkerLabeled" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Groups corresponding isotope-labeled features in a feature map.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FeatureLinkerLabeled</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="requirements"/>
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11 <expand macro="stdio"/>
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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13 @EXT_FOO@
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14 #import re
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16 ## Preprocessing
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17 mkdir in &&
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18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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19 mkdir out &&
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21 ## Main program call
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23 set -o pipefail &&
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24 @EXECUTABLE@ -write_ctd ./ &&
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25 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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26 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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27 -in
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28 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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29 -out
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30 'out/output.${gxy2omsext("consensusxml")}'
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31
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32 ## Postprocessing
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33 && mv 'out/output.${gxy2omsext("consensusxml")}' '$out'
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34 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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35 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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36 #end if]]></command>
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37 <configfiles>
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38 <inputs name="args_json" data_style="paths"/>
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39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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40 </configfiles>
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41 <inputs>
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42 <param argument="-in" type="data" format="featurexml" optional="false" label="Input file" help=" select featurexml data sets(s)"/>
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43 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
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44 <param name="rt_estimate" argument="-algorithm:rt_estimate" type="boolean" truevalue="true" falsevalue="false" checked="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="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"/>
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45 <param name="rt_pair_dist" argument="-algorithm:rt_pair_dist" type="float" optional="true" value="-20.0" label="optimal pair distance in RT [sec] from light to heavy feature" help=""/>
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46 <param name="rt_dev_low" argument="-algorithm:rt_dev_low" type="float" optional="true" min="0.0" value="15.0" label="maximum allowed deviation below optimal retention time distance" help=""/>
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47 <param name="rt_dev_high" argument="-algorithm:rt_dev_high" type="float" optional="true" min="0.0" value="15.0" label="maximum allowed deviation above optimal retention time distance" help=""/>
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48 <param name="mz_pair_dists" argument="-algorithm:mz_pair_dists" type="text" optional="true" value="4.0" label="optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3" help="by division through charge) (space separated list, in order to allow for spaces in list items surround them by single quotes)">
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49 <expand macro="list_float_valsan" name="mz_pair_dists"/>
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50 </param>
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51 <param name="mz_dev" argument="-algorithm:mz_dev" type="float" optional="true" min="0.0" value="0.05" label="maximum allowed deviation from optimal m/z distance" help=""/>
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52 <param name="mrm" argument="-algorithm:mrm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account)" help=""/>
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53 </section>
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54 <expand macro="adv_opts_macro">
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55 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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56 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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57 <expand macro="list_string_san" name="test"/>
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58 </param>
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59 </expand>
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60 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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61 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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62 </param>
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63 </inputs>
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64 <outputs>
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65 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/>
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66 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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67 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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68 </data>
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69 </outputs>
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70 <tests><!-- TOPP_FeatureLinkerLabeled_1 -->
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71 <test expect_num_outputs="2">
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72 <section name="adv_opts">
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73 <param name="force" value="false"/>
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74 <param name="test" value="true"/>
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75 </section>
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76 <param name="in" value="FeatureLinkerLabeled_1_input.featureXML"/>
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77 <output name="out" file="FeatureLinkerLabeled_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
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78 <section name="algorithm">
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79 <param name="rt_estimate" value="false"/>
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80 <param name="rt_pair_dist" value="-1.0"/>
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81 <param name="rt_dev_low" value="0.4"/>
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82 <param name="rt_dev_high" value="0.4"/>
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83 <param name="mz_pair_dists" value="8.0"/>
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84 <param name="mz_dev" value="0.1"/>
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85 <param name="mrm" value="false"/>
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86 </section>
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87 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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88 <output name="ctd_out" ftype="xml">
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89 <assert_contents>
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90 <is_valid_xml/>
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91 </assert_contents>
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92 </output>
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93 </test>
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94 <!-- TOPP_FeatureLinkerLabeled_2 -->
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95 <test expect_num_outputs="2">
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96 <section name="adv_opts">
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97 <param name="force" value="false"/>
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98 <param name="test" value="true"/>
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99 </section>
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100 <param name="in" value="FeatureLinkerLabeled_2_input.featureXML"/>
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101 <output name="out" file="FeatureLinkerLabeled_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
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102 <section name="algorithm">
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103 <param name="rt_estimate" value="true"/>
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104 <param name="rt_pair_dist" value="-121.0382"/>
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105 <param name="rt_dev_low" value="123.3965"/>
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106 <param name="rt_dev_high" value="123.3965"/>
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107 <param name="mz_pair_dists" value="4.0"/>
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108 <param name="mz_dev" value="0.1"/>
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109 <param name="mrm" value="false"/>
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110 </section>
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111 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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112 <output name="ctd_out" ftype="xml">
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113 <assert_contents>
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114 <is_valid_xml/>
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115 </assert_contents>
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116 </output>
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117 </test>
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118 </tests>
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119 <help><![CDATA[Groups corresponding isotope-labeled features in a feature map.
0
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120
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121
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122 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureLinkerLabeled.html]]></help>
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123 <expand macro="references"/>
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124 </tool>