Mercurial > repos > galaxyp > openms_featurelinkerunlabeled

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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 21:35:21 +0000
parents b46263c3ee99
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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: [Feature Linking]-->
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3 <tool id="FeatureLinkerUnlabeled" name="FeatureLinkerUnlabeled" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Groups corresponding features from multiple maps</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">FeatureLinkerUnlabeled</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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14
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15 ## Preprocessing
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16 mkdir in_cond.in &&
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17 #if $in_cond.in_select == "no"
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18 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
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19 ${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
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20 #else
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21 cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
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22 #end if
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23 mkdir out &&
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24 #if $design:
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25 mkdir design &&
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26 cp '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
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27 #end if
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29 ## Main program call
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31 set -o pipefail &&
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32 @EXECUTABLE@ -write_ctd ./ &&
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33 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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34 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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35 -in
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36 #if $in_cond.in_select == "no"
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37 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
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38 #else
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39 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
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40 #end if
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41 -out
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42 'out/output.${gxy2omsext("consensusxml")}'
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43 #if $design:
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44 -design
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45 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)'
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46 #end if
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48 ## Postprocessing
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49 && mv 'out/output.${gxy2omsext("consensusxml")}' '$out'
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50 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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51 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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52 #end if]]></command>
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53 <configfiles>
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54 <inputs name="args_json" data_style="paths"/>
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55 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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56 </configfiles>
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57 <inputs>
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58 <conditional name="in_cond">
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59 <param name="in_select" type="select" label="Run tool in batch mode for -in">
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60 <option value="no">No: process all datasets jointly</option>
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61 <option value="yes">Yes: process each dataset in an independent job</option>
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62 </param>
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63 <when value="no">
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64 <param argument="-in" type="data" format="consensusxml,featurexml" multiple="true" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
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65 </when>
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66 <when value="yes">
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67 <param argument="-in" type="data" format="consensusxml,featurexml" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
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68 </when>
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69 </conditional>
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70 <param 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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71 <param 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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72 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
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73 <param name="second_nearest_gap" argument="-algorithm:second_nearest_gap" type="float" 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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74 <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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75 <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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76 <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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77 <section name="distance_RT" title="Distance component based on RT differences" help="" expanded="false">
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78 <param name="max_difference" argument="-algorithm:distance_RT:max_difference" type="float" min="0.0" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help=""/>
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79 <param name="exponent" argument="-algorithm:distance_RT:exponent" type="float" 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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80 <param name="weight" argument="-algorithm:distance_RT:weight" type="float" min="0.0" value="1.0" label="Final RT distances are weighted by this facto" help=""/>
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81 </section>
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82 <section name="distance_MZ" title="Distance component based on m/z differences" help="" expanded="false">
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83 <param name="max_difference" argument="-algorithm:distance_MZ:max_difference" type="float" min="0.0" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help=""/>
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84 <param name="unit" argument="-algorithm:distance_MZ:unit" type="select" label="Unit of the 'max_difference' paramete" help="">
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85 <option value="Da" selected="true">Da</option>
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86 <option value="ppm">ppm</option>
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87 <expand macro="list_string_san" name="unit"/>
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88 </param>
16
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89 <param name="exponent" argument="-algorithm:distance_MZ:exponent" type="float" 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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90 <param name="weight" argument="-algorithm:distance_MZ:weight" type="float" min="0.0" value="1.0" label="Final m/z distances are weighted by this facto" help=""/>
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91 </section>
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92 <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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93 <param name="exponent" argument="-algorithm:distance_intensity:exponent" type="float" 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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94 <param name="weight" argument="-algorithm:distance_intensity:weight" type="float" min="0.0" value="0.0" label="Final intensity distances are weighted by this facto" help=""/>
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95 <param name="log_transform" argument="-algorithm:distance_intensity:log_transform" type="select" 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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96 <option value="enabled">enabled</option>
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97 <option value="disabled" selected="true">disabled</option>
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98 <expand macro="list_string_san" name="log_transform"/>
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99 </param>
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100 </section>
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101 </section>
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102 <expand macro="adv_opts_macro">
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103 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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104 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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105 <expand macro="list_string_san" name="test"/>
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106 </param>
0
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107 </expand>
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108 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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109 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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110 </param>
0
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111 </inputs>
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112 <outputs>
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113 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/>
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114 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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115 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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116 </data>
0
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117 </outputs>
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118 <tests>
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119 <!-- TOPP_FeatureLinkerUnlabeled_1 -->
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120 <test expect_num_outputs="2">
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121 <section name="adv_opts">
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122 <param name="force" value="false"/>
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123 <param name="test" value="true"/>
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124 </section>
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125 <conditional name="in_cond">
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126 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
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127 </conditional>
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128 <output name="out" value="FeatureLinkerUnlabeled_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
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129 <param name="keep_subelements" value="false"/>
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130 <section name="algorithm">
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131 <param name="second_nearest_gap" value="2.0"/>
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132 <param name="use_identifications" value="false"/>
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133 <param name="ignore_charge" value="true"/>
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134 <param name="ignore_adduct" value="true"/>
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135 <section name="distance_RT">
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136 <param name="max_difference" value="200.0"/>
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137 <param name="exponent" value="1.0"/>
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138 <param name="weight" value="1.0"/>
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139 </section>
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140 <section name="distance_MZ">
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141 <param name="max_difference" value="0.5"/>
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142 <param name="unit" value="Da"/>
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143 <param name="exponent" value="1.0"/>
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144 <param name="weight" value="1.0"/>
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145 </section>
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146 <section name="distance_intensity">
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147 <param name="exponent" value="1.0"/>
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148 <param name="weight" value="0.0"/>
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149 <param name="log_transform" value="disabled"/>
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150 </section>
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151 </section>
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152 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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153 <output name="ctd_out" ftype="xml">
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154 <assert_contents>
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155 <is_valid_xml/>
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156 </assert_contents>
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157 </output>
16
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158 <assert_stdout>
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159 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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160 </assert_stdout>
15
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161 </test>
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162 <!-- TOPP_FeatureLinkerUnlabeled_2 -->
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163 <test expect_num_outputs="2">
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164 <section name="adv_opts">
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165 <param name="force" value="false"/>
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166 <param name="test" value="true"/>
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167 </section>
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168 <conditional name="in_cond">
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169 <param name="in" value="FeatureLinkerUnlabeled_2_input1.featureXML,FeatureLinkerUnlabeled_2_input2.featureXML,FeatureLinkerUnlabeled_2_input3.featureXML"/>
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170 </conditional>
16
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171 <output name="out" value="FeatureLinkerUnlabeled_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
15
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172 <param name="keep_subelements" value="false"/>
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173 <section name="algorithm">
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174 <param name="second_nearest_gap" value="2.0"/>
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175 <param name="use_identifications" value="false"/>
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176 <param name="ignore_charge" value="false"/>
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177 <param name="ignore_adduct" value="true"/>
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178 <section name="distance_RT">
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179 <param name="max_difference" value="100.0"/>
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180 <param name="exponent" value="1.0"/>
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181 <param name="weight" value="1.0"/>
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182 </section>
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183 <section name="distance_MZ">
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184 <param name="max_difference" value="0.3"/>
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185 <param name="unit" value="Da"/>
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186 <param name="exponent" value="2.0"/>
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187 <param name="weight" value="1.0"/>
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188 </section>
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189 <section name="distance_intensity">
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190 <param name="exponent" value="1.0"/>
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191 <param name="weight" value="0.5"/>
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192 <param name="log_transform" value="disabled"/>
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193 </section>
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194 </section>
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195 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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196 <output name="ctd_out" ftype="xml">
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197 <assert_contents>
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198 <is_valid_xml/>
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199 </assert_contents>
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200 </output>
16
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201 <assert_stdout>
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202 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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203 </assert_stdout>
15
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204 </test>
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205 <!-- TOPP_FeatureLinkerUnlabeled_3 -->
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206 <test expect_num_outputs="2">
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207 <section name="adv_opts">
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208 <param name="force" value="false"/>
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209 <param name="test" value="true"/>
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210 </section>
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211 <conditional name="in_cond">
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212 <param name="in" value="FeatureLinkerUnlabeled_3_input1.featureXML,FeatureLinkerUnlabeled_3_input2.featureXML"/>
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213 </conditional>
16
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214 <output name="out" value="FeatureLinkerUnlabeled_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
15
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215 <param name="keep_subelements" value="false"/>
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216 <section name="algorithm">
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217 <param name="second_nearest_gap" value="1.5"/>
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218 <param name="use_identifications" value="false"/>
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219 <param name="ignore_charge" value="true"/>
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220 <param name="ignore_adduct" value="true"/>
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221 <section name="distance_RT">
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222 <param name="max_difference" value="30.0"/>
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223 <param name="exponent" value="1.0"/>
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224 <param name="weight" value="1.0"/>
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225 </section>
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226 <section name="distance_MZ">
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227 <param name="max_difference" value="0.3"/>
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228 <param name="unit" value="Da"/>
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229 <param name="exponent" value="2.0"/>
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230 <param name="weight" value="1.0"/>
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231 </section>
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232 <section name="distance_intensity">
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233 <param name="exponent" value="1.0"/>
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234 <param name="weight" value="0.0"/>
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235 <param name="log_transform" value="disabled"/>
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236 </section>
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237 </section>
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238 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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239 <output name="ctd_out" ftype="xml">
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240 <assert_contents>
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241 <is_valid_xml/>
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242 </assert_contents>
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243 </output>
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244 <assert_stdout>
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245 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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246 </assert_stdout>
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247 </test>
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248 <!-- TOPP_FeatureLinkerUnlabeled_4 -->
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249 <test expect_num_outputs="2">
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250 <section name="adv_opts">
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251 <param name="force" value="false"/>
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252 <param name="test" value="true"/>
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253 </section>
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254 <conditional name="in_cond">
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255 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
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256 </conditional>
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257 <output name="out" value="FeatureLinkerUnlabeled_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
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258 <param name="keep_subelements" value="false"/>
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259 <section name="algorithm">
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260 <param name="second_nearest_gap" value="2.0"/>
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261 <param name="use_identifications" value="true"/>
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262 <param name="ignore_charge" value="true"/>
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263 <param name="ignore_adduct" value="true"/>
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264 <section name="distance_RT">
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265 <param name="max_difference" value="200.0"/>
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266 <param name="exponent" value="2.0"/>
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267 <param name="weight" value="1.0"/>
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268 </section>
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269 <section name="distance_MZ">
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270 <param name="max_difference" value="0.5"/>
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271 <param name="unit" value="Da"/>
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272 <param name="exponent" value="2.0"/>
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273 <param name="weight" value="1.0"/>
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274 </section>
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275 <section name="distance_intensity">
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276 <param name="exponent" value="1.0"/>
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277 <param name="weight" value="0.0"/>
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278 <param name="log_transform" value="disabled"/>
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279 </section>
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280 </section>
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281 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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282 <output name="ctd_out" ftype="xml">
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283 <assert_contents>
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284 <is_valid_xml/>
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285 </assert_contents>
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286 </output>
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287 <assert_stdout>
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288 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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289 </assert_stdout>
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290 </test>
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291 </tests>
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292 <help><![CDATA[Groups corresponding features from multiple maps.
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293
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294
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295 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureLinkerUnlabeled.html]]></help>
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296 <expand macro="references"/>
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297 </tool>