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annotate FeatureFinderMetabo.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
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4
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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 CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Quantitation]-->
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4 <tool id="FeatureFinderMetabo" name="FeatureFinderMetabo" version="2.0.0">
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5 <description>Assembles metabolite features from singleton mass traces.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FeatureFinderMetabo</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>FeatureFinderMetabo
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 -threads \${GALAXY_SLOTS:-24}
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22 #if $param_algorithm_common_noise_threshold_int:
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23 -algorithm:common:noise_threshold_int $param_algorithm_common_noise_threshold_int
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24 #end if
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25 #if $param_algorithm_common_chrom_peak_snr:
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26 -algorithm:common:chrom_peak_snr $param_algorithm_common_chrom_peak_snr
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27 #end if
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28 #if $param_algorithm_common_chrom_fwhm:
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29 -algorithm:common:chrom_fwhm $param_algorithm_common_chrom_fwhm
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30 #end if
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31 #if $param_algorithm_mtd_mass_error_ppm:
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32 -algorithm:mtd:mass_error_ppm $param_algorithm_mtd_mass_error_ppm
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33 #end if
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34 #if $param_algorithm_mtd_reestimate_mt_sd:
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35 -algorithm:mtd:reestimate_mt_sd
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36 #end if
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37 #if $param_algorithm_epd_enabled:
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38 -algorithm:epd:enabled
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39 #end if
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40 #if $param_algorithm_epd_width_filtering:
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41 -algorithm:epd:width_filtering
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42 #if &quot; &quot; in str($param_algorithm_epd_width_filtering):
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43 &quot;$param_algorithm_epd_width_filtering&quot;
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44 #else
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45 $param_algorithm_epd_width_filtering
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46 #end if
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47 #end if
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48 #if $param_algorithm_ffm_quant_method:
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49 -algorithm:ffm:quant_method
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50 #if &quot; &quot; in str($param_algorithm_ffm_quant_method):
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51 &quot;$param_algorithm_ffm_quant_method&quot;
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52 #else
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53 $param_algorithm_ffm_quant_method
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54 #end if
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55 #end if
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56 #if $param_algorithm_ffm_charge_lower_bound:
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57 -algorithm:ffm:charge_lower_bound $param_algorithm_ffm_charge_lower_bound
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58 #end if
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59 #if $param_algorithm_ffm_charge_upper_bound:
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60 -algorithm:ffm:charge_upper_bound $param_algorithm_ffm_charge_upper_bound
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61 #end if
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62 #if $param_algorithm_ffm_enable_RT_filtering:
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63 -algorithm:ffm:enable_RT_filtering
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64 #end if
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65 #if $adv_opts.adv_opts_selector=='advanced':
4
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66 #if $adv_opts.param_force:
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67 -force
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68 #end if
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69 #if $adv_opts.param_algorithm_mtd_trace_termination_criterion:
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70 -algorithm:mtd:trace_termination_criterion
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71 #if &quot; &quot; in str($adv_opts.param_algorithm_mtd_trace_termination_criterion):
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72 &quot;$adv_opts.param_algorithm_mtd_trace_termination_criterion&quot;
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73 #else
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74 $adv_opts.param_algorithm_mtd_trace_termination_criterion
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75 #end if
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76 #end if
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77 #if $adv_opts.param_algorithm_mtd_trace_termination_outliers:
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78 -algorithm:mtd:trace_termination_outliers $adv_opts.param_algorithm_mtd_trace_termination_outliers
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79 #end if
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80 #if $adv_opts.param_algorithm_mtd_min_sample_rate:
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81 -algorithm:mtd:min_sample_rate $adv_opts.param_algorithm_mtd_min_sample_rate
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82 #end if
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83 #if $adv_opts.param_algorithm_mtd_min_trace_length:
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84 -algorithm:mtd:min_trace_length $adv_opts.param_algorithm_mtd_min_trace_length
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85 #end if
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86 #if $adv_opts.param_algorithm_mtd_max_trace_length:
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87 -algorithm:mtd:max_trace_length $adv_opts.param_algorithm_mtd_max_trace_length
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88 #end if
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89 #if $adv_opts.param_algorithm_epd_min_fwhm:
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90 -algorithm:epd:min_fwhm $adv_opts.param_algorithm_epd_min_fwhm
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91 #end if
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92 #if $adv_opts.param_algorithm_epd_max_fwhm:
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93 -algorithm:epd:max_fwhm $adv_opts.param_algorithm_epd_max_fwhm
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94 #end if
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95 #if $adv_opts.param_algorithm_epd_masstrace_snr_filtering:
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96 -algorithm:epd:masstrace_snr_filtering
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97 #end if
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98 #if $adv_opts.param_algorithm_ffm_local_rt_range:
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99 -algorithm:ffm:local_rt_range $adv_opts.param_algorithm_ffm_local_rt_range
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100 #end if
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101 #if $adv_opts.param_algorithm_ffm_local_mz_range:
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102 -algorithm:ffm:local_mz_range $adv_opts.param_algorithm_ffm_local_mz_range
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103 #end if
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104 #if $adv_opts.param_algorithm_ffm_report_summed_ints:
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105 -algorithm:ffm:report_summed_ints
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106 #end if
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107 #if $adv_opts.param_algorithm_ffm_disable_isotope_filtering:
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108 -algorithm:ffm:disable_isotope_filtering
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109 #end if
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110 #if $adv_opts.param_algorithm_ffm_isotope_model:
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111 -algorithm:ffm:isotope_model
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112 #if &quot; &quot; in str($adv_opts.param_algorithm_ffm_isotope_model):
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113 &quot;$adv_opts.param_algorithm_ffm_isotope_model&quot;
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114 #else
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115 $adv_opts.param_algorithm_ffm_isotope_model
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116 #end if
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117 #end if
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118 #if $adv_opts.param_algorithm_ffm_isotope_noisemodel:
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119 -algorithm:ffm:isotope_noisemodel
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120 #if &quot; &quot; in str($adv_opts.param_algorithm_ffm_isotope_noisemodel):
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121 &quot;$adv_opts.param_algorithm_ffm_isotope_noisemodel&quot;
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122 #else
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123 $adv_opts.param_algorithm_ffm_isotope_noisemodel
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124 #end if
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125 #end if
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126 #if $adv_opts.param_algorithm_ffm_use_smoothed_intensities:
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127 -algorithm:ffm:use_smoothed_intensities
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128 #end if
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129 #end if
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130 </command>
4
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131 <inputs>
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132 <param format="mzml" help="(-in) " label="Centroided mzML file" name="param_in" optional="False" type="data"/>
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133 <param help="(-noise_threshold_int) " label="Intensity threshold below which peaks are regarded as noise" name="param_algorithm_common_noise_threshold_int" type="float" value="10.0"/>
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134 <param help="(-chrom_peak_snr) " label="Minimum signal-to-noise a mass trace should have" name="param_algorithm_common_chrom_peak_snr" type="float" value="3.0"/>
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135 <param help="(-chrom_fwhm) " label="Expected chromatographic peak width (in seconds)" name="param_algorithm_common_chrom_fwhm" type="float" value="5.0"/>
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136 <param help="(-mass_error_ppm) " label="Allowed mass deviation (in ppm)" name="param_algorithm_mtd_mass_error_ppm" type="float" value="20.0"/>
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137 <param checked="true" falsevalue="" help="(-reestimate_mt_sd) " label="Enables dynamic re-estimation of m/z variance during mass trace collection stage" name="param_algorithm_mtd_reestimate_mt_sd" optional="True" truevalue="-algorithm:mtd:reestimate_mt_sd" type="boolean"/>
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138 <param checked="true" falsevalue="" help="(-enabled) Disable for direct injection" label="Enable splitting of isobaric mass traces by chromatographic peak detection" name="param_algorithm_epd_enabled" optional="True" truevalue="-algorithm:epd:enabled" type="boolean"/>
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139 <param help="(-width_filtering) The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution" label="Enable filtering of unlikely peak widths" name="param_algorithm_epd_width_filtering" optional="True" type="select" value="fixed">
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140 <option value="off">off</option>
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141 <option value="fixed">fixed</option>
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142 <option value="auto">auto</option>
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143 </param>
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144 <param help="(-quant_method) For LC data 'area' is recommended, 'median' for direct injection data" label="Method of quantification for mass traces" name="param_algorithm_ffm_quant_method" optional="True" type="select" value="area">
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145 <option value="area">area</option>
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146 <option value="median">median</option>
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147 </param>
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148 <param help="(-charge_lower_bound) " label="Lowest charge state to conside" name="param_algorithm_ffm_charge_lower_bound" type="integer" value="1"/>
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149 <param help="(-charge_upper_bound) " label="Highest charge state to conside" name="param_algorithm_ffm_charge_upper_bound" type="integer" value="3"/>
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150 <param checked="true" falsevalue="" help="(-enable_RT_filtering) Disable for direct injection data" label="Require sufficient overlap in RT while assembling mass traces" name="param_algorithm_ffm_enable_RT_filtering" optional="True" truevalue="-algorithm:ffm:enable_RT_filtering" type="boolean"/>
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151 <expand macro="advanced_options">
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152 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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153 <param help="(-trace_termination_criterion) In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold" label="Termination criterion for the extension of mass traces" name="param_algorithm_mtd_trace_termination_criterion" optional="True" type="select" value="outlier">
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154 <option value="outlier">outlier</option>
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155 <option value="sample_rate">sample_rate</option>
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156 </param>
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157 <param help="(-trace_termination_outliers) " label="Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached" name="param_algorithm_mtd_trace_termination_outliers" type="integer" value="5"/>
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158 <param help="(-min_sample_rate) " label="Minimum fraction of scans along the mass trace that must contain a peak" name="param_algorithm_mtd_min_sample_rate" type="float" value="0.5"/>
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159 <param help="(-min_trace_length) " label="Minimum expected length of a mass trace (in seconds)" name="param_algorithm_mtd_min_trace_length" type="float" value="5.0"/>
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160 <param help="(-max_trace_length) " label="Maximum expected length of a mass trace (in seconds)" name="param_algorithm_mtd_max_trace_length" type="float" value="300.0"/>
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161 <param help="(-min_fwhm) Ignored if parameter width_filtering is off or auto" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" name="param_algorithm_epd_min_fwhm" type="float" value="3.0"/>
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162 <param help="(-max_fwhm) Ignored if parameter width_filtering is off or auto" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds)" name="param_algorithm_epd_max_fwhm" type="float" value="60.0"/>
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163 <param checked="false" falsevalue="" help="(-masstrace_snr_filtering) " label="Apply post-filtering by signal-to-noise ratio after smoothing" name="param_algorithm_epd_masstrace_snr_filtering" optional="True" truevalue="-algorithm:epd:masstrace_snr_filtering" type="boolean"/>
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164 <param help="(-local_rt_range) " label="RT range where to look for coeluting mass traces" name="param_algorithm_ffm_local_rt_range" type="float" value="10.0"/>
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165 <param help="(-local_mz_range) " label="MZ range where to look for isotopic mass traces" name="param_algorithm_ffm_local_mz_range" type="float" value="6.5"/>
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166 <param checked="false" falsevalue="" help="(-report_summed_ints) " label="Set to true for a feature intensity summed up over all traces rather than using monoisotopic trace intensity alone" name="param_algorithm_ffm_report_summed_ints" optional="True" truevalue="-algorithm:ffm:report_summed_ints" type="boolean"/>
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167 <param checked="false" falsevalue="" help="(-disable_isotope_filtering) " label="Disable isotope filtering" name="param_algorithm_ffm_disable_isotope_filtering" optional="True" truevalue="-algorithm:ffm:disable_isotope_filtering" type="boolean"/>
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168 <param help="(-isotope_model) " label="Change type of isotope model" name="param_algorithm_ffm_isotope_model" optional="True" type="select" value="metabolites">
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169 <option value="metabolites">metabolites</option>
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170 <option value="peptides">peptides</option>
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171 </param>
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172 <param help="(-isotope_noisemodel) Select the appropriate noise model according to the quality of measurement or MS device" label="SVM isotope models were trained with either 2% or 5% RMS erro" name="param_algorithm_ffm_isotope_noisemodel" optional="True" type="select" value="5%RMS">
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173 <option value="5%RMS">5%RMS</option>
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174 <option value="2%RMS">2%RMS</option>
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175 </param>
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176 <param checked="true" falsevalue="" help="(-use_smoothed_intensities) " label="Use LOWESS intensities instead of raw intensities" name="param_algorithm_ffm_use_smoothed_intensities" optional="True" truevalue="-algorithm:ffm:use_smoothed_intensities" type="boolean"/>
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177 </expand>
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178 </inputs>
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179 <outputs>
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180 <data format="xml" name="param_out"/>
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181 </outputs>
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182 <help>Assembles metabolite features from singleton mass traces.
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183
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184
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185 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMetabo.html</help>
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186 </tool>