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1 <macros>
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2 <macro name="stdio">
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3 <stdio>
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4 <exit_code range="1:" level="fatal" description="Error running OpenMS tool." />
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5 </stdio>
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6 </macro>
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7 <macro name="requires">
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8 <requirements>
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9 <requirement type="package">openms</requirement>
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10 <yield />
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11 </requirements>
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12 </macro>
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13 <macro name="sampling_rate_param">
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14 <param name="sampling_rate_param" label="Sampling Rate" help="New sampling rate in m/z dimension." value="0.1" type="float" />
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15 </macro>
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16 <macro name="id_inputs">
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17 <param name="input1" label="Input Peak List (mzML)" type="data" format="mzml" />
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18 <param name="database" label="Database" type="data" format="fasta" />
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19 </macro>
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20 <macro name="id_outputs">
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21 <outputs>
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22 <data format="idxml" name="out" />
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23 </outputs>
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24 </macro>
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25 <macro name="precursor_mass_tolerance_param">
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26 <param name="precursor_mass_tolerance" label="Precursor Mass Tolerance" value="1.5" type="float" />
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27 </macro>
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28 <macro name="precursor_mass_tolerance_unit_param">
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29 <param name="precursor_mass_tolerance_unit" label="Precursor Mass Tolerance Units" type="select">
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30 <option value="Da" selected="true">Daltons</option>
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31 <option value="ppm">ppm</option>
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32 </param>
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33 </macro>
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34 <macro name="fragment_mass_tolerance_param">
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35 <param name="fragment_mass_tolerance" label="Fragment Mass Tolerance" value="0.3" type="float" />
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36 </macro>
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37 <macro name="fragment_mass_tolerance_unit_param">
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38 <param name="fragment_mass_tolerance_unit" label="Fragment Mass Tolerance Units" type="select">
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39 <option value="Da" selected="true">Daltons</option>
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40 <option value="ppm">ppm</option>
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41 </param>
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42 </macro>
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43 <macro name="fixed_modifications_param">
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44 <param name="fixed_modifications" type="select" label="Fixed Modification" multiple="true">
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45 <options from_file="openms_mods.loc">
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46 <column name="name" index="0" />
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47 <column name="value" index="0" />
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48 </options>
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49 </param>
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50 </macro>
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51 <macro name="variable_modifications_param">
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52 <param name="variable_modifications" type="select" label="Variable Modification" multiple="true">
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53 <options from_file="openms_mods.loc">
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54 <column name="name" index="0" />
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55 <column name="value" index="0" />
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56 </options>
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57 </param>
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58 </macro>
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59 <macro name="precursor_charge_params">
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60 <param name="min_precursor_charge" label="Minimum Precursor Charge" value="1" type="integer" />
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61 <param name="max_precursor_charge" label="Maximum Precursor Charge" value="4" type="integer" />
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62 </macro>
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63 <macro name="raw_feature_finder_params">
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64 <param name="rt_threshold" type="float" value="30" label="RT Threshold" help="Upper bound for the retention time [s] over which a characteristic peptide elutes." />
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65 <param name="rt_min" type="float" value="0" label="RT Minimum" help="Lower bound for the retention time [s]." />
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66 <param name="intensity_cutoff" type="float" value="10000" label="Intensity Cutoff" help="Lower bound for the intensity of isotopic peaks in a SILAC pattern." />
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67 <param name="intensity_correlation" type="float" value="0.7" label="Intensity Correlation" help="Lower bound for the Pearson correlation coefficient, which measures how well intensity profiles of different isotopic peaks correlate." />
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68 <param name="model_deviation" type="float" value="3" label="Model Deviation" help="Upper bound on the factor by which the ratios of observed isotopic peaks are allowed to differ from the ratios of the theoretic averagine model, i.e. ( theoretic_ratio / model_deviation ) < observed_ratio < ( theoretic_ratio * model_deviation )." />
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69 <param name="min_charge" type="integer" value="2" label="Minimum Charge" />
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70 <param name="max_charge" type="integer" value="4" label="Maximum Charge" />
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71 <param name="min_peaks_per_peptide" type="integer" value="3" label="Minimum Number of Peaks Per Peptide" />
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72 <param name="max_peaks_per_peptide" type="integer" value="5" label="Maximum Number of Peaks Per Peptide" />
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73 </macro>
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74 <macro name="map_input">
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75 </macro>
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76 <macro name="map_output">
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77 <data format="consensusxml" name="map_output">
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78 <change_format>
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79 <when input="input_type" value="featurexml" format="featurexml" />
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80 </change_format>
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81 </data>
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82 </macro>
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83 <macro name="aligner_model">
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84 <conditional name="model">
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85 <param name="model_type" type="select" label="Model Type">
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86 <option value="linear">Linear</option>
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87 <option value="b_spline" selected="true">Smoothing spline (non-linear)</option>
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88 <option value="interpolated">Interpolated</option>
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89 </param>
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90 <when value="linear">
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91 <!-- TODO: Add symmetric_regression -->
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92 </when>
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93 <when value="b_spline">
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94 <!-- TODO: Add num_breakpoints, break_positions -->
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95 </when>
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96 <when value="interpolated">
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97 <param name="interpolation_type" type="select" label="Interpolation Type">
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98 <option value="cspline" selected="true">cspline</option>
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99 <option value="linear">linear</option>
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100 <option value="akima">akima</option>
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101 </param>
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102 </when>
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103 </conditional>
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104 </macro>
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105 <macro name="feature_linker_input">
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106 <conditional name="type">
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107 <param name="input_type" type="select" label="Input Type">
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108 <option value="featurexml">Features (FeatureXML)</option>
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109 <option value="consensusxml">Consensus (ConsensusXML)</option>
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110 </param>
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111 <when value="featurexml">
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112 <param format="featurexml" name="inputs" type="data" label="Input Features" multiple="true" />
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113 </when>
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114 <when value="consensusxml">
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115 <param format="consensusxml" name="inputs" type="data" label="Input Consensus" multiple="true" />
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116 <param name="keep_subelements" type="boolean" label="Transfer sub-features of the inputs to the output." truevalue="keep_subelements=true" falsevalue="" />
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117 </when>
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118 </conditional>
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119 </macro>
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120 <macro name="feature_linker_algorithm_options">
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121 <param name="use_identifications" type="boolean" truevalue="algorithm!use_identifications=true" falsevalue="" label="Use Identifications" checked="false" help="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)." />
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122 <param name="ignore_charge" type="boolean" truevalue="algorithm!ignore_charge=true" falsevalue="" label="Use Charge" help="Compare features normally even if their charge states are different." checked="false" />
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123 <param name="rt_max_difference" type="float" label="Max Difference (RT)" value="100" help="Maximum allowed difference in RT in seconds." />
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124 <param name="mz_max_difference" type="float" label="Max Difference (m/z)" value="0.3" help="Maximum allowed difference in m/z" />
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125 <param name="mz_max_difference_unit" type="select" label="Max Difference Units (m/z)">
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126 <option value="Da" selected="true">Da</option>
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127 <option value="ppm" selected="true">ppm</option>
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128 </param>
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129 <conditional name="advanced">
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130 <param name="specify" type="boolean" label="Specify advanced exponents and weights for distances (RT, m/z, and intensity)" />
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131 <when value="true">
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132 <param name="rt_exponent" label="RT Exponent" help="Normalized RT differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" type="float" value="1" />
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133 <param name="mz_exponent" label="m/z Exponent" help="Normalized m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" type="float" value="1" />
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134 <param name="intensity_exponent" label="Intensity Exponent" help="Differences in relative intensity are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" type="float" value="1" />
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135 <param name="rt_weight" label="RT Exponent" help="RT distances are weighted by this factor" type="float" value="1" />
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136 <param name="mz_weight" label="m/z Exponent" help="m/z distances are weighted by this factor" type="float" value="2" />
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137 <param name="intensity_weight" label="Intensity Exponent" help="Distances based on relative intensity are weighted by this factor" type="float" value="0" />
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138 </when>
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139 <when value="false">
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140 </when>
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141 </conditional>
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142 </macro>
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143 </macros> |
