Mercurial > repos > galaxyp > openms
comparison macros.xml @ 4:1183846e70a1 draft
Uploaded
| author | galaxyp |
|---|---|
| date | Wed, 19 Jun 2013 13:15:44 -0400 |
| parents | cf0d72c7b482 |
| children |
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| 3:8fa16707e162 | 4:1183846e70a1 |
|---|---|
| 78 <change_format> | 78 <change_format> |
| 79 <when input="input_type" value="featurexml" format="featurexml" /> | 79 <when input="input_type" value="featurexml" format="featurexml" /> |
| 80 </change_format> | 80 </change_format> |
| 81 </data> | 81 </data> |
| 82 </macro> | 82 </macro> |
| 83 <macro name="aligner_model"> | |
| 84 <conditional name="model"> | |
| 85 <param name="model_type" type="select" label="Model Type"> | |
| 86 <option value="linear">Linear</option> | |
| 87 <option value="b_spline" selected="true">Smoothing spline (non-linear)</option> | |
| 88 <option value="interpolated">Interpolated</option> | |
| 89 </param> | |
| 90 <when value="linear"> | |
| 91 <!-- TODO: Add symmetric_regression --> | |
| 92 </when> | |
| 93 <when value="b_spline"> | |
| 94 <!-- TODO: Add num_breakpoints, break_positions --> | |
| 95 </when> | |
| 96 <when value="interpolated"> | |
| 97 <param name="interpolation_type" type="select" label="Interpolation Type"> | |
| 98 <option value="cspline" selected="true">cspline</option> | |
| 99 <option value="linear">linear</option> | |
| 100 <option value="akima">akima</option> | |
| 101 </param> | |
| 102 </when> | |
| 103 </conditional> | |
| 104 </macro> | |
| 105 <macro name="feature_linker_input"> | |
| 106 <conditional name="type"> | |
| 107 <param name="input_type" type="select" label="Input Type"> | |
| 108 <option value="featurexml">Features (FeatureXML)</option> | |
| 109 <option value="consensusxml">Consensus (ConsensusXML)</option> | |
| 110 </param> | |
| 111 <when value="featurexml"> | |
| 112 <param format="featurexml" name="inputs" type="data" label="Input Features" multiple="true" /> | |
| 113 </when> | |
| 114 <when value="consensusxml"> | |
| 115 <param format="consensusxml" name="inputs" type="data" label="Input Consensus" multiple="true" /> | |
| 116 <param name="keep_subelements" type="boolean" label="Transfer sub-features of the inputs to the output." truevalue="keep_subelements=true" falsevalue="" /> | |
| 117 </when> | |
| 118 </conditional> | |
| 119 </macro> | |
| 120 <macro name="feature_linker_algorithm_options"> | |
| 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)." /> | |
| 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" /> | |
| 123 <param name="rt_max_difference" type="float" label="Max Difference (RT)" value="100" help="Maximum allowed difference in RT in seconds." /> | |
| 124 <param name="mz_max_difference" type="float" label="Max Difference (m/z)" value="0.3" help="Maximum allowed difference in m/z" /> | |
| 125 <param name="mz_max_difference_unit" type="select" label="Max Difference Units (m/z)"> | |
| 126 <option value="Da" selected="true">Da</option> | |
| 127 <option value="ppm" selected="true">ppm</option> | |
| 128 </param> | |
| 129 <conditional name="advanced"> | |
| 130 <param name="specify" type="boolean" label="Specify advanced exponents and weights for distances (RT, m/z, and intensity)" /> | |
| 131 <when value="true"> | |
| 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" /> | |
| 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" /> | |
| 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" /> | |
| 135 <param name="rt_weight" label="RT Exponent" help="RT distances are weighted by this factor" type="float" value="1" /> | |
| 136 <param name="mz_weight" label="m/z Exponent" help="m/z distances are weighted by this factor" type="float" value="2" /> | |
| 137 <param name="intensity_weight" label="Intensity Exponent" help="Distances based on relative intensity are weighted by this factor" type="float" value="0" /> | |
| 138 </when> | |
| 139 <when value="false"> | |
| 140 </when> | |
| 141 </conditional> | |
| 142 </macro> | |
| 83 </macros> | 143 </macros> |