Mercurial > repos > galaxyp > openms
diff macros.xml @ 4:1183846e70a1 draft
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author | galaxyp |
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date | Wed, 19 Jun 2013 13:15:44 -0400 |
parents | cf0d72c7b482 |
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--- a/macros.xml Fri May 10 17:31:59 2013 -0400 +++ b/macros.xml Wed Jun 19 13:15:44 2013 -0400 @@ -80,4 +80,64 @@ </change_format> </data> </macro> + <macro name="aligner_model"> + <conditional name="model"> + <param name="model_type" type="select" label="Model Type"> + <option value="linear">Linear</option> + <option value="b_spline" selected="true">Smoothing spline (non-linear)</option> + <option value="interpolated">Interpolated</option> + </param> + <when value="linear"> + <!-- TODO: Add symmetric_regression --> + </when> + <when value="b_spline"> + <!-- TODO: Add num_breakpoints, break_positions --> + </when> + <when value="interpolated"> + <param name="interpolation_type" type="select" label="Interpolation Type"> + <option value="cspline" selected="true">cspline</option> + <option value="linear">linear</option> + <option value="akima">akima</option> + </param> + </when> + </conditional> + </macro> + <macro name="feature_linker_input"> + <conditional name="type"> + <param name="input_type" type="select" label="Input Type"> + <option value="featurexml">Features (FeatureXML)</option> + <option value="consensusxml">Consensus (ConsensusXML)</option> + </param> + <when value="featurexml"> + <param format="featurexml" name="inputs" type="data" label="Input Features" multiple="true" /> + </when> + <when value="consensusxml"> + <param format="consensusxml" name="inputs" type="data" label="Input Consensus" multiple="true" /> + <param name="keep_subelements" type="boolean" label="Transfer sub-features of the inputs to the output." truevalue="keep_subelements=true" falsevalue="" /> + </when> + </conditional> + </macro> + <macro name="feature_linker_algorithm_options"> + <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)." /> + <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" /> + <param name="rt_max_difference" type="float" label="Max Difference (RT)" value="100" help="Maximum allowed difference in RT in seconds." /> + <param name="mz_max_difference" type="float" label="Max Difference (m/z)" value="0.3" help="Maximum allowed difference in m/z" /> + <param name="mz_max_difference_unit" type="select" label="Max Difference Units (m/z)"> + <option value="Da" selected="true">Da</option> + <option value="ppm" selected="true">ppm</option> + </param> + <conditional name="advanced"> + <param name="specify" type="boolean" label="Specify advanced exponents and weights for distances (RT, m/z, and intensity)" /> + <when value="true"> + <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" /> + <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" /> + <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" /> + <param name="rt_weight" label="RT Exponent" help="RT distances are weighted by this factor" type="float" value="1" /> + <param name="mz_weight" label="m/z Exponent" help="m/z distances are weighted by this factor" type="float" value="2" /> + <param name="intensity_weight" label="Intensity Exponent" help="Distances based on relative intensity are weighted by this factor" type="float" value="0" /> + </when> + <when value="false"> + </when> + </conditional> + </macro> </macros> \ No newline at end of file