Mercurial > repos > galaxyp > openms
diff feature_linker_unlabeled_qt.xml @ 4:1183846e70a1 draft
Uploaded
author | galaxyp |
---|---|
date | Wed, 19 Jun 2013 13:15:44 -0400 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/feature_linker_unlabeled_qt.xml Wed Jun 19 13:15:44 2013 -0400 @@ -0,0 +1,58 @@ +<tool id="openms_feature_linker_unlabeled_qt" version="0.1.0" name="Feature Linker (Unlabeled QT)"> + <description> + Groups corresponding features from multiple maps using a QT clustering approach. + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="stdio" /> + <expand macro="requires" /> + <command interpreter="python"> + openms_wrapper.py --executable 'FeatureLinkerUnlabeledQT' --config $config + </command> + <configfiles> + <configfile name="config">[simple_options] +in=${",".join(map(str, $inputs))} +out=$output +#if $type.input_type == "consensusxml" +$keep_subelements +#end if +$ignore_charge +$use_identifications +algorithm!distance_RT!max_difference=$rt_max_difference +algorithm!distance_MZ!max_difference=$mz_max_difference +algorithm!distance_MZ!unit=$mz_max_difference_unit +#if $advanced.specify +algorithm!distance_RT!weight=$advanced.rt_weight +algorithm!distance_MZ!weight=$advanced.mz_weight +algorithm!distance_intensity!weight=$advanced.intensity_weight +algorithm!distance_RT!exponent=$advanced.rt_exponent +algorithm!distance_MZ!exponent=$advanced.mz_exponent +algorithm!distance_intensity!exponent=$advanced.intensity_exponent +#end if +</configfile> + </configfiles> + <inputs> + <expand macro="feature_linker_input" /> + + <expand macro="feature_linker_algorithm_options" /> + </inputs> + <outputs> + <data format="consensusxml" name="output" /> + </outputs> + <help> +**What it does** + +This tool provides an algorithm for grouping corresponding features in multiple runs of label-free experiments. For more details and algorithm-specific parameters (set in the INI file) see "Detailed Description" in the algorithm documentation or the INI file table below. + +FeatureLinkerUnlabeled takes several feature maps (featureXML files) and stores the corresponding features in a consensus map (consensusXML file). Feature maps can be created from MS experiments (peak data) using one of the FeatureFinder TOPP tools. + +Advanced users can convert the consensusXML generated by this tool to EDTA using FileConverter and plot the distribution of distances in RT (or m/z) between different input files (can be done in Excel). The distribution should be Gaussian-like with very few points beyond the tails. Points far away from the Gaussian indicate a too wide tolerance. A Gaussian with its left/right tail trimmed indicates a too narrow tolerance. + +**Citation** + +For the underlying tool, please cite ``Weisser et al.: An automated pipeline for high-throughput label-free quantitative proteomics (J. Proteome Res., 2013, PMID: 23391308).`` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms + </help> +</tool>