diff feature_linker_unlabeled_qt.xml @ 4:1183846e70a1 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/feature_linker_unlabeled_qt.xml	Wed Jun 19 13:15:44 2013 -0400
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+<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>