Mercurial > repos > galaxyp > openms_featurefindermetabo
diff FeatureFinderMetabo.xml @ 9:b6e4da302f66 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author | galaxyp |
---|---|
date | Wed, 15 May 2019 08:25:30 -0400 |
parents | 1473223a9595 |
children | 21dc135961b5 |
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--- a/FeatureFinderMetabo.xml Tue Mar 20 14:52:17 2018 -0400 +++ b/FeatureFinderMetabo.xml Wed May 15 08:25:30 2019 -0400 @@ -10,7 +10,7 @@ <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> - <command>FeatureFinderMetabo + <command detect_errors="aggressive"><![CDATA[FeatureFinderMetabo #if $param_in: -in $param_in @@ -88,7 +88,7 @@ #end if #end if #if $param_algorithm_ffm_mz_scoring_13C: - -algorithm:ffm:mz_scoring_13C + -algorithm:ffm:mz_scoring_13C true #end if #if $param_algorithm_ffm_report_convex_hulls: -algorithm:ffm:report_convex_hulls @@ -144,7 +144,7 @@ #end if #end if #end if -</command> +]]></command> <inputs> <param name="param_in" type="data" format="mzml" optional="False" label="Centroided mzML file" help="(-in) "/> <param name="param_algorithm_common_noise_threshold_int" type="float" value="10.0" label="Intensity threshold below which peaks are regarded as noise" help="(-noise_threshold_int) "/> @@ -179,6 +179,12 @@ <option value="metabolites (5% RMS)" selected="true">metabolites (5% RMS)</option> <option value="peptides">peptides</option> <option value="none">none</option> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> </param> <param name="param_algorithm_ffm_mz_scoring_13C" display="radio" type="boolean" truevalue="-algorithm:ffm:mz_scoring_13C" falsevalue="" checked="false" optional="True" label="Use the 13C isotope peak position (~1.003355 Da) as the expected shift in m/z for isotope mass traces (highly recommended for lipidomics!)" help="(-mz_scoring_13C) Disable for general metabolites (as described in Kenar et al. 2014, MCP.)"/> <param name="param_algorithm_ffm_report_convex_hulls" display="radio" type="boolean" truevalue="-algorithm:ffm:report_convex_hulls" falsevalue="" checked="false" optional="True" label="Augment each reported feature with the convex hull of the underlying mass traces (increases featureXML file size considerably)" help="(-report_convex_hulls) "/> @@ -211,5 +217,5 @@ <help>Assembles metabolite features from centroided (LC-)MS data using the mass trace approach. -For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMetabo.html</help> +For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FeatureFinderMetabo.html</help> </tool>