Mercurial > repos > galaxyp > openms_featurefindercentroided

comparison FeatureFinderCentroided.xml @ 9:c56b544a3fb2 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 08:05:28 -0400
parents 077ba692e138
children 6eda2adf7613
comparison
equal deleted inserted replaced
8:d7f016292d95 9:c56b544a3fb2
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
10 <expand macro="references"/> 10 <expand macro="references"/>
11 <expand macro="stdio"/> 11 <expand macro="stdio"/>
12 <expand macro="requirements"/> 12 <expand macro="requirements"/>
13 <command>FeatureFinderCentroided 13 <command detect_errors="aggressive"><![CDATA[FeatureFinderCentroided
14 14
15 #if $param_in: 15 #if $param_in:
16 -in $param_in 16 -in $param_in
17 #end if 17 #end if
18 #if $param_out: 18 #if $param_out:
121 #end if 121 #end if
122 #if $adv_opts.param_algorithm_feature_max_intersection: 122 #if $adv_opts.param_algorithm_feature_max_intersection:
123 -algorithm:feature:max_intersection $adv_opts.param_algorithm_feature_max_intersection 123 -algorithm:feature:max_intersection $adv_opts.param_algorithm_feature_max_intersection
124 #end if 124 #end if
125 #end if 125 #end if
126 </command> 126 -threads "\${GALAXY_SLOTS:-1}"
127 ]]></command>
127 <inputs> 128 <inputs>
128 <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/> 129 <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/>
129 <param name="param_seeds" type="data" format="featurexml" optional="True" label="User specified seed list" help="(-seeds) "/> 130 <param name="param_seeds" type="data" format="featurexml" optional="True" label="User specified seed list" help="(-seeds) "/>
130 <param name="param_algorithm_intensity_bins" type="integer" min="1" optional="True" value="10" label="Number of bins per dimension (RT and m/z)" help="(-bins) The higher this value, the more local the intensity significance score is. &lt;br&gt;This parameter should be decreased, if the algorithm is used on small regions of a map"/> 131 <param name="param_algorithm_intensity_bins" type="integer" min="1" optional="True" value="10" label="Number of bins per dimension (RT and m/z)" help="(-bins) The higher this value, the more local the intensity significance score is. &lt;br&gt;This parameter should be decreased, if the algorithm is used on small regions of a map"/>
131 <param name="param_algorithm_mass_trace_mz_tolerance" type="float" min="0.0" optional="True" value="0.03" label="Tolerated m/z deviation of peaks belonging to the same mass trace" help="(-mz_tolerance) &lt;br&gt;It should be larger than the m/z resolution of the instrument. &lt;br&gt;This value must be smaller than that 1/charge_high!"/> 132 <param name="param_algorithm_mass_trace_mz_tolerance" type="float" min="0.0" optional="True" value="0.03" label="Tolerated m/z deviation of peaks belonging to the same mass trace" help="(-mz_tolerance) &lt;br&gt;It should be larger than the m/z resolution of the instrument. &lt;br&gt;This value must be smaller than that 1/charge_high!"/>
171 <data name="param_out_mzq" format="mzq"/> 172 <data name="param_out_mzq" format="mzq"/>
172 </outputs> 173 </outputs>
173 <help>Detects two-dimensional features in LC-MS data. 174 <help>Detects two-dimensional features in LC-MS data.
174 175
175 176
176 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderCentroided.html</help> 177 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FeatureFinderCentroided.html</help>
177 </tool> 178 </tool>