Mercurial > repos > galaxyp > openms_metaprosip

comparison MetaProSIP.xml @ 5:fdb3fbfef4cc draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
author galaxyp
date Mon, 12 Feb 2018 12:54:44 -0500
parents 21644dec106d
children 96cc79adfadb
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4:05f78b9d5874 5:fdb3fbfef4cc
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="MetaProSIP" name="MetaProSIP" version="2.2.0.1"> 4 <tool id="MetaProSIP" name="MetaProSIP" version="2.3.0">
5 <description>Performs proteinSIP on peptide features for elemental flux analysis.</description> 5 <description>Performs proteinSIP on peptide features for elemental flux analysis.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MetaProSIP</token> 7 <token name="@EXECUTABLE@">MetaProSIP</token>
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 <requirement type="package" version="3.3.1">r-base</requirement> 13 <requirement type="package" version="3.4.1">r-base</requirement>
14 </expand> 14 </expand>
15 <command>MetaProSIP 15 <command>MetaProSIP
16 16
17 #if $param_in_mzML: 17 #if $param_in_mzML:
18 -in_mzML $param_in_mzML 18 -in_mzML $param_in_mzML
27 -out_peptide_centric_csv $param_out_peptide_centric_csv 27 -out_peptide_centric_csv $param_out_peptide_centric_csv
28 #end if 28 #end if
29 #if $param_in_featureXML: 29 #if $param_in_featureXML:
30 -in_featureXML $param_in_featureXML 30 -in_featureXML $param_in_featureXML
31 #end if 31 #end if
32
33 -r_executable 'R'
34
35 #if $param_mz_tolerance_ppm: 32 #if $param_mz_tolerance_ppm:
36 -mz_tolerance_ppm $param_mz_tolerance_ppm 33 -mz_tolerance_ppm $param_mz_tolerance_ppm
37 #end if 34 #end if
38 #if $param_rt_tolerance_s: 35 #if $param_rt_tolerance_s:
39 -rt_tolerance_s $param_rt_tolerance_s 36 -rt_tolerance_s $param_rt_tolerance_s
138 <param name="param_mz_tolerance_ppm" type="float" value="10.0" label="Tolerance in ppm" help="(-mz_tolerance_ppm) "/> 135 <param name="param_mz_tolerance_ppm" type="float" value="10.0" label="Tolerance in ppm" help="(-mz_tolerance_ppm) "/>
139 <param name="param_rt_tolerance_s" type="float" value="30.0" label="Rolerance window around feature rt for XIC extraction" help="(-rt_tolerance_s) "/> 136 <param name="param_rt_tolerance_s" type="float" value="30.0" label="Rolerance window around feature rt for XIC extraction" help="(-rt_tolerance_s) "/>
140 <param name="param_intensity_threshold" type="float" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help="(-intensity_threshold) "/> 137 <param name="param_intensity_threshold" type="float" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help="(-intensity_threshold) "/>
141 <param name="param_correlation_threshold" type="float" value="0.7" label="Correlation threshold for reporting a RIA" help="(-correlation_threshold) "/> 138 <param name="param_correlation_threshold" type="float" value="0.7" label="Correlation threshold for reporting a RIA" help="(-correlation_threshold) "/>
142 <param name="param_xic_threshold" type="float" value="0.7" label="Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak" help="(-xic_threshold) If featureXML from reference file is used it should be disabled (set to -1) as no mono-isotopic peak is expected to be present"/> 139 <param name="param_xic_threshold" type="float" value="0.7" label="Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak" help="(-xic_threshold) If featureXML from reference file is used it should be disabled (set to -1) as no mono-isotopic peak is expected to be present"/>
143 <param name="param_decomposition_threshold" type="float" value="0.7" label="Minimum R^2 of decomposition that must be achieved for a peptide to be reported" help="(-decomposition_threshold) "/> 140 <param name="param_decomposition_threshold" type="float" value="0.7" label="Minimum R² of decomposition that must be achieved for a peptide to be reported" help="(-decomposition_threshold) "/>
144 <param name="param_weight_merge_window" type="float" value="5.0" label="Decomposition coefficients within +- this rate window will be combined" help="(-weight_merge_window) "/> 141 <param name="param_weight_merge_window" type="float" value="5.0" label="Decomposition coefficients within +- this rate window will be combined" help="(-weight_merge_window) "/>
145 <param name="param_plot_extension" display="radio" type="select" optional="False" value="png" label="Extension used for plots (png|svg|pdf)" help="(-plot_extension) "> 142 <param name="param_plot_extension" display="radio" type="select" optional="False" value="png" label="Extension used for plots (png|svg|pdf)" help="(-plot_extension) ">
146 <option value="png" selected="true">png</option> 143 <option value="png" selected="true">png</option>
147 <option value="svg">svg</option> 144 <option value="svg">svg</option>
148 <option value="pdf">pdf</option> 145 <option value="pdf">pdf</option>
189 <data name="param_out_peptide_centric_csv" format="tabular"/> 186 <data name="param_out_peptide_centric_csv" format="tabular"/>
190 </outputs> 187 </outputs>
191 <help>Performs proteinSIP on peptide features for elemental flux analysis. 188 <help>Performs proteinSIP on peptide features for elemental flux analysis.
192 189
193 190
194 For more information, visit http://www.openms.de/comp/metaprosip/</help> 191 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MetaProSIP.html</help>
195 </tool> 192 </tool>