Mercurial > repos > galaxyp > openms_assaygeneratormetabo

comparison AssayGeneratorMetabo.xml @ 2:d30e724536fc draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:26:23 +0000
parents cb9d2162b340
children 11ac8ae77fb7
comparison
equal deleted inserted replaced
1:2c3d2c216ff9 2:d30e724536fc
40 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS 40 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
41 && mv '@EXECUTABLE@.ctd' '$ctd_out' 41 && mv '@EXECUTABLE@.ctd' '$ctd_out'
42 #end if]]></command> 42 #end if]]></command>
43 <configfiles> 43 <configfiles>
44 <inputs name="args_json" data_style="paths"/> 44 <inputs name="args_json" data_style="paths"/>
45 <configfile name="hardcoded_json"><![CDATA[{"executable": "\$(which sirius)", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 45 <configfile name="hardcoded_json"><![CDATA[{"executable": "\$(which sirius)", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true, "sirius": {"cores": "\${GALAXY_SLOTS:-1}"}}]]></configfile>
46 </configfiles> 46 </configfiles>
47 <inputs> 47 <inputs>
48 <param name="in" argument="-in" type="data" format="mzml" multiple="true" optional="false" label="MzML input file(s) used for assay library generation" help=" select mzml data sets(s)"/> 48 <param name="in" argument="-in" type="data" format="mzml" multiple="true" optional="false" label="MzML input file(s) used for assay library generation" help=" select mzml data sets(s)"/>
49 <param name="in_id" argument="-in_id" type="data" format="featurexml" multiple="true" optional="false" label="FeatureXML input file(s) containing identification information" help="(e.g. AccurateMassSearch) select featurexml data sets(s)"/> 49 <param name="in_id" argument="-in_id" type="data" format="featurexml" multiple="true" optional="false" label="FeatureXML input file(s) containing identification information" help="(e.g. AccurateMassSearch) select featurexml data sets(s)"/>
50 <param name="out_type" type="select" optional="false" label="File type of output out (Assay library output file)"> 50 <param name="out_type" type="select" optional="false" label="File type of output out (Assay library output file)">
143 <expand macro="list_string_san"/> 143 <expand macro="list_string_san"/>
144 </param> 144 </param>
145 <param name="compound_timeout" argument="-sirius:compound_timeout" type="integer" optional="true" min="0" value="10" label="Time out in seconds per compound" help="To disable the timeout set the value to 0"/> 145 <param name="compound_timeout" argument="-sirius:compound_timeout" type="integer" optional="true" min="0" value="10" label="Time out in seconds per compound" help="To disable the timeout set the value to 0"/>
146 <param name="tree_timeout" argument="-sirius:tree_timeout" type="integer" optional="true" min="0" value="0" label="Time out in seconds per fragmentation tree computation" help=""/> 146 <param name="tree_timeout" argument="-sirius:tree_timeout" type="integer" optional="true" min="0" value="0" label="Time out in seconds per fragmentation tree computation" help=""/>
147 <param name="top_n_hits" argument="-sirius:top_n_hits" type="integer" optional="true" min="1" value="10" label="The number of top hits for each compound written to the CSI:FingerID output" help=""/> 147 <param name="top_n_hits" argument="-sirius:top_n_hits" type="integer" optional="true" min="1" value="10" label="The number of top hits for each compound written to the CSI:FingerID output" help=""/>
148 <param name="cores" argument="-sirius:cores" type="integer" optional="true" min="1" value="1" label="The number of cores SIRIUS is allowed to use on the system" help=""/>
149 <param name="auto_charge" argument="-sirius:auto_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this option if the charge of your compounds is unknown and you do not want to assume [M+H]+ as default" help="With the auto charge option SIRIUS will not care about charges and allow arbitrary adducts for the precursor peak"/> 148 <param name="auto_charge" argument="-sirius:auto_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this option if the charge of your compounds is unknown and you do not want to assume [M+H]+ as default" help="With the auto charge option SIRIUS will not care about charges and allow arbitrary adducts for the precursor peak"/>
150 <param name="ion_tree" argument="-sirius:ion_tree" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Print molecular formulas and node labels with the ion formula instead of the neutral formula" help=""/> 149 <param name="ion_tree" argument="-sirius:ion_tree" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Print molecular formulas and node labels with the ion formula instead of the neutral formula" help=""/>
151 <param name="no_recalibration" argument="-sirius:no_recalibration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this option is set, SIRIUS will not recalibrate the spectrum during the analysis" help=""/> 150 <param name="no_recalibration" argument="-sirius:no_recalibration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this option is set, SIRIUS will not recalibrate the spectrum during the analysis" help=""/>
152 <param name="most_intense_ms2" argument="-sirius:most_intense_ms2" type="boolean" truevalue="true" falsevalue="false" checked="false" label="SIRIUS uses the fragmentation spectrum with the most intense precursor peak (for each spectrum)" help=""/> 151 <param name="most_intense_ms2" argument="-sirius:most_intense_ms2" type="boolean" truevalue="true" falsevalue="false" checked="false" label="SIRIUS uses the fragmentation spectrum with the most intense precursor peak (for each spectrum)" help=""/>
153 </section> 152 </section>
158 <option value="ppm">ppm</option> 157 <option value="ppm">ppm</option>
159 <expand macro="list_string_san"/> 158 <expand macro="list_string_san"/>
160 </param> 159 </param>
161 <param name="min_fragment_mz" argument="-min_fragment_mz" type="float" optional="true" value="0.0" label="Minimal m/z of a fragment ion choosen as a transition" help=""/> 160 <param name="min_fragment_mz" argument="-min_fragment_mz" type="float" optional="true" value="0.0" label="Minimal m/z of a fragment ion choosen as a transition" help=""/>
162 <param name="max_fragment_mz" argument="-max_fragment_mz" type="float" optional="true" value="2000.0" label="Maximal m/z of a fragment ion choosen as a transition" help=""/> 161 <param name="max_fragment_mz" argument="-max_fragment_mz" type="float" optional="true" value="2000.0" label="Maximal m/z of a fragment ion choosen as a transition" help=""/>
163 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 162 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
164 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 163 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
165 <expand macro="list_string_san"/> 164 <expand macro="list_string_san"/>
166 </param> 165 </param>
167 </expand> 166 </expand>
168 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> 167 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
169 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 168 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
170 </param> 169 </param>
171 </inputs> 170 </inputs>
172 <outputs> 171 <outputs>
173 <data name="out" label="${tool.name} on ${on_string}: out"> 172 <data name="out" label="${tool.name} on ${on_string}: out">
186 <expand macro="manutest_AssayGeneratorMetabo"/> 185 <expand macro="manutest_AssayGeneratorMetabo"/>
187 </tests> 186 </tests>
188 <help><![CDATA[Assay library generation from DDA data (Metabolomics) 187 <help><![CDATA[Assay library generation from DDA data (Metabolomics)
189 188
190 189
191 For more information, visit http://www.openms.de/documentation/UTILS_AssayGeneratorMetabo.html]]></help> 190 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_AssayGeneratorMetabo.html]]></help>
192 <expand macro="references"/> 191 <expand macro="references"/>
193 </tool> 192 </tool>