Mercurial > repos > galaxyp > openms_mapalignertreeguided

comparison MapAlignerTreeGuided.xml @ 2:25c08f95cdf4 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 20:39:15 +0000
parents 759648882c3c
children 502c7e321ba5
comparison
equal deleted inserted replaced
1:4bdaddb03b67 2:25c08f95cdf4
55 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS 55 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
56 && mv '@EXECUTABLE@.ctd' '$ctd_out' 56 && mv '@EXECUTABLE@.ctd' '$ctd_out'
57 #end if]]></command> 57 #end if]]></command>
58 <configfiles> 58 <configfiles>
59 <inputs name="args_json" data_style="paths"/> 59 <inputs name="args_json" data_style="paths"/>
60 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 60 <configfile name="hardcoded_json"><![CDATA[{"copy_data": "false", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
61 </configfiles> 61 </configfiles>
62 <inputs> 62 <inputs>
63 <param name="in" argument="-in" type="data" format="featurexml" multiple="true" optional="false" label="Input files to align (all must have the same file type)" help=" select featurexml data sets(s)"/> 63 <param name="in" argument="-in" type="data" format="featurexml" multiple="true" optional="false" label="Input files to align (all must have the same file type)" help=" select featurexml data sets(s)"/>
64 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> 64 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
65 <param name="model_type" argument="-algorithm:model_type" display="radio" type="select" optional="false" label="Options to control the modeling of retention time transformations from data" help=""> 65 <param name="model_type" argument="-algorithm:model_type" display="radio" type="select" optional="false" label="Options to control the modeling of retention time transformations from data" help="">
152 <param name="use_unassigned_peptides" argument="-algorithm:align_algorithm:use_unassigned_peptides" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Should unassigned peptide identifications be used when computing an alignment of feature or consensus maps" help="If 'false', only peptide IDs assigned to features will be used"/> 152 <param name="use_unassigned_peptides" argument="-algorithm:align_algorithm:use_unassigned_peptides" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Should unassigned peptide identifications be used when computing an alignment of feature or consensus maps" help="If 'false', only peptide IDs assigned to features will be used"/>
153 <param name="use_feature_rt" argument="-algorithm:align_algorithm:use_feature_rt" type="boolean" truevalue="true" falsevalue="false" checked="true" label="When aligning feature or consensus maps, don't use the retention time of a peptide identification directly; instead, use the retention time of the centroid of the feature (apex of the elution profile) that the peptide was matched to" help="If different identifications are matched to one feature, only the peptide closest to the centroid in RT is used.. Precludes 'use_unassigned_peptides'"/> 153 <param name="use_feature_rt" argument="-algorithm:align_algorithm:use_feature_rt" type="boolean" truevalue="true" falsevalue="false" checked="true" label="When aligning feature or consensus maps, don't use the retention time of a peptide identification directly; instead, use the retention time of the centroid of the feature (apex of the elution profile) that the peptide was matched to" help="If different identifications are matched to one feature, only the peptide closest to the centroid in RT is used.. Precludes 'use_unassigned_peptides'"/>
154 </section> 154 </section>
155 </section> 155 </section>
156 <expand macro="adv_opts_macro"> 156 <expand macro="adv_opts_macro">
157 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 157 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
158 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 158 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
159 <expand macro="list_string_san"/> 159 <expand macro="list_string_san"/>
160 </param> 160 </param>
161 </expand> 161 </expand>
162 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false"> 162 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
163 <option value="out_FLAG">out (When aligning feature or consensus maps, don't use the retention time of a peptide identification directly; instead, use the retention time of the centroid of the feature (apex of the elution profile) that the peptide was matched to)</option> 163 <option value="out_FLAG">out (Output files (same file type as 'in'))</option>
164 <option value="trafo_out_FLAG">trafo_out (When aligning feature or consensus maps, don't use the retention time of a peptide identification directly; instead, use the retention time of the centroid of the feature (apex of the elution profile) that the peptide was matched to)</option> 164 <option value="trafo_out_FLAG">trafo_out (Transformation output files)</option>
165 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 165 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
166 </param> 166 </param>
167 </inputs> 167 </inputs>
168 <outputs> 168 <outputs>
169 <collection type="list" name="out" label="${tool.name} on ${on_string}: out"> 169 <collection type="list" name="out" label="${tool.name} on ${on_string}: out">
186 <expand macro="manutest_MapAlignerTreeGuided"/> 186 <expand macro="manutest_MapAlignerTreeGuided"/>
187 </tests> 187 </tests>
188 <help><![CDATA[Tree guided correction of retention time distortions between maps. 188 <help><![CDATA[Tree guided correction of retention time distortions between maps.
189 189
190 190
191 For more information, visit http://www.openms.de/documentation/TOPP_MapAlignerTreeGuided.html]]></help> 191 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_MapAlignerTreeGuided.html]]></help>
192 <expand macro="references"/> 192 <expand macro="references"/>
193 </tool> 193 </tool>