Mercurial > repos > galaxyp > openms_mapalignerposeclustering
annotate MapAlignerPoseClustering.xml @ 4:e86e83ac0cd3 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author | galaxyp |
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date | Wed, 15 May 2019 08:10:13 -0400 |
parents | 304c13ce9577 |
children | e237cb433a92 |
rev | line source |
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2
304c13ce9577
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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1 <?xml version='1.0' encoding='UTF-8'?> |
304c13ce9577
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> |
304c13ce9577
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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3 <!--Proposed Tool Section: [Map Alignment]--> |
304c13ce9577
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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4 <tool id="MapAlignerPoseClustering" name="MapAlignerPoseClustering" version="2.3.0"> |
0
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
galaxyp
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5 <description>Corrects retention time distortions between maps using a pose clustering approach.</description> |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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6 <macros> |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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7 <token name="@EXECUTABLE@">MapAlignerPoseClustering</token> |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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8 <import>macros.xml</import> |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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9 </macros> |
2
304c13ce9577
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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10 <expand macro="references"/> |
0
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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11 <expand macro="stdio"/> |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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12 <expand macro="requirements"/> |
4
e86e83ac0cd3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
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13 <command detect_errors="aggressive"><![CDATA[ |
e86e83ac0cd3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
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14 |
e86e83ac0cd3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
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15 #import re |
1
40ca4302e603
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 42171f39c42277bcfb50271180dcc9c82d3e8e74
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16 |
40ca4302e603
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 42171f39c42277bcfb50271180dcc9c82d3e8e74
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17 mkdir -p ./results_trafoxml ./results_out && |
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70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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18 MapAlignerPoseClustering |
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40ca4302e603
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 42171f39c42277bcfb50271180dcc9c82d3e8e74
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19 |
40ca4302e603
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 42171f39c42277bcfb50271180dcc9c82d3e8e74
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20 -in |
40ca4302e603
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 42171f39c42277bcfb50271180dcc9c82d3e8e74
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21 #for $infile in $param_in: |
40ca4302e603
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 42171f39c42277bcfb50271180dcc9c82d3e8e74
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22 '$infile' |
40ca4302e603
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 42171f39c42277bcfb50271180dcc9c82d3e8e74
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23 #end for |
40ca4302e603
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 42171f39c42277bcfb50271180dcc9c82d3e8e74
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24 |
40ca4302e603
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 42171f39c42277bcfb50271180dcc9c82d3e8e74
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25 -out |
4
e86e83ac0cd3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
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26 #for $infile in $param_in: |
e86e83ac0cd3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
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27 #set escaped_element_identifier = re.sub('[^\w\-\s]', '_', str($infile.element_identifier)) |
e86e83ac0cd3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
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28 './results_out/${escaped_element_identifier}.${infile.extension}' |
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40ca4302e603
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 42171f39c42277bcfb50271180dcc9c82d3e8e74
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29 #end for |
40ca4302e603
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 42171f39c42277bcfb50271180dcc9c82d3e8e74
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30 |
40ca4302e603
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 42171f39c42277bcfb50271180dcc9c82d3e8e74
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31 -trafo_out |
4
e86e83ac0cd3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
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32 #for $infile in $param_in: |
e86e83ac0cd3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
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33 #set escaped_element_identifier = re.sub('[^\w\-\s]', '_', str($infile.element_identifier)) |
e86e83ac0cd3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
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34 './results_trafoxml/${escaped_element_identifier}.trafoxml' |
1
40ca4302e603
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 42171f39c42277bcfb50271180dcc9c82d3e8e74
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35 #end for |
0
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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36 |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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37 #if $param_reference_file: |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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38 -reference:file $param_reference_file |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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39 #end if |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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40 #if $param_reference_index: |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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41 -reference:index $param_reference_index |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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42 #end if |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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43 #if $param_algorithm_max_num_peaks_considered: |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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44 -algorithm:max_num_peaks_considered $param_algorithm_max_num_peaks_considered |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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45 #end if |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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46 #if $param_algorithm_superimposer_mz_pair_max_distance: |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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47 -algorithm:superimposer:mz_pair_max_distance $param_algorithm_superimposer_mz_pair_max_distance |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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48 #end if |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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49 #if $param_algorithm_superimposer_num_used_points: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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50 -algorithm:superimposer:num_used_points $param_algorithm_superimposer_num_used_points |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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51 #end if |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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52 #if $param_algorithm_superimposer_scaling_bucket_size: |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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53 -algorithm:superimposer:scaling_bucket_size $param_algorithm_superimposer_scaling_bucket_size |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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54 #end if |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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55 #if $param_algorithm_superimposer_shift_bucket_size: |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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56 -algorithm:superimposer:shift_bucket_size $param_algorithm_superimposer_shift_bucket_size |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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57 #end if |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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58 #if $param_algorithm_pairfinder_second_nearest_gap: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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59 -algorithm:pairfinder:second_nearest_gap $param_algorithm_pairfinder_second_nearest_gap |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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60 #end if |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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61 #if $param_algorithm_pairfinder_use_identifications: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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62 -algorithm:pairfinder:use_identifications |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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63 #end if |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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64 #if $param_algorithm_pairfinder_ignore_charge: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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65 -algorithm:pairfinder:ignore_charge |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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66 #end if |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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67 #if $param_algorithm_pairfinder_distance_RT_max_difference: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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68 -algorithm:pairfinder:distance_RT:max_difference $param_algorithm_pairfinder_distance_RT_max_difference |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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69 #end if |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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70 #if $param_algorithm_pairfinder_distance_MZ_max_difference: |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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71 -algorithm:pairfinder:distance_MZ:max_difference $param_algorithm_pairfinder_distance_MZ_max_difference |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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72 #end if |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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73 #if $param_algorithm_pairfinder_distance_MZ_unit: |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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74 -algorithm:pairfinder:distance_MZ:unit |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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75 #if " " in str($param_algorithm_pairfinder_distance_MZ_unit): |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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76 "$param_algorithm_pairfinder_distance_MZ_unit" |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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77 #else |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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78 $param_algorithm_pairfinder_distance_MZ_unit |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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79 #end if |
70f729e59244
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
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80 #end if |
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81 #if $adv_opts.adv_opts_selector=='advanced': |
2
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82 #if $adv_opts.param_force: |
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83 -force |
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84 #end if |
0
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85 #if $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction: |
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86 -algorithm:superimposer:rt_pair_distance_fraction $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction |
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87 #end if |
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88 #if $adv_opts.param_algorithm_superimposer_max_shift: |
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89 -algorithm:superimposer:max_shift $adv_opts.param_algorithm_superimposer_max_shift |
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90 #end if |
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91 #if $adv_opts.param_algorithm_superimposer_max_scaling: |
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92 -algorithm:superimposer:max_scaling $adv_opts.param_algorithm_superimposer_max_scaling |
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93 #end if |
2
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94 #if $adv_opts.param_algorithm_superimposer_dump_buckets: |
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95 -algorithm:superimposer:dump_buckets "$adv_opts.param_algorithm_superimposer_dump_buckets" |
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96 #end if |
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97 #if $adv_opts.param_algorithm_superimposer_dump_pairs: |
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98 -algorithm:superimposer:dump_pairs "$adv_opts.param_algorithm_superimposer_dump_pairs" |
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99 #end if |
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100 #if $adv_opts.param_algorithm_pairfinder_distance_RT_exponent: |
0
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101 -algorithm:pairfinder:distance_RT:exponent $adv_opts.param_algorithm_pairfinder_distance_RT_exponent |
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102 #end if |
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103 #if $adv_opts.param_algorithm_pairfinder_distance_RT_weight: |
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104 -algorithm:pairfinder:distance_RT:weight $adv_opts.param_algorithm_pairfinder_distance_RT_weight |
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105 #end if |
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106 #if $adv_opts.param_algorithm_pairfinder_distance_MZ_exponent: |
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107 -algorithm:pairfinder:distance_MZ:exponent $adv_opts.param_algorithm_pairfinder_distance_MZ_exponent |
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108 #end if |
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109 #if $adv_opts.param_algorithm_pairfinder_distance_MZ_weight: |
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110 -algorithm:pairfinder:distance_MZ:weight $adv_opts.param_algorithm_pairfinder_distance_MZ_weight |
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111 #end if |
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112 #if $adv_opts.param_algorithm_pairfinder_distance_intensity_exponent: |
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113 -algorithm:pairfinder:distance_intensity:exponent $adv_opts.param_algorithm_pairfinder_distance_intensity_exponent |
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114 #end if |
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115 #if $adv_opts.param_algorithm_pairfinder_distance_intensity_weight: |
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116 -algorithm:pairfinder:distance_intensity:weight $adv_opts.param_algorithm_pairfinder_distance_intensity_weight |
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117 #end if |
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118 #if $adv_opts.param_algorithm_pairfinder_distance_intensity_log_transform: |
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119 -algorithm:pairfinder:distance_intensity:log_transform |
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120 #if " " in str($adv_opts.param_algorithm_pairfinder_distance_intensity_log_transform): |
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121 "$adv_opts.param_algorithm_pairfinder_distance_intensity_log_transform" |
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122 #else |
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123 $adv_opts.param_algorithm_pairfinder_distance_intensity_log_transform |
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124 #end if |
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125 #end if |
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126 #end if |
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127 ]]> |
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128 </command> |
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129 <inputs> |
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130 <param name="param_in" type="data" format="mzML,featureXML" multiple="true" label="Input files to align (all must have the same file type)" help="(-in) "/> |
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131 <param name="param_reference_file" type="data" format="mzML,featureXML" optional="True" label="File to use as reference (same file format as input files required)" help="(-file) "/> |
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132 <param name="param_reference_index" type="integer" min="0" optional="True" value="0" label="Use one of the input files as reference ('1' for the first file, etc.)" help="(-index) <br>If '0', no explicit reference is set - the algorithm will select a reference"/> |
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133 <param name="param_algorithm_max_num_peaks_considered" type="integer" min="-1" optional="True" value="1000" label="The maximal number of peaks/features to be considered per map" help="(-max_num_peaks_considered) To use all, set to '-1'"/> |
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134 <param name="param_algorithm_superimposer_mz_pair_max_distance" type="float" min="0.0" optional="True" value="0.5" label="Maximum of m/z deviation of corresponding elements in different maps" help="(-mz_pair_max_distance) This condition applies to the pairs considered in hashing"/> |
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135 <param name="param_algorithm_superimposer_num_used_points" type="integer" min="-1" optional="True" value="2000" label="Maximum number of elements considered in each map (selected by intensity)" help="(-num_used_points) Use this to reduce the running time and to disregard weak signals during alignment. For using all points, set this to -1"/> |
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136 <param name="param_algorithm_superimposer_scaling_bucket_size" type="float" min="0.0" optional="True" value="0.005" label="The scaling of the retention time interval is being hashed into buckets of this size during pose clustering" help="(-scaling_bucket_size) A good choice for this would be a bit smaller than the error you would expect from repeated runs"/> |
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137 <param name="param_algorithm_superimposer_shift_bucket_size" type="float" min="0.0" optional="True" value="3.0" label="The shift at the lower (respectively, higher) end of the retention time interval is being hashed into buckets of this size during pose clustering" help="(-shift_bucket_size) A good choice for this would be about the time between consecutive MS scans"/> |
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138 <param name="param_algorithm_pairfinder_second_nearest_gap" type="float" min="1.0" optional="True" value="2.0" label="Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself" help="(-second_nearest_gap) "/> |
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139 <param name="param_algorithm_pairfinder_use_identifications" display="radio" type="boolean" truevalue="-algorithm:pairfinder:use_identifications" falsevalue="" checked="false" optional="True" label="Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered)" help="(-use_identifications) "/> |
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140 <param name="param_algorithm_pairfinder_ignore_charge" display="radio" type="boolean" truevalue="-algorithm:pairfinder:ignore_charge" falsevalue="" checked="false" optional="True" label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" help="(-ignore_charge) "/> |
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141 <param name="param_algorithm_pairfinder_distance_RT_max_difference" type="float" min="0.0" optional="True" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help="(-max_difference) "/> |
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142 <param name="param_algorithm_pairfinder_distance_MZ_max_difference" type="float" min="0.0" optional="True" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help="(-max_difference) "/> |
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143 <param name="param_algorithm_pairfinder_distance_MZ_unit" display="radio" type="select" optional="False" value="Da" label="Unit of the 'max_difference' paramete" help="(-unit) "> |
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144 <option value="Da" selected="true">Da</option> |
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145 <option value="ppm">ppm</option> |
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146 </param> |
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147 <expand macro="advanced_options"> |
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148 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> |
0
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149 <param name="param_algorithm_superimposer_rt_pair_distance_fraction" type="float" min="0.0" max="1.0" optional="True" value="0.1" label="Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval (i.e., max - min)" help="(-rt_pair_distance_fraction) "/> |
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150 <param name="param_algorithm_superimposer_max_shift" type="float" min="0.0" optional="True" value="1000.0" label="Maximal shift which is considered during histogramming (in seconds)" help="(-max_shift) This applies for both directions"/> |
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151 <param name="param_algorithm_superimposer_max_scaling" type="float" min="1.0" optional="True" value="2.0" label="Maximal scaling which is considered during histogramming" help="(-max_scaling) The minimal scaling is the reciprocal of this"/> |
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152 <param name="param_algorithm_superimposer_dump_buckets" type="text" size="30" label="[DEBUG] If non-empty, base filename where hash table buckets will be dumped to" help="(-dump_buckets) A serial number for each invocation will be appended automatically"> |
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153 <sanitizer> |
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154 <valid initial="string.printable"> |
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155 <remove value="'"/> |
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156 <remove value="""/> |
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157 </valid> |
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158 </sanitizer> |
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159 </param> |
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160 <param name="param_algorithm_superimposer_dump_pairs" type="text" size="30" label="[DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!)" help="(-dump_pairs) A serial number for each invocation will be appended automatically"> |
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161 <sanitizer> |
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162 <valid initial="string.printable"> |
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163 <remove value="'"/> |
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164 <remove value="""/> |
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165 </valid> |
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166 </sanitizer> |
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167 </param> |
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168 <param name="param_algorithm_pairfinder_distance_RT_exponent" type="float" min="0.0" optional="True" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/> |
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169 <param name="param_algorithm_pairfinder_distance_RT_weight" type="float" min="0.0" optional="True" value="1.0" label="Final RT distances are weighted by this facto" help="(-weight) "/> |
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170 <param name="param_algorithm_pairfinder_distance_MZ_exponent" type="float" min="0.0" optional="True" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/> |
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171 <param name="param_algorithm_pairfinder_distance_MZ_weight" type="float" min="0.0" optional="True" value="1.0" label="Final m/z distances are weighted by this facto" help="(-weight) "/> |
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172 <param name="param_algorithm_pairfinder_distance_intensity_exponent" type="float" min="0.0" optional="True" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/> |
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173 <param name="param_algorithm_pairfinder_distance_intensity_weight" type="float" min="0.0" optional="True" value="0.0" label="Final intensity distances are weighted by this facto" help="(-weight) "/> |
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174 <param name="param_algorithm_pairfinder_distance_intensity_log_transform" display="radio" type="select" optional="False" value="disabled" label="Log-transform intensities?" help="(-log_transform) If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))"> |
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175 <option value="enabled">enabled</option> |
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176 <option value="disabled" selected="true">disabled</option> |
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177 </param> |
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178 </expand> |
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179 </inputs> |
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180 <outputs> |
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181 <collection name="out" type="list"> |
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182 <discover_datasets pattern="__designation_and_ext__" directory="results_out"/> |
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183 </collection> |
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184 |
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185 <collection name="trafo_out" type="list"> |
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186 <discover_datasets pattern="__designation_and_ext__" directory="results_trafoxml"/> |
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187 </collection> |
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188 </outputs> |
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189 <help>Corrects retention time distortions between maps using a pose clustering approach. |
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190 |
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191 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_MapAlignerPoseClustering.html</help> |
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192 </tool> |