Mercurial > repos > galaxyp > openms_consensusid
annotate ConsensusID.xml @ 5:1bcd7ee6edaf draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
| author | galaxyp |
|---|---|
| date | Wed, 23 Aug 2017 13:30:10 -0400 |
| parents | 9d7e3e5da94a |
| children | fd633fe1d7d7 |
| rev | line source |
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5c56387ff06a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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1 <?xml version='1.0' encoding='UTF-8'?> |
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5c56387ff06a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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 CTD2Galaxy.--> |
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5c56387ff06a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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3 <!--Proposed Tool Section: [ID Processing]--> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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4 <tool id="ConsensusID" name="ConsensusID" version="2.2.0"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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5 <description>Computes a consensus of peptide identifications of several identification engines.</description> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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6 <macros> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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7 <token name="@EXECUTABLE@">ConsensusID</token> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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8 <import>macros.xml</import> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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9 </macros> |
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5c56387ff06a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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10 <expand macro="references"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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11 <expand macro="stdio"/> |
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5c56387ff06a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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12 <expand macro="requirements"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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13 <command>ConsensusID |
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5c56387ff06a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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14 |
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5c56387ff06a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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15 #if $param_in: |
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5c56387ff06a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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16 -in $param_in |
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5c56387ff06a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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17 #end if |
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5c56387ff06a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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18 #if $param_out: |
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5c56387ff06a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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19 -out $param_out |
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5c56387ff06a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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20 #end if |
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5c56387ff06a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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21 #if $param_rt_delta: |
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5c56387ff06a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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22 -rt_delta $param_rt_delta |
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5c56387ff06a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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23 #end if |
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5c56387ff06a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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24 #if $param_mz_delta: |
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5c56387ff06a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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25 -mz_delta $param_mz_delta |
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5c56387ff06a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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26 #end if |
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5c56387ff06a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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27 #if $param_algorithm: |
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66388c2e2f38
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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28 -algorithm |
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66388c2e2f38
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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29 #if " " in str($param_algorithm): |
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66388c2e2f38
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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30 "$param_algorithm" |
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66388c2e2f38
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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31 #else |
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66388c2e2f38
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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32 $param_algorithm |
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66388c2e2f38
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
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33 #end if |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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34 #end if |
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5c56387ff06a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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35 #if $param_filter_considered_hits: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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36 -filter:considered_hits $param_filter_considered_hits |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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37 #end if |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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38 #if $param_filter_min_support: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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39 -filter:min_support $param_filter_min_support |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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40 #end if |
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41 #if $param_filter_count_empty: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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42 -filter:count_empty |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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43 #end if |
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44 #if $param_PEPIons_mass_tolerance: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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45 -PEPIons:mass_tolerance $param_PEPIons_mass_tolerance |
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46 #end if |
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47 #if $param_PEPIons_min_shared: |
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48 -PEPIons:min_shared $param_PEPIons_min_shared |
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49 #end if |
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50 #if $param_PEPMatrix_matrix: |
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51 -PEPMatrix:matrix |
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52 #if " " in str($param_PEPMatrix_matrix): |
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53 "$param_PEPMatrix_matrix" |
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54 #else |
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55 $param_PEPMatrix_matrix |
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56 #end if |
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57 #end if |
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58 #if $param_PEPMatrix_penalty: |
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59 -PEPMatrix:penalty $param_PEPMatrix_penalty |
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60 #end if |
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61 #if $adv_opts.adv_opts_selector=='advanced': |
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62 #if $adv_opts.param_force: |
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63 -force |
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64 #end if |
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65 #end if |
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66 </command> |
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67 <inputs> |
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68 <param name="param_in" type="data" format="idxml,featurexml,consensusxml" optional="False" label="input file" help="(-in) "/> |
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69 <param name="param_rt_delta" type="float" min="0.0" optional="True" value="0.1" label="[idXML input only] Maximum allowed retention time deviation between identifications belonging to the same spectrum" help="(-rt_delta) "/> |
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70 <param name="param_mz_delta" type="float" min="0.0" optional="True" value="0.1" label="[idXML input only] Maximum allowed precursor m/z deviation between identifications belonging to the same spectrum" help="(-mz_delta) "/> |
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5c56387ff06a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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71 <param name="param_algorithm" type="select" optional="False" value="PEPMatrix" label="Algorithm used for consensus scoring" help="(-algorithm) <br>* PEPMatrix: Scoring based on posterior error probabilities (PEPs) and peptide sequence similarities (scored by a substitution matrix). Requires PEPs as scores. <br>* PEPIons: Scoring based on posterior error probabilities (PEPs) and fragment ion similarities ('shared peak count'). Requires PEPs as scores. <br>* best: For each peptide ID, use the best score of any search engine as the consensus score. Requires the same score type in all ID runs. <br>* worst: For each peptide ID, use the worst score of any search engine as the consensus score. Requires the same score type in all ID runs. <br>* average: For each peptide ID, use the average score of all search engines as the consensus. Requires the same score type in all ID runs. <br>* ranks: Calculates a consensus score based on the ranks of peptide IDs in the results of different search engines. The final score is in the range (0, 1], with 1 being the best score. No requirements about score types"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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72 <option value="PEPMatrix" selected="true">PEPMatrix</option> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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73 <option value="PEPIons">PEPIons</option> |
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74 <option value="best">best</option> |
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75 <option value="worst">worst</option> |
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76 <option value="average">average</option> |
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77 <option value="ranks">ranks</option> |
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78 </param> |
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79 <param name="param_filter_considered_hits" type="integer" min="0" optional="True" value="0" label="The number of top hits in each ID run that are considered for consensus scoring ('0' for all hits)" help="(-considered_hits) "/> |
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80 <param name="param_filter_min_support" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="For each peptide hit from an ID run, the fraction of other ID runs that must support that hit (otherwise it is removed)" help="(-min_support) "/> |
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81 <param name="param_filter_count_empty" display="radio" type="boolean" truevalue="-filter:count_empty" falsevalue="" checked="false" optional="True" label="Count empty ID runs (i.e" help="(-count_empty) those containing no peptide hit for the current spectrum) when calculating 'min_support'?"/> |
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82 <param name="param_PEPIons_mass_tolerance" type="float" min="0.0" optional="True" value="0.5" label="Maximum difference between fragment masses (in Da) for fragments to be considered 'shared' between peptides" help="(-mass_tolerance) "/> |
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83 <param name="param_PEPIons_min_shared" type="integer" min="1" optional="True" value="2" label="The minimal number of 'shared' fragments (between two suggested peptides) that is necessary to evaluate the similarity based on shared peak count (SPC)" help="(-min_shared) "/> |
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84 <param name="param_PEPMatrix_matrix" display="radio" type="select" optional="False" value="identity" label="Substitution matrix to use for alignment-based similarity scoring" help="(-matrix) "> |
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85 <option value="identity" selected="true">identity</option> |
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86 <option value="PAM30MS">PAM30MS</option> |
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87 </param> |
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88 <param name="param_PEPMatrix_penalty" type="integer" min="1" optional="True" value="5" label="Alignment gap penalty (the same value is used for gap opening and extension)" help="(-penalty) "/> |
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89 <expand macro="advanced_options"> |
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90 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> |
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91 </expand> |
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92 </inputs> |
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93 <outputs> |
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94 <data name="param_out" metadata_source="param_in" format="input"/> |
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95 </outputs> |
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96 <help>Computes a consensus of peptide identifications of several identification engines. |
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97 |
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98 |
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99 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConsensusID.html</help> |
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100 </tool> |