Mercurial > repos > galaxyp > openms_consensusid

comparison ConsensusID.xml @ 3:9d7e3e5da94a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:30:14 -0400
parents 66388c2e2f38
children fd633fe1d7d7
comparison
equal deleted inserted replaced
2:8960fb791701 3:9d7e3e5da94a
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 CTD2Galaxy.-->
3 <!--Proposed Tool Section: [ID Processing]--> 3 <!--Proposed Tool Section: [ID Processing]-->
4 <tool id="ConsensusID" name="ConsensusID" version="2.1.0"> 4 <tool id="ConsensusID" name="ConsensusID" version="2.2.0">
5 <description>Computes a consensus of peptide identifications of several identification engines.</description> 5 <description>Computes a consensus of peptide identifications of several identification engines.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">ConsensusID</token> 7 <token name="@EXECUTABLE@">ConsensusID</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
63 -force 63 -force
64 #end if 64 #end if
65 #end if 65 #end if
66 </command> 66 </command>
67 <inputs> 67 <inputs>
68 <param name="param_in" type="data" format="featurexml,consensusxml,idxml" optional="False" label="input file" help="(-in) "/> 68 <param name="param_in" type="data" format="idxml,featurexml,consensusxml" optional="False" label="input file" help="(-in) "/>
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) "/> 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) "/>
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) "/> 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) "/>
71 <param name="param_algorithm" type="select" optional="False" value="PEPMatrix" label="Algorithm used for consensus scoring" help="(-algorithm) &lt;br&gt;* PEPMatrix: Scoring based on posterior error probabilities (PEPs) and peptide sequence similarities (scored by a substitution matrix). Requires PEPs as scores. &lt;br&gt;* PEPIons: Scoring based on posterior error probabilities (PEPs) and fragment ion similarities ('shared peak count'). Requires PEPs as scores. &lt;br&gt;* 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. &lt;br&gt;* 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. &lt;br&gt;* 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. &lt;br&gt;* 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"> 71 <param name="param_algorithm" type="select" optional="False" value="PEPMatrix" label="Algorithm used for consensus scoring" help="(-algorithm) &lt;br&gt;* PEPMatrix: Scoring based on posterior error probabilities (PEPs) and peptide sequence similarities (scored by a substitution matrix). Requires PEPs as scores. &lt;br&gt;* PEPIons: Scoring based on posterior error probabilities (PEPs) and fragment ion similarities ('shared peak count'). Requires PEPs as scores. &lt;br&gt;* 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. &lt;br&gt;* 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. &lt;br&gt;* 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. &lt;br&gt;* 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">
72 <option value="PEPMatrix" selected="true">PEPMatrix</option> 72 <option value="PEPMatrix" selected="true">PEPMatrix</option>
73 <option value="PEPIons">PEPIons</option> 73 <option value="PEPIons">PEPIons</option>