Mercurial > repos > galaxyp > openms_fidoadapter

comparison FidoAdapter.xml @ 12:ea92ae2382ef draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 05:41:32 -0400
parents 0245664f3b6d
children 671bc82cdb4a
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11:be0565773ece 12:ea92ae2382ef
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 CTDConverter.-->
3 <!--Proposed Tool Section: [ID Processing]--> 3 <!--Proposed Tool Section: [ID Processing]-->
4 <tool id="FidoAdapter" name="FidoAdapter" version="2.2.0.1"> 4 <tool id="FidoAdapter" name="FidoAdapter" version="2.3.0">
5 <description>Runs the protein inference engine Fido.</description> 5 <description>Runs the protein inference engine Fido.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FidoAdapter</token> 7 <token name="@EXECUTABLE@">FidoAdapter</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
10 <expand macro="references"/> 10 <expand macro="references"/>
11 <expand macro="stdio"/> 11 <expand macro="stdio"/>
12 <expand macro="requirements"/> 12 <expand macro="requirements"/>
13 <command>FidoAdapter 13 <command detect_errors="aggressive"><![CDATA[FidoAdapter
14 -fidocp_executable FidoChooseParameters 14 -fidocp_executable FidoChooseParameters
15 -fido_executable Fido 15 -fido_executable Fido
16 16
17 #if $param_in: 17 #if $param_in:
18 -in $param_in 18 -in $param_in
64 #end if 64 #end if
65 #if $adv_opts.param_force: 65 #if $adv_opts.param_force:
66 -force 66 -force
67 #end if 67 #end if
68 #end if 68 #end if
69 </command> 69 ]]></command>
70 <inputs> 70 <inputs>
71 <param name="param_in" type="data" format="idxml" optional="False" label="Input: identification results" help="(-in) "/> 71 <param name="param_in" type="data" format="idxml" optional="False" label="Input: identification results" help="(-in) "/>
72 <param name="param_separate_runs" display="radio" type="boolean" truevalue="-separate_runs" falsevalue="" checked="false" optional="True" label="Process multiple protein identification runs in the input separately, don't merge them" help="(-separate_runs) Merging results in loss of descriptive information of the single protein identification runs"/> 72 <param name="param_separate_runs" display="radio" type="boolean" truevalue="-separate_runs" falsevalue="" checked="false" optional="True" label="Process multiple protein identification runs in the input separately, don't merge them" help="(-separate_runs) Merging results in loss of descriptive information of the single protein identification runs"/>
73 <param name="param_greedy_group_resolution" display="radio" type="boolean" truevalue="-greedy_group_resolution" falsevalue="" checked="false" optional="True" label="Post-process Fido output with greedy resolution of shared peptides based on the protein probabilities" help="(-greedy_group_resolution) Also adds the resolved ambiguity groups to output"/> 73 <param name="param_greedy_group_resolution" display="radio" type="boolean" truevalue="-greedy_group_resolution" falsevalue="" checked="false" optional="True" label="Post-process Fido output with greedy resolution of shared peptides based on the protein probabilities" help="(-greedy_group_resolution) Also adds the resolved ambiguity groups to output"/>
74 <param name="param_no_cleanup" display="radio" type="boolean" truevalue="-no_cleanup" falsevalue="" checked="false" optional="True" label="Omit clean-up of peptide sequences (removal of non-letter characters, replacement of I with L)" help="(-no_cleanup) "/> 74 <param name="param_no_cleanup" display="radio" type="boolean" truevalue="-no_cleanup" falsevalue="" checked="false" optional="True" label="Omit clean-up of peptide sequences (removal of non-letter characters, replacement of I with L)" help="(-no_cleanup) "/>
94 <data name="param_out" format="idxml"/> 94 <data name="param_out" format="idxml"/>
95 </outputs> 95 </outputs>
96 <help>Runs the protein inference engine Fido. 96 <help>Runs the protein inference engine Fido.
97 97
98 98
99 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FidoAdapter.html</help> 99 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FidoAdapter.html</help>
100 </tool> 100 </tool>