Mercurial > repos > galaxyp > openms_xtandemadapter

comparison XTandemAdapter.xml @ 8:9459f73208e0 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 08:12:20 -0400
parents b09039836cb1
children 9e16ba5b88e8
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7:269f95c18fa1 8:9459f73208e0
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>XTandemAdapter 13 <command detect_errors="aggressive"><![CDATA[XTandemAdapter
14 -xtandem_executable xtandem 14 -xtandem_executable xtandem
15 15
16 #if $param_in: 16 #if $param_in:
17 -in $param_in 17 -in $param_in
18 #end if 18 #end if
112 #if $adv_opts.adv_opts_selector=='advanced': 112 #if $adv_opts.adv_opts_selector=='advanced':
113 #if $adv_opts.param_force: 113 #if $adv_opts.param_force:
114 -force 114 -force
115 #end if 115 #end if
116 #end if 116 #end if
117 </command> 117 ]]></command>
118 <inputs> 118 <inputs>
119 <param name="param_in" type="data" format="mzml" optional="False" label="Input file containing MS2 spectra" help="(-in) "/> 119 <param name="param_in" type="data" format="mzml" optional="False" label="Input file containing MS2 spectra" help="(-in) "/>
120 <param name="param_database" type="data" format="fasta" optional="False" label="FASTA file or pro file" help="(-database) Non-existing relative file-names are looked up via'OpenMS.ini:id_db_dir'"/> 120 <param name="param_database" type="data" format="fasta" optional="False" label="FASTA file or pro file" help="(-database) Non-existing relative file-names are looked up via'OpenMS.ini:id_db_dir'"/>
121 <param name="param_default_config_file" type="data" format="xml" optional="True" label="Default X! Tandem configuration file" help="(-default_config_file) All parameters of this adapter take precedence over the file - use it for parameters not available here. A template file can be found at 'OpenMS/share/CHEMISTRY/XTandem_default_input.xml'"/> 121 <param name="param_default_config_file" type="data" format="xml" optional="True" label="Default X! Tandem configuration file" help="(-default_config_file) All parameters of this adapter take precedence over the file - use it for parameters not available here. A template file can be found at 'OpenMS/share/CHEMISTRY/XTandem_default_input.xml'"/>
122 <param name="param_ignore_adapter_param" display="radio" type="boolean" truevalue="-ignore_adapter_param" falsevalue="" checked="false" optional="True" label="Set this to use the configuration given in 'default_config_file' exclusively, ignoring other parameters (apart from 'in', 'out', 'database', 'xtandem_executable') set via this adapte" help="(-ignore_adapter_param) "/> 122 <param name="param_ignore_adapter_param" display="radio" type="boolean" truevalue="-ignore_adapter_param" falsevalue="" checked="false" optional="True" label="Set this to use the configuration given in 'default_config_file' exclusively, ignoring other parameters (apart from 'in', 'out', 'database', 'xtandem_executable') set via this adapte" help="(-ignore_adapter_param) "/>
5241 <data name="param_xml_out" format="xml"/> 5241 <data name="param_xml_out" format="xml"/>
5242 </outputs> 5242 </outputs>
5243 <help>Annotates MS/MS spectra using X! Tandem. 5243 <help>Annotates MS/MS spectra using X! Tandem.
5244 5244
5245 5245
5246 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_XTandemAdapter.html</help> 5246 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_XTandemAdapter.html</help>
5247 </tool> 5247 </tool>