Mercurial > repos > galaxyp > openms_luciphoradapter

comparison LuciphorAdapter.xml @ 12:772d236ead0a 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 06:03:33 -0400
parents 561679970134
children 114b3afda8ec
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11:2a5738ecd2fc 12:772d236ead0a
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="LuciphorAdapter" name="LuciphorAdapter" version="2.2.0"> 4 <tool id="LuciphorAdapter" name="LuciphorAdapter" version="2.3.0">
5 <description>Modification site localisation using LuciPHOr2.</description> 5 <description>Modification site localisation using LuciPHOr2.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">LuciphorAdapter</token> 7 <token name="@EXECUTABLE@">LuciphorAdapter</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>LuciphorAdapter 13 <command detect_errors="aggressive"><![CDATA[LuciphorAdapter
14 14
15 #if $param_in: 15 #if $param_in:
16 -in $param_in 16 -in $param_in
17 #end if 17 #end if
18 #if $param_id: 18 #if $param_id:
111 #if $adv_opts.adv_opts_selector=='advanced': 111 #if $adv_opts.adv_opts_selector=='advanced':
112 #if $adv_opts.param_force: 112 #if $adv_opts.param_force:
113 -force 113 -force
114 #end if 114 #end if
115 #end if 115 #end if
116 </command> 116 ]]></command>
117 <inputs> 117 <inputs>
118 <param name="param_in" type="data" format="mzml" optional="False" label="Input spectrum file" help="(-in) "/> 118 <param name="param_in" type="data" format="mzml" optional="False" label="Input spectrum file" help="(-in) "/>
119 <param name="param_id" type="data" format="idxml" optional="False" label="Protein/peptide identifications file" help="(-id) "/> 119 <param name="param_id" type="data" format="idxml" optional="False" label="Protein/peptide identifications file" help="(-id) "/>
120 <param name="param_fragment_method" display="radio" type="select" optional="False" value="CID" label="Fragmentation method" help="(-fragment_method) "> 120 <param name="param_fragment_method" display="radio" type="select" optional="False" value="CID" label="Fragmentation method" help="(-fragment_method) ">
121 <option value="CID" selected="true">CID</option> 121 <option value="CID" selected="true">CID</option>
2700 <data name="param_out" format="idxml"/> 2700 <data name="param_out" format="idxml"/>
2701 </outputs> 2701 </outputs>
2702 <help>Modification site localisation using LuciPHOr2. 2702 <help>Modification site localisation using LuciPHOr2.
2703 2703
2704 2704
2705 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_LuciphorAdapter.html</help> 2705 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_LuciphorAdapter.html</help>
2706 </tool> 2706 </tool>