Mercurial > repos > galaxyp > openms_inspectadapter

comparison InspectAdapter.xml @ 13:04f649bc6e79 draft default tip

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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 06:56:59 -0400
parents 31c9e6e1bcb3
children
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12:6286f32cdf64 13:04f649bc6e79
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: [Identification]--> 3 <!--Proposed Tool Section: [Identification]-->
4 <tool id="InspectAdapter" name="InspectAdapter" version="2.2.0.1"> 4 <tool id="InspectAdapter" name="InspectAdapter" version="2.3.0">
5 <description>Annotates MS/MS spectra using Inspect.</description> 5 <description>Annotates MS/MS spectra using Inspect.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">InspectAdapter</token> 7 <token name="@EXECUTABLE@">InspectAdapter</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>InspectAdapter 13 <command detect_errors="aggressive"><![CDATA[InspectAdapter
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_out: 18 #if $param_out:
116 #if $adv_opts.adv_opts_selector=='advanced': 116 #if $adv_opts.adv_opts_selector=='advanced':
117 #if $adv_opts.param_force: 117 #if $adv_opts.param_force:
118 -force 118 -force
119 #end if 119 #end if
120 #end if 120 #end if
121 </command> 121 ]]></command>
122 <inputs> 122 <inputs>
123 <param name="param_in" type="data" format="mzxml,mzData" optional="False" label="input file in mzXML or mzData format" help="(-in) &lt;br&gt;Note: In mode 'inspect_out' an Inspect results file is read"/> 123 <param name="param_in" type="data" format="mzxml,mzData" optional="False" label="input file in mzXML or mzData format" help="(-in) &lt;br&gt;Note: In mode 'inspect_out' an Inspect results file is read"/>
124 <param name="param_inspect_in" display="radio" type="boolean" truevalue="-inspect_in" falsevalue="" checked="false" optional="True" label="if this flag is set the InspectAdapter will read in mzXML, &lt;br&gt;write an Inspect input file and generate a trie database" help="(-inspect_in) "/> 124 <param name="param_inspect_in" display="radio" type="boolean" truevalue="-inspect_in" falsevalue="" checked="false" optional="True" label="if this flag is set the InspectAdapter will read in mzXML, &lt;br&gt;write an Inspect input file and generate a trie database" help="(-inspect_in) "/>
125 <param name="param_inspect_out" display="radio" type="boolean" truevalue="-inspect_out" falsevalue="" checked="false" optional="True" label="if this flag is set the InspectAdapter will read in a Inspect results file &lt;br&gt;and write idXML" help="(-inspect_out) "/> 125 <param name="param_inspect_out" display="radio" type="boolean" truevalue="-inspect_out" falsevalue="" checked="false" optional="True" label="if this flag is set the InspectAdapter will read in a Inspect results file &lt;br&gt;and write idXML" help="(-inspect_out) "/>
126 <param name="param_inspect_directory" type="text" size="30" label="the directory in which Inspect is located" help="(-inspect_directory) "> 126 <param name="param_inspect_directory" type="text" size="30" label="the directory in which Inspect is located" help="(-inspect_directory) ">
247 <data name="param_inspect_output" format="data"/> 247 <data name="param_inspect_output" format="data"/>
248 </outputs> 248 </outputs>
249 <help>Annotates MS/MS spectra using Inspect. 249 <help>Annotates MS/MS spectra using Inspect.
250 250
251 251
252 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InspectAdapter.html</help> 252 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_InspectAdapter.html</help>
253 </tool> 253 </tool>