Mercurial > repos > galaxyp > openms_inspectadapter

comparison InspectAdapter.xml @ 1:15ebe1509e0d 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 08:59:58 -0400
parents 4fba18bcca36
children f66061c92e2d
comparison
equal deleted inserted replaced
0:4fba18bcca36 1:15ebe1509e0d
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: [Identification]--> 3 <!--Proposed Tool Section: [Identification]-->
4 <tool id="InspectAdapter" name="InspectAdapter" version="2.1.0"> 4 <tool id="InspectAdapter" name="InspectAdapter" version="2.2.0.1">
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>
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" 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) ">
127 <sanitizer> 127 <sanitizer>
128 <valid initial="string.printable"> 128 <valid initial="string.printable">
194 <remove value="'"/> 194 <remove value="'"/>
195 <remove value="&quot;"/> 195 <remove value="&quot;"/>
196 </valid> 196 </valid>
197 </sanitizer> 197 </sanitizer>
198 </param> 198 </param>
199 <param name="param_inspect_input" type="data" format="text" label="name for the input file of Inspect (may only be used in a full run)" help="(-inspect_input) "/> 199 <param name="param_inspect_input" type="data" format="txt" label="name for the input file of Inspect (may only be used in a full run)" help="(-inspect_input) "/>
200 <param name="param_multicharge" display="radio" type="boolean" truevalue="-multicharge" falsevalue="" checked="false" optional="True" label="attempt to guess the precursor charge and mass, &lt;br&gt;and consider multiple charge states if feasible" help="(-multicharge) "/> 200 <param name="param_multicharge" display="radio" type="boolean" truevalue="-multicharge" falsevalue="" checked="false" optional="True" label="attempt to guess the precursor charge and mass, &lt;br&gt;and consider multiple charge states if feasible" help="(-multicharge) "/>
201 <param name="param_max_modifications_pp" type="integer" value="-1" label="number of PTMs permitted in a single peptide" help="(-max_modifications_pp) "/> 201 <param name="param_max_modifications_pp" type="integer" value="-1" label="number of PTMs permitted in a single peptide" help="(-max_modifications_pp) "/>
202 <param name="param_tag_count" type="integer" value="-1" label="number of tags to generate" help="(-tag_count) "/> 202 <param name="param_tag_count" type="integer" value="-1" label="number of tags to generate" help="(-tag_count) "/>
203 <param name="param_no_tmp_dbs" display="radio" type="boolean" truevalue="-no_tmp_dbs" falsevalue="" checked="false" optional="True" label="no temporary databases are used" help="(-no_tmp_dbs) "/> 203 <param name="param_no_tmp_dbs" display="radio" type="boolean" truevalue="-no_tmp_dbs" falsevalue="" checked="false" optional="True" label="no temporary databases are used" help="(-no_tmp_dbs) "/>
204 <param name="param_p_value" type="float" value="1.0" label="annotations with inferior p-value are ignored" help="(-p_value) "/> 204 <param name="param_p_value" type="float" value="1.0" label="annotations with inferior p-value are ignored" help="(-p_value) "/>