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comparison CompNovoCID.xml @ 12:2a753cefc663 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 06:49:37 -0400
parents 8693073cb9ff
children 79fbe62996d9
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equal deleted inserted replaced
11:938f123bb44f 12:2a753cefc663
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="CompNovoCID" name="CompNovoCID" version="2.2.0"> 4 <tool id="CompNovoCID" name="CompNovoCID" version="2.3.0">
5 <description>Performs a de novo peptide identification using the CompNovo engine.</description> 5 <description>Performs a de novo peptide identification using the CompNovo engine.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">CompNovoCID</token> 7 <token name="@EXECUTABLE@">CompNovoCID</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>CompNovoCID 13 <command detect_errors="aggressive"><![CDATA[CompNovoCID
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:
102 #end if 102 #end if
103 #if $adv_opts.param_algorithm_residue_set: 103 #if $adv_opts.param_algorithm_residue_set:
104 -algorithm:residue_set "$adv_opts.param_algorithm_residue_set" 104 -algorithm:residue_set "$adv_opts.param_algorithm_residue_set"
105 #end if 105 #end if
106 #end if 106 #end if
107 </command> 107 ]]></command>
108 <inputs> 108 <inputs>
109 <param name="param_in" type="data" format="mzml" optional="False" label="input file in mzML format" help="(-in) "/> 109 <param name="param_in" type="data" format="mzml" optional="False" label="input file in mzML format" help="(-in) "/>
110 <param name="param_algorithm_tryptic_only" type="text" size="30" value="true" label="if set to true only tryptic peptides are reported" help="(-tryptic_only) "> 110 <param name="param_algorithm_tryptic_only" type="text" size="30" value="true" label="if set to true only tryptic peptides are reported" help="(-tryptic_only) ">
111 <sanitizer> 111 <sanitizer>
112 <valid initial="string.printable"> 112 <valid initial="string.printable">
123 <param name="param_algorithm_number_of_hits" type="integer" value="100" label="maximal number of hits which are reported per spectrum" help="(-number_of_hits) "/> 123 <param name="param_algorithm_number_of_hits" type="integer" value="100" label="maximal number of hits which are reported per spectrum" help="(-number_of_hits) "/>
124 <param name="param_algorithm_estimate_precursor_mz" display="radio" type="select" optional="False" value="true" label="If set to true, the precursor charge will be estimated," help="(-estimate_precursor_mz) e.g. from the precursor peaks of the ETD spectrum. &lt;br&gt;The input is believed otherwise"> 124 <param name="param_algorithm_estimate_precursor_mz" display="radio" type="select" optional="False" value="true" label="If set to true, the precursor charge will be estimated," help="(-estimate_precursor_mz) e.g. from the precursor peaks of the ETD spectrum. &lt;br&gt;The input is believed otherwise">
125 <option value="true" selected="true">true</option> 125 <option value="true" selected="true">true</option>
126 <option value="false">false</option> 126 <option value="false">false</option>
127 </param> 127 </param>
128 <repeat name="rep_param_algorithm_fixed_modifications" min="0" max="1" title="param_algorithm_fixed_modifications"> 128 <repeat name="rep_param_algorithm_fixed_modifications" min="0" title="param_algorithm_fixed_modifications">
129 <param name="param_algorithm_fixed_modifications" type="select" optional="True" label="fixed modifications, specified using UniMod (www.unimod.org) terms," help="(-fixed_modifications) e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'"> 129 <param name="param_algorithm_fixed_modifications" type="select" optional="True" label="fixed modifications, specified using UniMod (www.unimod.org) terms," help="(-fixed_modifications) e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
130 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 130 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
131 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 131 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
132 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 132 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
133 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option> 133 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>
2656 <option value="sulfo+amino (Y)">sulfo+amino (Y)</option> 2656 <option value="sulfo+amino (Y)">sulfo+amino (Y)</option>
2657 <option value="thioacylPA (K)">thioacylPA (K)</option> 2657 <option value="thioacylPA (K)">thioacylPA (K)</option>
2658 <option value="trifluoro (L)">trifluoro (L)</option> 2658 <option value="trifluoro (L)">trifluoro (L)</option>
2659 </param> 2659 </param>
2660 </repeat> 2660 </repeat>
2661 <repeat name="rep_param_algorithm_variable_modifications" min="0" max="1" title="param_algorithm_variable_modifications"> 2661 <repeat name="rep_param_algorithm_variable_modifications" min="0" title="param_algorithm_variable_modifications">
2662 <param name="param_algorithm_variable_modifications" type="select" optional="True" label="variable modifications, specified using UniMod (www.unimod.org) terms," help="(-variable_modifications) e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'"> 2662 <param name="param_algorithm_variable_modifications" type="select" optional="True" label="variable modifications, specified using UniMod (www.unimod.org) terms," help="(-variable_modifications) e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
2663 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 2663 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
2664 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 2664 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
2665 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 2665 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
2666 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option> 2666 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>
5216 <data name="param_out" format="idxml"/> 5216 <data name="param_out" format="idxml"/>
5217 </outputs> 5217 </outputs>
5218 <help>Performs a de novo peptide identification using the CompNovo engine. 5218 <help>Performs a de novo peptide identification using the CompNovo engine.
5219 5219
5220 5220
5221 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_CompNovoCID.html</help> 5221 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_CompNovoCID.html</help>
5222 </tool> 5222 </tool>