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comparison StaticModification.xml @ 2:9989f6be8bea draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:15:09 +0000
parents e030fdaaf631
children ace4851c8c37
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equal deleted inserted replaced
1:8030f8ff8afa 2:9989f6be8bea
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 CTDConverter.--> 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: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="StaticModification" name="StaticModification" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="StaticModification" name="StaticModification" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Applies a set of modifications to all PeptideIDs in an idXML file.</description> 5 <description>Applies a set of modifications to all PeptideIDs in an idXML file.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">StaticModification</token> 7 <token name="@EXECUTABLE@">StaticModification</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
39 <configfiles> 37 <configfiles>
40 <inputs name="args_json" data_style="paths"/> 38 <inputs name="args_json" data_style="paths"/>
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
42 </configfiles> 40 </configfiles>
43 <inputs> 41 <inputs>
44 <param name="in" argument="-in" type="data" format="idxml" optional="false" label="Input: identification results" help=" select idxml data sets(s)"/> 42 <param argument="-in" type="data" format="idxml" optional="false" label="Input: identification results" help=" select idxml data sets(s)"/>
45 <param name="mods" argument="-mods" multiple="true" type="select" optional="true" label="List of manual modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'"> 43 <param argument="-mods" multiple="true" type="select" optional="true" label="List of manual modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
46 <option value="">default (nothing chosen)</option>
47 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 44 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
48 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> 45 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
49 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> 46 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
50 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 47 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
51 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 48 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
1410 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option> 1407 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
1411 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 1408 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
1412 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 1409 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
1413 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 1410 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
1414 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option> 1411 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
1415 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
1416 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option> 1412 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
1417 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option> 1413 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
1418 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option> 1414 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
1419 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option> 1415 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
1420 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 1416 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
2970 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option> 2966 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
2971 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option> 2967 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
2972 <option value="ZGB (K)">ZGB (K)</option> 2968 <option value="ZGB (K)">ZGB (K)</option>
2973 <option value="ZGB (N-term)">ZGB (N-term)</option> 2969 <option value="ZGB (N-term)">ZGB (N-term)</option>
2974 <option value="ZQG (K)">ZQG (K)</option> 2970 <option value="ZQG (K)">ZQG (K)</option>
2975 <expand macro="list_string_san"/> 2971 <expand macro="list_string_san" name="mods"/>
2976 </param> 2972 </param>
2977 <param name="presets" argument="-presets" display="radio" type="select" optional="false" label="Add predefined sets, as shortcut to manually specifying a lot of modifications" help=""> 2973 <param argument="-presets" type="select" optional="true" label="Add predefined sets, as shortcut to manually specifying a lot of modifications" help="">
2978 <option value="none" selected="true">none</option> 2974 <option value="none" selected="true">none</option>
2979 <option value="N15">N15</option> 2975 <option value="N15">N15</option>
2980 <expand macro="list_string_san"/> 2976 <expand macro="list_string_san" name="presets"/>
2981 </param> 2977 </param>
2982 <expand macro="adv_opts_macro"> 2978 <expand macro="adv_opts_macro">
2983 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 2979 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
2984 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 2980 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
2985 <expand macro="list_string_san"/> 2981 <expand macro="list_string_san" name="test"/>
2986 </param> 2982 </param>
2987 </expand> 2983 </expand>
2988 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 2984 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
2989 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 2985 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
2990 </param> 2986 </param>
2993 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> 2989 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
2994 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 2990 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
2995 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 2991 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
2996 </data> 2992 </data>
2997 </outputs> 2993 </outputs>
2998 <tests> 2994 <tests/>
2999 <expand macro="autotest_StaticModification"/>
3000 <expand macro="manutest_StaticModification"/>
3001 </tests>
3002 <help><![CDATA[Applies a set of modifications to all PeptideIDs in an idXML file. 2995 <help><![CDATA[Applies a set of modifications to all PeptideIDs in an idXML file.
3003 2996
3004 2997
3005 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_StaticModification.html]]></help> 2998 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_StaticModification.html]]></help>
3006 <expand macro="references"/> 2999 <expand macro="references"/>
3007 </tool> 3000 </tool>