Mercurial > repos > galaxyp > openms_staticmodification
diff StaticModification.xml @ 2:9989f6be8bea draft
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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--- a/StaticModification.xml Fri Nov 06 19:48:19 2020 +0000 +++ b/StaticModification.xml Thu Dec 01 19:15:09 2022 +0000 @@ -1,13 +1,11 @@ <?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> <!--Proposed Tool Section: [Utilities]--> -<tool id="StaticModification" name="StaticModification" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="StaticModification" name="StaticModification" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Applies a set of modifications to all PeptideIDs in an idXML file.</description> <macros> <token name="@EXECUTABLE@">StaticModification</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -41,9 +39,8 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param name="in" argument="-in" type="data" format="idxml" optional="false" label="Input: identification results" help=" select idxml data sets(s)"/> - <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)'"> - <option value="">default (nothing chosen)</option> + <param argument="-in" type="data" format="idxml" optional="false" label="Input: identification results" help=" select idxml data sets(s)"/> + <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)'"> <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> @@ -1413,7 +1410,6 @@ <option value="Glu->Pro (E)">Glu->Pro (E)</option> <option value="Glu->pyro-Glu (N-term E)">Glu->pyro-Glu (N-term E)</option> <option value="Glu->pyro-Glu+Methyl (N-term E)">Glu->pyro-Glu+Methyl (N-term E)</option> - <option value="Glu->pyro-Glu+Methyl (N-term E)">Glu->pyro-Glu+Methyl (N-term E)</option> <option value="Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)</option> <option value="Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option> <option value="Glu->Ser (E)">Glu->Ser (E)</option> @@ -2972,17 +2968,17 @@ <option value="ZGB (K)">ZGB (K)</option> <option value="ZGB (N-term)">ZGB (N-term)</option> <option value="ZQG (K)">ZQG (K)</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="mods"/> </param> - <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=""> + <param argument="-presets" type="select" optional="true" label="Add predefined sets, as shortcut to manually specifying a lot of modifications" help=""> <option value="none" selected="true">none</option> <option value="N15">N15</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="presets"/> </param> <expand macro="adv_opts_macro"> - <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> - <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> - <expand macro="list_string_san"/> + <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> + <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <expand macro="list_string_san" name="test"/> </param> </expand> <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> @@ -2995,13 +2991,10 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_StaticModification"/> - <expand macro="manutest_StaticModification"/> - </tests> + <tests/> <help><![CDATA[Applies a set of modifications to all PeptideIDs in an idXML file. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_StaticModification.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_StaticModification.html]]></help> <expand macro="references"/> </tool>