Mercurial > repos > galaxyp > openms_rnamasscalculator

comparison RNAMassCalculator.xml @ 2:f8475273db10 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:14:33 +0000
parents 4f8478024146
children cb0f5beef55f
comparison
equal deleted inserted replaced
1:1af5b39289b8 2:f8475273db10
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="RNAMassCalculator" name="RNAMassCalculator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="RNAMassCalculator" name="RNAMassCalculator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Calculates masses and mass-to-charge ratios of RNA sequences</description> 5 <description>Calculates masses, mass-to-charge ratios and sum formulas of RNA sequences</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">RNAMassCalculator</token> 7 <token name="@EXECUTABLE@">RNAMassCalculator</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import> 9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import> 10 <import>macros_test.xml</import>
60 <expand macro="list_string_san"/> 60 <expand macro="list_string_san"/>
61 </param> 61 </param>
62 <param name="charge" argument="-charge" type="text" optional="true" value="0" label="List of charge states; required if 'in_seq' is given" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 62 <param name="charge" argument="-charge" type="text" optional="true" value="0" label="List of charge states; required if 'in_seq' is given" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
63 <expand macro="list_integer_valsan"/> 63 <expand macro="list_integer_valsan"/>
64 </param> 64 </param>
65 <param name="format" argument="-format" display="radio" type="select" optional="false" label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)" help=""> 65 <param name="format" argument="-format" type="select" optional="false" label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only, 'formula_only': sum formula only)" help="">
66 <option value="list" selected="true">list</option> 66 <option value="list" selected="true">list</option>
67 <option value="table">table</option> 67 <option value="table">table</option>
68 <option value="mass_only">mass_only</option> 68 <option value="mass_only">mass_only</option>
69 <option value="mz_only">mz_only</option> 69 <option value="mz_only">mz_only</option>
70 <option value="formula_only">formula_only</option>
70 <expand macro="list_string_san"/> 71 <expand macro="list_string_san"/>
71 </param> 72 </param>
72 <param name="average_mass" argument="-average_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute average (instead of monoisotopic) oligonucleotide masses" help=""/> 73 <param name="average_mass" argument="-average_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute average (instead of monoisotopic) oligonucleotide masses" help=""/>
73 <param name="fragment_type" argument="-fragment_type" type="select" optional="false" label="For what type of sequence/fragment the mass should be computed" help=""> 74 <param name="fragment_type" argument="-fragment_type" type="select" optional="false" label="For what type of sequence/fragment the mass should be computed" help="">
74 <option value="full" selected="true">full</option> 75 <option value="full" selected="true">full</option>
88 </param> 89 </param>
89 <param name="separator" argument="-separator" type="text" optional="true" value="" label="Field separator for 'table' output format; by default, the 'tab' character is used" help=""> 90 <param name="separator" argument="-separator" type="text" optional="true" value="" label="Field separator for 'table' output format; by default, the 'tab' character is used" help="">
90 <expand macro="list_string_san"/> 91 <expand macro="list_string_san"/>
91 </param> 92 </param>
92 <expand macro="adv_opts_macro"> 93 <expand macro="adv_opts_macro">
93 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 94 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
94 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 95 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
95 <expand macro="list_string_san"/> 96 <expand macro="list_string_san"/>
96 </param> 97 </param>
97 </expand> 98 </expand>
98 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false"> 99 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
99 <option value="out_FLAG">out (Enables the test mode (needed for internal use only))</option> 100 <option value="out_FLAG">out (Output file; if empty, output is written to the screen)</option>
100 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 101 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
101 </param> 102 </param>
102 </inputs> 103 </inputs>
103 <outputs> 104 <outputs>
104 <data name="out" label="${tool.name} on ${on_string}: out" format="txt"> 105 <data name="out" label="${tool.name} on ${on_string}: out" format="txt">
113 </outputs> 114 </outputs>
114 <tests> 115 <tests>
115 <expand macro="autotest_RNAMassCalculator"/> 116 <expand macro="autotest_RNAMassCalculator"/>
116 <expand macro="manutest_RNAMassCalculator"/> 117 <expand macro="manutest_RNAMassCalculator"/>
117 </tests> 118 </tests>
118 <help><![CDATA[Calculates masses and mass-to-charge ratios of RNA sequences 119 <help><![CDATA[Calculates masses, mass-to-charge ratios and sum formulas of RNA sequences
119 120
120 121
121 For more information, visit http://www.openms.de/documentation/UTILS_RNAMassCalculator.html]]></help> 122 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_RNAMassCalculator.html]]></help>
122 <expand macro="references"/> 123 <expand macro="references"/>
123 </tool> 124 </tool>