Mercurial > repos > galaxyp > openms_rnamasscalculator

comparison RNAMassCalculator.xml @ 4:cb0f5beef55f 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 19:20:12 +0000
parents f8475273db10
children 148c000ea2ec
comparison
equal deleted inserted replaced
3:bb58f2f266e8 4:cb0f5beef55f
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@VERSION_SUFFIX@" profile="21.05">
5 <description>Calculates masses, mass-to-charge ratios and sum formulas 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>
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@
52 <configfiles> 50 <configfiles>
53 <inputs name="args_json" data_style="paths"/> 51 <inputs name="args_json" data_style="paths"/>
54 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 52 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
55 </configfiles> 53 </configfiles>
56 <inputs> 54 <inputs>
57 <param name="in" argument="-in" type="data" format="txt" optional="true" label="Input file with RNA sequences and optionally charge numbers (mutually exclusive to 'in_seq')" help=" select txt data sets(s)"/> 55 <param argument="-in" type="data" format="txt" optional="true" label="Input file with RNA sequences and optionally charge numbers (mutually exclusive to 'in_seq')" help=" select txt data sets(s)"/>
58 <param name="in_seq" argument="-in_seq" type="text" optional="true" value="" label="List of RNA sequences (mutually exclusive to 'in')" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 56 <param argument="-in_seq" type="text" optional="true" value="" label="List of RNA sequences (mutually exclusive to 'in')" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
59 <expand macro="list_string_val"/> 57 <expand macro="list_string_val" name="in_seq"/>
60 <expand macro="list_string_san"/> 58 <expand macro="list_string_san" name="in_seq"/>
61 </param> 59 </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)"> 60 <param 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"/> 61 <expand macro="list_integer_valsan" name="charge"/>
64 </param> 62 </param>
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=""> 63 <param argument="-format" type="select" optional="true" 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> 64 <option value="list" selected="true">list</option>
67 <option value="table">table</option> 65 <option value="table">table</option>
68 <option value="mass_only">mass_only</option> 66 <option value="mass_only">mass_only</option>
69 <option value="mz_only">mz_only</option> 67 <option value="mz_only">mz_only</option>
70 <option value="formula_only">formula_only</option> 68 <option value="formula_only">formula_only</option>
71 <expand macro="list_string_san"/> 69 <expand macro="list_string_san" name="format"/>
72 </param> 70 </param>
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=""/> 71 <param argument="-average_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute average (instead of monoisotopic) oligonucleotide masses" 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=""> 72 <param argument="-fragment_type" type="select" optional="true" label="For what type of sequence/fragment the mass should be computed" help="">
75 <option value="full" selected="true">full</option> 73 <option value="full" selected="true">full</option>
76 <option value="internal">internal</option> 74 <option value="internal">internal</option>
77 <option value="5-prime">5-prime</option> 75 <option value="5-prime">5-prime</option>
78 <option value="3-prime">3-prime</option> 76 <option value="3-prime">3-prime</option>
79 <option value="a-B-ion">a-B-ion</option> 77 <option value="a-B-ion">a-B-ion</option>
83 <option value="d-ion">d-ion</option> 81 <option value="d-ion">d-ion</option>
84 <option value="w-ion">w-ion</option> 82 <option value="w-ion">w-ion</option>
85 <option value="x-ion">x-ion</option> 83 <option value="x-ion">x-ion</option>
86 <option value="y-ion">y-ion</option> 84 <option value="y-ion">y-ion</option>
87 <option value="z-ion">z-ion</option> 85 <option value="z-ion">z-ion</option>
88 <expand macro="list_string_san"/> 86 <expand macro="list_string_san" name="fragment_type"/>
89 </param> 87 </param>
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=""> 88 <param argument="-separator" type="text" optional="true" value="" label="Field separator for 'table' output format; by default, the 'tab' character is used" help="">
91 <expand macro="list_string_san"/> 89 <expand macro="list_string_san" name="separator"/>
92 </param> 90 </param>
93 <expand macro="adv_opts_macro"> 91 <expand macro="adv_opts_macro">
94 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 92 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
95 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 93 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
96 <expand macro="list_string_san"/> 94 <expand macro="list_string_san" name="test"/>
97 </param> 95 </param>
98 </expand> 96 </expand>
99 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 97 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
100 <option value="out_FLAG">out (Output file; if empty, output is written to the screen)</option> 98 <option value="out_FLAG">out (Output file; if empty, output is written to the screen)</option>
101 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 99 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
110 </data> 108 </data>
111 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 109 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
112 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 110 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
113 </data> 111 </data>
114 </outputs> 112 </outputs>
115 <tests> 113 <tests><!-- UTILS_RNAMassCalculator_1 -->
116 <expand macro="autotest_RNAMassCalculator"/> 114 <test expect_num_outputs="2">
117 <expand macro="manutest_RNAMassCalculator"/> 115 <section name="adv_opts">
116 <param name="force" value="false"/>
117 <param name="test" value="true"/>
118 </section>
119 <param name="in_seq" value="&quot;AUCGGC&quot;"/>
120 <output name="out" file="RNAMassCalculator_1.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
121 <param name="charge" value="-1 -2"/>
122 <param name="format" value="list"/>
123 <param name="average_mass" value="false"/>
124 <param name="fragment_type" value="full"/>
125 <param name="separator" value=""/>
126 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
127 <output name="ctd_out" ftype="xml">
128 <assert_contents>
129 <is_valid_xml/>
130 </assert_contents>
131 </output>
132 </test>
118 </tests> 133 </tests>
119 <help><![CDATA[Calculates masses, mass-to-charge ratios and sum formulas of RNA sequences 134 <help><![CDATA[Calculates masses, mass-to-charge ratios and sum formulas of RNA sequences
120 135
121 136
122 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_RNAMassCalculator.html]]></help> 137 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_RNAMassCalculator.html]]></help>
123 <expand macro="references"/> 138 <expand macro="references"/>
124 </tool> 139 </tool>