Mercurial > repos > galaxyp > openms_rnamasscalculator

comparison RNAMassCalculator.xml @ 5:148c000ea2ec draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:33:05 +0000
parents cb0f5beef55f
children
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4:cb0f5beef55f 5:148c000ea2ec
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.--> 1 <!--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]--> 2 <!--Proposed Tool Section: [RNA]-->
4 <tool id="RNAMassCalculator" name="RNAMassCalculator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <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> 4 <description>Calculates masses, mass-to-charge ratios and sum formulas of RNA sequences</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">RNAMassCalculator</token> 6 <token name="@EXECUTABLE@">RNAMassCalculator</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 #if $in: 16 #if $in:
18 mkdir in && 17 mkdir in &&
19 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 18 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
20 #end if 19 #end if
21 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 20 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
22 mkdir out && 21 mkdir out &&
23 #end if 22 #end if
24 23
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)"/> 54 <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)"/>
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)"> 55 <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)">
57 <expand macro="list_string_val" name="in_seq"/> 56 <expand macro="list_string_val" name="in_seq"/>
58 <expand macro="list_string_san" name="in_seq"/> 57 <expand macro="list_string_san" name="in_seq"/>
59 </param> 58 </param>
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)"> 59 <param argument="-charge" type="text" 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)">
61 <expand macro="list_integer_valsan" name="charge"/> 60 <expand macro="list_integer_valsan" name="charge"/>
62 </param> 61 </param>
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=""> 62 <param argument="-format" type="select" 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="">
64 <option value="list" selected="true">list</option> 63 <option value="list" selected="true">list</option>
65 <option value="table">table</option> 64 <option value="table">table</option>
66 <option value="mass_only">mass_only</option> 65 <option value="mass_only">mass_only</option>
67 <option value="mz_only">mz_only</option> 66 <option value="mz_only">mz_only</option>
68 <option value="formula_only">formula_only</option> 67 <option value="formula_only">formula_only</option>
69 <expand macro="list_string_san" name="format"/> 68 <expand macro="list_string_san" name="format"/>
70 </param> 69 </param>
71 <param argument="-average_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute average (instead of monoisotopic) oligonucleotide masses" help=""/> 70 <param argument="-average_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute average (instead of monoisotopic) oligonucleotide masses" help=""/>
72 <param argument="-fragment_type" type="select" optional="true" label="For what type of sequence/fragment the mass should be computed" help=""> 71 <param argument="-fragment_type" type="select" label="For what type of sequence/fragment the mass should be computed" help="">
73 <option value="full" selected="true">full</option> 72 <option value="full" selected="true">full</option>
74 <option value="internal">internal</option> 73 <option value="internal">internal</option>
75 <option value="5-prime">5-prime</option> 74 <option value="5-prime">5-prime</option>
76 <option value="3-prime">3-prime</option> 75 <option value="3-prime">3-prime</option>
77 <option value="a-B-ion">a-B-ion</option> 76 <option value="a-B-ion">a-B-ion</option>
88 <param argument="-separator" type="text" optional="true" value="" label="Field separator for 'table' output format; by default, the 'tab' character is used" help=""> 87 <param argument="-separator" type="text" optional="true" value="" label="Field separator for 'table' output format; by default, the 'tab' character is used" help="">
89 <expand macro="list_string_san" name="separator"/> 88 <expand macro="list_string_san" name="separator"/>
90 </param> 89 </param>
91 <expand macro="adv_opts_macro"> 90 <expand macro="adv_opts_macro">
92 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 91 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
93 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 92 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
94 <expand macro="list_string_san" name="test"/> 93 <expand macro="list_string_san" name="test"/>
95 </param> 94 </param>
96 </expand> 95 </expand>
97 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 96 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
98 <option value="out_FLAG">out (Output file; if empty, output is written to the screen)</option> 97 <option value="out_FLAG">out (Output file; if empty, output is written to the screen)</option>
108 </data> 107 </data>
109 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 108 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
110 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 109 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
111 </data> 110 </data>
112 </outputs> 111 </outputs>
113 <tests><!-- UTILS_RNAMassCalculator_1 --> 112 <tests>
113 <!-- TOPP_RNAMassCalculator_1 -->
114 <test expect_num_outputs="2"> 114 <test expect_num_outputs="2">
115 <section name="adv_opts"> 115 <section name="adv_opts">
116 <param name="force" value="false"/> 116 <param name="force" value="false"/>
117 <param name="test" value="true"/> 117 <param name="test" value="true"/>
118 </section> 118 </section>
119 <param name="in_seq" value="&quot;AUCGGC&quot;"/> 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"/> 120 <output name="out" value="RNAMassCalculator_1.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
121 <param name="charge" value="-1 -2"/> 121 <param name="charge" value="-1 -2"/>
122 <param name="format" value="list"/> 122 <param name="format" value="list"/>
123 <param name="average_mass" value="false"/> 123 <param name="average_mass" value="false"/>
124 <param name="fragment_type" value="full"/> 124 <param name="fragment_type" value="full"/>
125 <param name="separator" value=""/> 125 <param name="separator" value=""/>
127 <output name="ctd_out" ftype="xml"> 127 <output name="ctd_out" ftype="xml">
128 <assert_contents> 128 <assert_contents>
129 <is_valid_xml/> 129 <is_valid_xml/>
130 </assert_contents> 130 </assert_contents>
131 </output> 131 </output>
132 <assert_stdout>
133 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
134 </assert_stdout>
132 </test> 135 </test>
133 </tests> 136 </tests>
134 <help><![CDATA[Calculates masses, mass-to-charge ratios and sum formulas of RNA sequences 137 <help><![CDATA[Calculates masses, mass-to-charge ratios and sum formulas of RNA sequences
135 138
136 139
137 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_RNAMassCalculator.html]]></help> 140 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_RNAMassCalculator.html]]></help>
138 <expand macro="references"/> 141 <expand macro="references"/>
139 </tool> 142 </tool>