Mercurial > repos > galaxyp > openms_masscalculator

comparison MassCalculator.xml @ 13:bcd50cd4fe42 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 19:08:33 +0000
parents 65c6e741ddf3
children d905af02ce63
comparison
equal deleted inserted replaced
12:17ce97f931d3 13:bcd50cd4fe42
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="MassCalculator" name="MassCalculator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="MassCalculator" name="MassCalculator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Calculates masses and mass-to-charge ratios of peptide sequences</description> 5 <description>Calculates masses and mass-to-charge ratios of peptide sequences</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MassCalculator</token> 7 <token name="@EXECUTABLE@">MassCalculator</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="tabular" optional="true" label="Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq')" help=" select tabular data sets(s)"/> 55 <param argument="-in" type="data" format="tabular" optional="true" label="Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq')" help=" select tabular data sets(s)"/>
58 <param name="in_seq" argument="-in_seq" type="text" optional="true" value="" label="List of peptide 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 peptide 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" 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=""> 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)" 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 <expand macro="list_string_san"/> 68 <expand macro="list_string_san" name="format"/>
71 </param> 69 </param>
72 <param name="average_mass" argument="-average_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute average (instead of monoisotopic) peptide masses" help=""/> 70 <param argument="-average_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute average (instead of monoisotopic) peptide 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=""> 71 <param argument="-fragment_type" type="select" optional="true" label="For what type of sequence/fragment the mass should be computed" help="">
74 <option value="full" selected="true">full</option> 72 <option value="full" selected="true">full</option>
75 <option value="internal">internal</option> 73 <option value="internal">internal</option>
76 <option value="N-terminal">N-terminal</option> 74 <option value="N-terminal">N-terminal</option>
77 <option value="C-terminal">C-terminal</option> 75 <option value="C-terminal">C-terminal</option>
78 <option value="a-ion">a-ion</option> 76 <option value="a-ion">a-ion</option>
79 <option value="b-ion">b-ion</option> 77 <option value="b-ion">b-ion</option>
80 <option value="c-ion">c-ion</option> 78 <option value="c-ion">c-ion</option>
81 <option value="x-ion">x-ion</option> 79 <option value="x-ion">x-ion</option>
82 <option value="y-ion">y-ion</option> 80 <option value="y-ion">y-ion</option>
83 <option value="z-ion">z-ion</option> 81 <option value="z-ion">z-ion</option>
84 <expand macro="list_string_san"/> 82 <expand macro="list_string_san" name="fragment_type"/>
85 </param> 83 </param>
86 <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=""> 84 <param argument="-separator" type="text" optional="true" value="" label="Field separator for 'table' output format; by default, the 'tab' character is used" help="">
87 <expand macro="list_string_san"/> 85 <expand macro="list_string_san" name="separator"/>
88 </param> 86 </param>
89 <expand macro="adv_opts_macro"> 87 <expand macro="adv_opts_macro">
90 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 88 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
91 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 89 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
92 <expand macro="list_string_san"/> 90 <expand macro="list_string_san" name="test"/>
93 </param> 91 </param>
94 </expand> 92 </expand>
95 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 93 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
96 <option value="out_FLAG">out (Output file; if empty, output is written to the screen)</option> 94 <option value="out_FLAG">out (Output file; if empty, output is written to the screen)</option>
97 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 95 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
106 </data> 104 </data>
107 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 105 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
108 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 106 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
109 </data> 107 </data>
110 </outputs> 108 </outputs>
111 <tests> 109 <tests><!-- UTILS_MassCalculator_1 -->
112 <expand macro="autotest_MassCalculator"/> 110 <test expect_num_outputs="2">
113 <expand macro="manutest_MassCalculator"/> 111 <section name="adv_opts">
112 <param name="force" value="false"/>
113 <param name="test" value="true"/>
114 </section>
115 <param name="in" value="MassCalculator_1_input.tsv" ftype="tabular"/>
116 <param name="in_seq" value=""/>
117 <output name="out" file="MassCalculator_1_output.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
118 <param name="charge" value="0 1"/>
119 <param name="format" value="table"/>
120 <param name="average_mass" value="false"/>
121 <param name="fragment_type" value="full"/>
122 <param name="separator" value=","/>
123 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
124 <output name="ctd_out" ftype="xml">
125 <assert_contents>
126 <is_valid_xml/>
127 </assert_contents>
128 </output>
129 </test>
130 <!-- UTILS_MassCalculator_2 -->
131 <test expect_num_outputs="2">
132 <section name="adv_opts">
133 <param name="force" value="false"/>
134 <param name="test" value="true"/>
135 </section>
136 <param name="in_seq" value="&quot;LDQWLC(Carbamidomethyl)EKL&quot; &quot;(Glu-&gt;pyro-Glu)EAM(Oxidation)APKHK&quot; &quot;RANVM(Oxidation)DYR&quot; &quot;FGVEQDVDMVFASFIR&quot;"/>
137 <output name="out" file="MassCalculator_2_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
138 <param name="charge" value="1 2 3"/>
139 <param name="format" value="list"/>
140 <param name="average_mass" value="false"/>
141 <param name="fragment_type" value="full"/>
142 <param name="separator" value=""/>
143 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
144 <output name="ctd_out" ftype="xml">
145 <assert_contents>
146 <is_valid_xml/>
147 </assert_contents>
148 </output>
149 </test>
114 </tests> 150 </tests>
115 <help><![CDATA[Calculates masses and mass-to-charge ratios of peptide sequences 151 <help><![CDATA[Calculates masses and mass-to-charge ratios of peptide sequences
116 152
117 153
118 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MassCalculator.html]]></help> 154 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MassCalculator.html]]></help>
119 <expand macro="references"/> 155 <expand macro="references"/>
120 </tool> 156 </tool>