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comparison MassCalculator.xml @ 14:d905af02ce63 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 21:36:45 +0000
parents bcd50cd4fe42
children
comparison
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13:bcd50cd4fe42 14:d905af02ce63
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: [Misc / Helpers]-->
4 <tool id="MassCalculator" name="MassCalculator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <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> 4 <description>Calculates masses and mass-to-charge ratios of peptide sequences</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">MassCalculator</token> 6 <token name="@EXECUTABLE@">MassCalculator</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="tabular" optional="true" label="Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq')" help=" select tabular data sets(s)"/> 54 <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)"/>
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)"> 55 <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)">
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)" 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)" 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 <expand macro="list_string_san" name="format"/> 67 <expand macro="list_string_san" name="format"/>
69 </param> 68 </param>
70 <param argument="-average_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute average (instead of monoisotopic) peptide masses" help=""/> 69 <param argument="-average_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute average (instead of monoisotopic) peptide masses" help=""/>
71 <param argument="-fragment_type" type="select" optional="true" label="For what type of sequence/fragment the mass should be computed" help=""> 70 <param argument="-fragment_type" type="select" label="For what type of sequence/fragment the mass should be computed" help="">
72 <option value="full" selected="true">full</option> 71 <option value="full" selected="true">full</option>
73 <option value="internal">internal</option> 72 <option value="internal">internal</option>
74 <option value="N-terminal">N-terminal</option> 73 <option value="N-terminal">N-terminal</option>
75 <option value="C-terminal">C-terminal</option> 74 <option value="C-terminal">C-terminal</option>
76 <option value="a-ion">a-ion</option> 75 <option value="a-ion">a-ion</option>
84 <param argument="-separator" type="text" optional="true" value="" label="Field separator for 'table' output format; by default, the 'tab' character is used" help=""> 83 <param argument="-separator" type="text" optional="true" value="" label="Field separator for 'table' output format; by default, the 'tab' character is used" help="">
85 <expand macro="list_string_san" name="separator"/> 84 <expand macro="list_string_san" name="separator"/>
86 </param> 85 </param>
87 <expand macro="adv_opts_macro"> 86 <expand macro="adv_opts_macro">
88 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 87 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
89 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 88 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
90 <expand macro="list_string_san" name="test"/> 89 <expand macro="list_string_san" name="test"/>
91 </param> 90 </param>
92 </expand> 91 </expand>
93 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 92 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
94 <option value="out_FLAG">out (Output file; if empty, output is written to the screen)</option> 93 <option value="out_FLAG">out (Output file; if empty, output is written to the screen)</option>
104 </data> 103 </data>
105 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 104 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
106 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 105 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
107 </data> 106 </data>
108 </outputs> 107 </outputs>
109 <tests><!-- UTILS_MassCalculator_1 --> 108 <tests>
109 <!-- TOPP_MassCalculator_1 -->
110 <test expect_num_outputs="2"> 110 <test expect_num_outputs="2">
111 <section name="adv_opts"> 111 <section name="adv_opts">
112 <param name="force" value="false"/> 112 <param name="force" value="false"/>
113 <param name="test" value="true"/> 113 <param name="test" value="true"/>
114 </section> 114 </section>
115 <param name="in" value="MassCalculator_1_input.tsv" ftype="tabular"/> 115 <param name="in" value="MassCalculator_1_input.tsv" ftype="tabular"/>
116 <param name="in_seq" value=""/> 116 <output name="out" value="MassCalculator_1_output.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
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"/> 117 <param name="charge" value="0 1"/>
119 <param name="format" value="table"/> 118 <param name="format" value="table"/>
120 <param name="average_mass" value="false"/> 119 <param name="average_mass" value="false"/>
121 <param name="fragment_type" value="full"/> 120 <param name="fragment_type" value="full"/>
122 <param name="separator" value=","/> 121 <param name="separator" value=","/>
124 <output name="ctd_out" ftype="xml"> 123 <output name="ctd_out" ftype="xml">
125 <assert_contents> 124 <assert_contents>
126 <is_valid_xml/> 125 <is_valid_xml/>
127 </assert_contents> 126 </assert_contents>
128 </output> 127 </output>
128 <assert_stdout>
129 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
130 </assert_stdout>
129 </test> 131 </test>
130 <!-- UTILS_MassCalculator_2 --> 132 <!-- TOPP_MassCalculator_2 -->
131 <test expect_num_outputs="2"> 133 <test expect_num_outputs="2">
132 <section name="adv_opts"> 134 <section name="adv_opts">
133 <param name="force" value="false"/> 135 <param name="force" value="false"/>
134 <param name="test" value="true"/> 136 <param name="test" value="true"/>
135 </section> 137 </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;"/> 138 <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"/> 139 <output name="out" value="MassCalculator_2_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
138 <param name="charge" value="1 2 3"/> 140 <param name="charge" value="1 2 3"/>
139 <param name="format" value="list"/> 141 <param name="format" value="list"/>
140 <param name="average_mass" value="false"/> 142 <param name="average_mass" value="false"/>
141 <param name="fragment_type" value="full"/> 143 <param name="fragment_type" value="full"/>
142 <param name="separator" value=""/> 144 <param name="separator" value=""/>
144 <output name="ctd_out" ftype="xml"> 146 <output name="ctd_out" ftype="xml">
145 <assert_contents> 147 <assert_contents>
146 <is_valid_xml/> 148 <is_valid_xml/>
147 </assert_contents> 149 </assert_contents>
148 </output> 150 </output>
151 <assert_stdout>
152 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
153 </assert_stdout>
149 </test> 154 </test>
150 </tests> 155 </tests>
151 <help><![CDATA[Calculates masses and mass-to-charge ratios of peptide sequences 156 <help><![CDATA[Calculates masses and mass-to-charge ratios of peptide sequences
152 157
153 158
154 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MassCalculator.html]]></help> 159 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MassCalculator.html]]></help>
155 <expand macro="references"/> 160 <expand macro="references"/>
156 </tool> 161 </tool>