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comparison PSMFeatureExtractor.xml @ 11:c68cd6e1d3dc 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 21:40:34 +0000
parents 63fea23042c4
children
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10:63fea23042c4 11:c68cd6e1d3dc
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: [Identification Processing]-->
4 <tool id="PSMFeatureExtractor" name="PSMFeatureExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="PSMFeatureExtractor" name="PSMFeatureExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Computes extra features for each input PSM.</description> 4 <description>Computes extra features for each input PSM</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">PSMFeatureExtractor</token> 6 <token name="@EXECUTABLE@">PSMFeatureExtractor</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in_cond.in && 16 mkdir in_cond.in &&
18 #if $in_cond.in_select == "no" 17 #if $in_cond.in_select == "no"
19 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 18 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
20 ${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} 19 ${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
21 #else 20 #else
22 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && 21 cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
23 #end if 22 #end if
24 mkdir out && 23 mkdir out &&
25 24
26 ## Main program call 25 ## Main program call
27 26
52 <param name="in_select" type="select" label="Run tool in batch mode for -in"> 51 <param name="in_select" type="select" label="Run tool in batch mode for -in">
53 <option value="no">No: process all datasets jointly</option> 52 <option value="no">No: process all datasets jointly</option>
54 <option value="yes">Yes: process each dataset in an independent job</option> 53 <option value="yes">Yes: process each dataset in an independent job</option>
55 </param> 54 </param>
56 <when value="no"> 55 <when value="no">
57 <param argument="-in" type="data" format="idxml,mzid" multiple="true" optional="false" label="Input file(s)" help=" select idxml,mzid data sets(s)"/> 56 <param argument="-in" type="data" format="idxml,mzid" multiple="true" label="Input file(s)" help=" select idxml,mzid data sets(s)"/>
58 </when> 57 </when>
59 <when value="yes"> 58 <when value="yes">
60 <param argument="-in" type="data" format="idxml,mzid" multiple="false" optional="false" label="Input file(s)" help=" select idxml,mzid data sets(s)"/> 59 <param argument="-in" type="data" format="idxml,mzid" label="Input file(s)" help=" select idxml,mzid data sets(s)"/>
61 </when> 60 </when>
62 </conditional> 61 </conditional>
63 <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help=""> 62 <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help="">
64 <option value="idXML">idxml</option> 63 <option value="idXML">idxml</option>
65 <option value="mzid">mzid</option> 64 <option value="mzid">mzid</option>
65 <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
66 <expand macro="list_string_san" name="out_type"/> 66 <expand macro="list_string_san" name="out_type"/>
67 </param> 67 </param>
68 <param argument="-extra" type="text" optional="true" value="" label="List of the MetaData parameters to be included in a feature set for precolato" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 68 <param argument="-extra" type="text" optional="true" value="" label="List of the MetaData parameters to be included in a feature set for precolato" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
69 <expand macro="list_string_val" name="extra"/> 69 <expand macro="list_string_val" name="extra"/>
70 <expand macro="list_string_san" name="extra"/> 70 <expand macro="list_string_san" name="extra"/>
74 <param argument="-skip_db_check" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Manual override to skip the check if same settings for multiple search engines were applied" help="Only valid together with -multiple_search_engines flag"/> 74 <param argument="-skip_db_check" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Manual override to skip the check if same settings for multiple search engines were applied" help="Only valid together with -multiple_search_engines flag"/>
75 <param argument="-concat" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Naive merging of PSMs from different search engines: concatenate multiple search results instead of merging on scan level" help="Only valid together with -multiple_search_engines flag"/> 75 <param argument="-concat" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Naive merging of PSMs from different search engines: concatenate multiple search results instead of merging on scan level" help="Only valid together with -multiple_search_engines flag"/>
76 <param argument="-impute" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Will instead of discarding all PSM not unanimously detected by all SE, impute missing values by their respective scores min/max observed" help="Only valid together with -multiple_search_engines flag"/> 76 <param argument="-impute" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Will instead of discarding all PSM not unanimously detected by all SE, impute missing values by their respective scores min/max observed" help="Only valid together with -multiple_search_engines flag"/>
77 <param argument="-limit_imputation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Will impute missing scores with the worst numerical limit (instead of min/max observed) of the respective score" help="Only valid together with -multiple_search_engines flag"/> 77 <param argument="-limit_imputation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Will impute missing scores with the worst numerical limit (instead of min/max observed) of the respective score" help="Only valid together with -multiple_search_engines flag"/>
78 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 78 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
79 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 79 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
80 <expand macro="list_string_san" name="test"/> 80 <expand macro="list_string_san" name="test"/>
81 </param> 81 </param>
82 </expand> 82 </expand>
83 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 83 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
84 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 84 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
92 </data> 92 </data>
93 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 93 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
94 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 94 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
95 </data> 95 </data>
96 </outputs> 96 </outputs>
97 <tests><test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible --> 97 <tests>
98 <param name="adv_opts|test" value="true"/> 98 <!-- TOPP_PSMFeatureExtractor_1 -->
99 <param name="adv_opts|skip_db_check" value="true"/> 99 <test expect_num_outputs="2">
100 <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/> 100 <section name="adv_opts">
101 <param name="multiple_search_engines" value="true"/> 101 <param name="skip_db_check" value="true"/>
102 <param name="out_type" value="idxml"/> 102 <param name="concat" value="false"/>
103 <output name="out" ftype="idxml" value="PSMFeatureExtractor.idxml" compare="sim_size" delta="500"/> 103 <param name="impute" value="false"/>
104 </test> 104 <param name="limit_imputation" value="false"/>
105 <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible --> 105 <param name="force" value="false"/>
106 <param name="adv_opts|test" value="true"/> 106 <param name="test" value="true"/>
107 <param name="adv_opts|skip_db_check" value="true"/> 107 </section>
108 <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/> 108 <conditional name="in_cond">
109 <param name="multiple_search_engines" value="true"/> 109 <param name="in" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
110 <param name="out_type" value="mzid"/> 110 </conditional>
111 <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" compare="sim_size" delta="500"/> 111 <output name="out" value="PSMFeatureExtractor_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
112 </test> 112 <param name="out_type" value="idXML"/>
113 <!-- test for the batch conditional crated for data parameters with multiple="true" --> 113 <param name="multiple_search_engines" value="true"/>
114 <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible --> 114 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
115 <param name="adv_opts|test" value="true"/> 115 <output name="ctd_out" ftype="xml">
116 <param name="in_select" value="yes"/> 116 <assert_contents>
117 <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/> 117 <is_valid_xml/>
118 <param name="out_type" value="idxml"/> 118 </assert_contents>
119 <output name="out" ftype="idxml" value="PSMFeatureExtractor_3.idXML" compare="sim_size" delta="500"/> 119 </output>
120 </test> 120 <assert_stdout>
121 </tests> 121 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
122 </assert_stdout>
123 </test>
124 <!-- TOPP_PSMFeatureExtractor_2 -->
125 <test expect_num_outputs="2">
126 <section name="adv_opts">
127 <param name="skip_db_check" value="true"/>
128 <param name="concat" value="false"/>
129 <param name="impute" value="false"/>
130 <param name="limit_imputation" value="false"/>
131 <param name="force" value="false"/>
132 <param name="test" value="true"/>
133 </section>
134 <conditional name="in_cond">
135 <param name="in" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
136 </conditional>
137 <output name="out" value="PSMFeatureExtractor_2_out.mzid" compare="sim_size" delta_frac="0.7" ftype="mzid"/>
138 <param name="out_type" value="mzid"/>
139 <param name="multiple_search_engines" value="true"/>
140 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
141 <output name="ctd_out" ftype="xml">
142 <assert_contents>
143 <is_valid_xml/>
144 </assert_contents>
145 </output>
146 <assert_stdout>
147 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
148 </assert_stdout>
149 </test>
150 <!-- TOPP_PSMFeatureExtractor_3 -->
151 <test expect_num_outputs="2">
152 <section name="adv_opts">
153 <param name="skip_db_check" value="false"/>
154 <param name="concat" value="false"/>
155 <param name="impute" value="false"/>
156 <param name="limit_imputation" value="false"/>
157 <param name="force" value="false"/>
158 <param name="test" value="true"/>
159 </section>
160 <conditional name="in_cond">
161 <param name="in" value="MSGFPlusAdapter_1_out.idXML"/>
162 </conditional>
163 <output name="out" value="PSMFeatureExtractor_3_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
164 <param name="out_type" value="idXML"/>
165 <param name="multiple_search_engines" value="false"/>
166 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
167 <output name="ctd_out" ftype="xml">
168 <assert_contents>
169 <is_valid_xml/>
170 </assert_contents>
171 </output>
172 <assert_stdout>
173 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
174 </assert_stdout>
175 </test>
176 </tests>
122 <help><![CDATA[Computes extra features for each input PSM. 177 <help><![CDATA[Computes extra features for each input PSM.
123 178
124 179
125 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_PSMFeatureExtractor.html]]></help> 180 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_PSMFeatureExtractor.html]]></help>
126 <expand macro="references"/> 181 <expand macro="references"/>
127 </tool> 182 </tool>