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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 21:33:43 +0000
parents e3fb590554fd
children
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4:e3fb590554fd 5:d0a7080ddf67
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: [File Converter]-->
4 <tool id="MSstatsConverter" name="MSstatsConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="MSstatsConverter" name="MSstatsConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Converter to input for MSstats</description> 4 <description>Converter to input for MSstats</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">MSstatsConverter</token> 6 <token name="@EXECUTABLE@">MSstatsConverter</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir in_design && 18 mkdir in_design &&
20 ln -s '$in_design' 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)' && 19 cp '$in_design' 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)' &&
21 mkdir out && 20 mkdir out &&
21 ## advanced options
22 #if $adv_opts.reannotate_filenames_cond.reannotate_filenames: 22 #if $adv_opts.reannotate_filenames_cond.reannotate_filenames:
23 mkdir adv_opts.reannotate_filenames_cond.reannotate_filenames && 23 mkdir adv_opts.reannotate_filenames_cond.reannotate_filenames &&
24 #if $adv_opts.reannotate_filenames_cond.reannotate_filenames_select == "no" 24 #if $adv_opts.reannotate_filenames_cond.reannotate_filenames_select == "no"
25 mkdir ${' '.join(["'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s'" % (i) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])} && 25 mkdir ${' '.join(["'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s'" % (i) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])} &&
26 ${' '.join(["ln -s '%s' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])} 26 ${' '.join(["cp '%s' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])}
27 #else 27 #else
28 ln -s '$adv_opts.reannotate_filenames_cond.reannotate_filenames' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)' && 28 cp '$adv_opts.reannotate_filenames_cond.reannotate_filenames' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)' &&
29 #end if 29 #end if
30 #end if 30 #end if
31
31 32
32 ## Main program call 33 ## Main program call
33 34
34 set -o pipefail && 35 set -o pipefail &&
35 @EXECUTABLE@ -write_ctd ./ && 36 @EXECUTABLE@ -write_ctd ./ &&
39 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' 40 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
40 -in_design 41 -in_design
41 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)' 42 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)'
42 -out 43 -out
43 'out/output.${gxy2omsext("csv")}' 44 'out/output.${gxy2omsext("csv")}'
45 ## advanced options
44 #if $adv_opts.reannotate_filenames_cond.reannotate_filenames: 46 #if $adv_opts.reannotate_filenames_cond.reannotate_filenames:
45 -reannotate_filenames 47 -reannotate_filenames
46 #if $adv_opts.reannotate_filenames_cond.reannotate_filenames_select == "no" 48 #if $adv_opts.reannotate_filenames_cond.reannotate_filenames_select == "no"
47 ${' '.join(["'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])} 49 ${' '.join(["'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])}
48 #else 50 #else
49 'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)' 51 'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)'
50 #end if 52 #end if
51 #end if 53 #end if
54
52 55
53 ## Postprocessing 56 ## Postprocessing
54 && mv 'out/output.${gxy2omsext("csv")}' '$out' 57 && mv 'out/output.${gxy2omsext("csv")}' '$out'
55 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS 58 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
56 && mv '@EXECUTABLE@.ctd' '$ctd_out' 59 && mv '@EXECUTABLE@.ctd' '$ctd_out'
58 <configfiles> 61 <configfiles>
59 <inputs name="args_json" data_style="paths"/> 62 <inputs name="args_json" data_style="paths"/>
60 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 63 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
61 </configfiles> 64 </configfiles>
62 <inputs> 65 <inputs>
63 <param argument="-in" type="data" format="consensusxml" optional="false" label="Input consensusXML with peptide intensities" help=" select consensusxml data sets(s)"/> 66 <param argument="-in" type="data" format="consensusxml" label="Input consensusXML with peptide intensities" help=" select consensusxml data sets(s)"/>
64 <param argument="-in_design" type="data" format="tabular" optional="false" label="Experimental Design file" help=" select tabular data sets(s)"/> 67 <param argument="-in_design" type="data" format="tabular" label="Experimental Design file" help=" select tabular data sets(s)"/>
65 <param argument="-method" type="select" optional="true" label="Method used in the experiment(label free [LFQ], isobaric labeling [ISO]))" help=""> 68 <param argument="-method" type="select" label="Method used in the experiment(label free [LFQ], isobaric labeling [ISO]))" help="">
66 <option value="LFQ" selected="true">LFQ</option> 69 <option value="LFQ" selected="true">LFQ</option>
67 <option value="ISO">ISO</option> 70 <option value="ISO">ISO</option>
68 <expand macro="list_string_san" name="method"/> 71 <expand macro="list_string_san" name="method"/>
69 </param> 72 </param>
70 <param argument="-msstats_bioreplicate" type="text" optional="true" value="MSstats_BioReplicate" label="Which column in the condition table should be used for MSstats 'BioReplicate'" help=""> 73 <param argument="-msstats_bioreplicate" type="text" value="MSstats_BioReplicate" label="Which column in the condition table should be used for MSstats 'BioReplicate'" help="">
71 <expand macro="list_string_san" name="msstats_bioreplicate"/> 74 <expand macro="list_string_san" name="msstats_bioreplicate"/>
72 </param> 75 </param>
73 <param argument="-msstats_condition" type="text" optional="true" value="MSstats_Condition" label="Which column in the condition table should be used for MSstats 'Condition'" help=""> 76 <param argument="-msstats_condition" type="text" value="MSstats_Condition" label="Which column in the condition table should be used for MSstats 'Condition'" help="">
74 <expand macro="list_string_san" name="msstats_condition"/> 77 <expand macro="list_string_san" name="msstats_condition"/>
75 </param> 78 </param>
76 <param argument="-msstats_mixture" type="text" optional="true" value="MSstats_Mixture" label="Which column in the condition table should be used for MSstats 'Mixture'" help=""> 79 <param argument="-msstats_mixture" type="text" value="MSstats_Mixture" label="Which column in the condition table should be used for MSstats 'Mixture'" help="">
77 <expand macro="list_string_san" name="msstats_mixture"/> 80 <expand macro="list_string_san" name="msstats_mixture"/>
78 </param> 81 </param>
79 <param argument="-labeled_reference_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, IsotopeLabelType is 'H', else 'L'" help=""/> 82 <param argument="-labeled_reference_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, IsotopeLabelType is 'H', else 'L'" help=""/>
80 <expand macro="adv_opts_macro"> 83 <expand macro="adv_opts_macro">
81 <conditional name="reannotate_filenames_cond"> 84 <conditional name="reannotate_filenames_cond">
85 </param> 88 </param>
86 <when value="no"> 89 <when value="no">
87 <param argument="-reannotate_filenames" type="data" format="mzml" multiple="true" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/> 90 <param argument="-reannotate_filenames" type="data" format="mzml" multiple="true" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/>
88 </when> 91 </when>
89 <when value="yes"> 92 <when value="yes">
90 <param argument="-reannotate_filenames" type="data" format="mzml" multiple="false" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/> 93 <param argument="-reannotate_filenames" type="data" format="mzml" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/>
91 </when> 94 </when>
92 </conditional> 95 </conditional>
93 <param argument="-retention_time_summarization_method" type="select" optional="true" label="How indistinguishable peptidoforms at different retention times should be treated" help="This is usually necessary for LFQ experiments and therefore defaults to 'max'. In case of TMT/iTRAQ, MSstatsTMT does the aggregation itself later and the parameter always resets to manual (i.e. is unused)"> 96 <param argument="-retention_time_summarization_method" type="select" label="How indistinguishable peptidoforms at different retention times should be treated" help="This is usually necessary for LFQ experiments and therefore defaults to 'max'. In case of TMT/iTRAQ, MSstatsTMT does the aggregation itself later and the parameter always resets to manual (i.e. is unused)">
94 <option value="manual">manual</option> 97 <option value="manual">manual</option>
95 <option value="max" selected="true">max</option> 98 <option value="max" selected="true">max</option>
96 <option value="min">min</option> 99 <option value="min">min</option>
97 <option value="mean">mean</option> 100 <option value="mean">mean</option>
98 <option value="sum">sum</option> 101 <option value="sum">sum</option>
99 <expand macro="list_string_san" name="retention_time_summarization_method"/> 102 <expand macro="list_string_san" name="retention_time_summarization_method"/>
100 </param> 103 </param>
101 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 104 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
102 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 105 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
103 <expand macro="list_string_san" name="test"/> 106 <expand macro="list_string_san" name="test"/>
104 </param> 107 </param>
105 </expand> 108 </expand>
106 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 109 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
107 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 110 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
111 <data name="out" label="${tool.name} on ${on_string}: out" format="csv"/> 114 <data name="out" label="${tool.name} on ${on_string}: out" format="csv"/>
112 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 115 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
113 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 116 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
114 </data> 117 </data>
115 </outputs> 118 </outputs>
116 <tests><!-- TOPP_MSstatsConverter_1 --> 119 <tests>
120 <!-- TOPP_MSstatsConverter_1 -->
117 <test expect_num_outputs="2"> 121 <test expect_num_outputs="2">
118 <section name="adv_opts"> 122 <section name="adv_opts">
119 <param name="retention_time_summarization_method" value="max"/> 123 <param name="retention_time_summarization_method" value="max"/>
120 <param name="force" value="false"/> 124 <param name="force" value="false"/>
121 <param name="test" value="true"/> 125 <param name="test" value="true"/>
125 <param name="method" value="LFQ"/> 129 <param name="method" value="LFQ"/>
126 <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/> 130 <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/>
127 <param name="msstats_condition" value="MSstats_Condition"/> 131 <param name="msstats_condition" value="MSstats_Condition"/>
128 <param name="msstats_mixture" value="MSstats_Mixture"/> 132 <param name="msstats_mixture" value="MSstats_Mixture"/>
129 <param name="labeled_reference_peptides" value="false"/> 133 <param name="labeled_reference_peptides" value="false"/>
130 <output name="out" file="MSstatsConverter_1_out.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/> 134 <output name="out" value="MSstatsConverter_1_out.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
131 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 135 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
132 <output name="ctd_out" ftype="xml"> 136 <output name="ctd_out" ftype="xml">
133 <assert_contents> 137 <assert_contents>
134 <is_valid_xml/> 138 <is_valid_xml/>
135 </assert_contents> 139 </assert_contents>
136 </output> 140 </output>
141 <assert_stdout>
142 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
143 </assert_stdout>
137 </test> 144 </test>
138 <!-- TOPP_MSstatsConverter_2 --> 145 <!-- TOPP_MSstatsConverter_2 -->
139 <test expect_num_outputs="2"> 146 <test expect_num_outputs="2">
140 <section name="adv_opts"> 147 <section name="adv_opts">
141 <param name="retention_time_summarization_method" value="manual"/> 148 <param name="retention_time_summarization_method" value="manual"/>
147 <param name="method" value="ISO"/> 154 <param name="method" value="ISO"/>
148 <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/> 155 <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/>
149 <param name="msstats_condition" value="MSstats_Condition"/> 156 <param name="msstats_condition" value="MSstats_Condition"/>
150 <param name="msstats_mixture" value="MSstats_Mixture"/> 157 <param name="msstats_mixture" value="MSstats_Mixture"/>
151 <param name="labeled_reference_peptides" value="false"/> 158 <param name="labeled_reference_peptides" value="false"/>
152 <output name="out" file="MSstatsConverter_2_out.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/> 159 <output name="out" value="MSstatsConverter_2_out.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
153 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 160 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
154 <output name="ctd_out" ftype="xml"> 161 <output name="ctd_out" ftype="xml">
155 <assert_contents> 162 <assert_contents>
156 <is_valid_xml/> 163 <is_valid_xml/>
157 </assert_contents> 164 </assert_contents>
158 </output> 165 </output>
166 <assert_stdout>
167 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
168 </assert_stdout>
159 </test> 169 </test>
160 <!-- TOPP_MSstatsConverter_3 --> 170 <!-- TOPP_MSstatsConverter_3 -->
161 <test expect_num_outputs="2"> 171 <test expect_num_outputs="2">
162 <section name="adv_opts"> 172 <section name="adv_opts">
163 <param name="retention_time_summarization_method" value="manual"/> 173 <param name="retention_time_summarization_method" value="manual"/>
169 <param name="method" value="ISO"/> 179 <param name="method" value="ISO"/>
170 <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/> 180 <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/>
171 <param name="msstats_condition" value="MSstats_Condition"/> 181 <param name="msstats_condition" value="MSstats_Condition"/>
172 <param name="msstats_mixture" value="MSstats_Mixture"/> 182 <param name="msstats_mixture" value="MSstats_Mixture"/>
173 <param name="labeled_reference_peptides" value="false"/> 183 <param name="labeled_reference_peptides" value="false"/>
174 <output name="out" file="MSstatsConverter_3_out.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/> 184 <output name="out" value="MSstatsConverter_3_out.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
175 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 185 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
176 <output name="ctd_out" ftype="xml"> 186 <output name="ctd_out" ftype="xml">
177 <assert_contents> 187 <assert_contents>
178 <is_valid_xml/> 188 <is_valid_xml/>
179 </assert_contents> 189 </assert_contents>
180 </output> 190 </output>
191 <assert_stdout>
192 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
193 </assert_stdout>
181 </test> 194 </test>
182 </tests> 195 </tests>
183 <help><![CDATA[Converter to input for MSstats 196 <help><![CDATA[Converter to input for MSstats
184 197
185 198
186 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MSstatsConverter.html]]></help> 199 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MSstatsConverter.html]]></help>
187 <expand macro="references"/> 200 <expand macro="references"/>
188 </tool> 201 </tool>