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comparison MSstatsConverter.xml @ 4:e3fb590554fd 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 19:13:23 +0000
parents e444b158fb20
children d0a7080ddf67
comparison
equal deleted inserted replaced
3:ef71714a330e 4:e3fb590554fd
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="MSstatsConverter" name="MSstatsConverter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="MSstatsConverter" name="MSstatsConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Converter to input for MSstats</description> 5 <description>Converter to input for MSstats</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MSstatsConverter</token> 7 <token name="@EXECUTABLE@">MSstatsConverter</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@
19 mkdir in && 17 mkdir in &&
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
21 mkdir in_design && 19 mkdir in_design &&
22 ln -s '$in_design' 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)' && 20 ln -s '$in_design' 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)' &&
23 mkdir out && 21 mkdir out &&
24 #if $adv_opts_cond.adv_opts_selector=='advanced': 22 #if $adv_opts.reannotate_filenames_cond.reannotate_filenames:
25 #if $adv_opts_cond.reannotate_filenames: 23 mkdir adv_opts.reannotate_filenames_cond.reannotate_filenames &&
26 mkdir adv_opts_cond.reannotate_filenames && 24 #if $adv_opts.reannotate_filenames_cond.reannotate_filenames_select == "no"
27 ${ ' '.join(["ln -s '%s' 'adv_opts_cond.reannotate_filenames/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $adv_opts_cond.reannotate_filenames if _]) } 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])}
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($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)' &&
29 #end if
28 #end if 30 #end if
29 #end if
30 31
31 ## Main program call 32 ## Main program call
32 33
33 set -o pipefail && 34 set -o pipefail &&
34 @EXECUTABLE@ -write_ctd ./ && 35 @EXECUTABLE@ -write_ctd ./ &&
38 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' 39 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
39 -in_design 40 -in_design
40 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)' 41 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)'
41 -out 42 -out
42 'out/output.${gxy2omsext("csv")}' 43 'out/output.${gxy2omsext("csv")}'
43 #if $adv_opts_cond.adv_opts_selector=='advanced': 44 #if $adv_opts.reannotate_filenames_cond.reannotate_filenames:
44 #if $adv_opts_cond.reannotate_filenames:
45 -reannotate_filenames 45 -reannotate_filenames
46 ${' '.join(["'adv_opts_cond.reannotate_filenames/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $adv_opts_cond.reannotate_filenames if _])} 46 #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])}
48 #else
49 'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)'
50 #end if
47 #end if 51 #end if
48 #end if
49 52
50 ## Postprocessing 53 ## Postprocessing
51 && mv 'out/output.${gxy2omsext("csv")}' '$out' 54 && mv 'out/output.${gxy2omsext("csv")}' '$out'
52 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS 55 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
53 && mv '@EXECUTABLE@.ctd' '$ctd_out' 56 && mv '@EXECUTABLE@.ctd' '$ctd_out'
55 <configfiles> 58 <configfiles>
56 <inputs name="args_json" data_style="paths"/> 59 <inputs name="args_json" data_style="paths"/>
57 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 60 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
58 </configfiles> 61 </configfiles>
59 <inputs> 62 <inputs>
60 <param name="in" argument="-in" type="data" format="consensusxml" optional="false" label="Input consensusXML with peptide intensities" help=" select consensusxml data sets(s)"/> 63 <param argument="-in" type="data" format="consensusxml" optional="false" label="Input consensusXML with peptide intensities" help=" select consensusxml data sets(s)"/>
61 <param name="in_design" argument="-in_design" type="data" format="tabular" optional="false" label="Experimental Design file" help=" select tabular data sets(s)"/> 64 <param argument="-in_design" type="data" format="tabular" optional="false" label="Experimental Design file" help=" select tabular data sets(s)"/>
62 <param name="method" argument="-method" display="radio" type="select" optional="false" label="Method used in the experiment(label free [LFQ], isobaric labeling [ISO]))" help=""> 65 <param argument="-method" type="select" optional="true" label="Method used in the experiment(label free [LFQ], isobaric labeling [ISO]))" help="">
63 <option value="LFQ" selected="true">LFQ</option> 66 <option value="LFQ" selected="true">LFQ</option>
64 <option value="ISO">ISO</option> 67 <option value="ISO">ISO</option>
65 <expand macro="list_string_san"/> 68 <expand macro="list_string_san" name="method"/>
66 </param> 69 </param>
67 <param name="msstats_bioreplicate" argument="-msstats_bioreplicate" type="text" optional="true" value="MSstats_BioReplicate" label="Which column in the condition table should be used for MSstats 'BioReplicate'" help=""> 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="">
68 <expand macro="list_string_san"/> 71 <expand macro="list_string_san" name="msstats_bioreplicate"/>
69 </param> 72 </param>
70 <param name="msstats_condition" argument="-msstats_condition" type="text" optional="true" value="MSstats_Condition" label="Which column in the condition table should be used for MSstats 'Condition'" help=""> 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="">
71 <expand macro="list_string_san"/> 74 <expand macro="list_string_san" name="msstats_condition"/>
72 </param> 75 </param>
73 <param name="msstats_mixture" argument="-msstats_mixture" type="text" optional="true" value="MSstats_Mixture" label="Which column in the condition table should be used for MSstats 'Mixture'" help=""> 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="">
74 <expand macro="list_string_san"/> 77 <expand macro="list_string_san" name="msstats_mixture"/>
75 </param> 78 </param>
76 <param name="labeled_reference_peptides" argument="-labeled_reference_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, IsotopeLabelType is 'H', else 'L'" help=""/> 79 <param argument="-labeled_reference_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, IsotopeLabelType is 'H', else 'L'" help=""/>
77 <expand macro="adv_opts_macro"> 80 <expand macro="adv_opts_macro">
78 <param name="reannotate_filenames" argument="-reannotate_filenames" type="data" format="mzml" multiple="true" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/> 81 <conditional name="reannotate_filenames_cond">
79 <param name="retention_time_summarization_method" argument="-retention_time_summarization_method" type="select" optional="false" 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)"> 82 <param name="reannotate_filenames_select" type="select" label="Run tool in batch mode for -reannotate_filenames">
83 <option value="no">No: process all datasets jointly</option>
84 <option value="yes">Yes: process each dataset in an independent job</option>
85 </param>
86 <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)"/>
88 </when>
89 <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)"/>
91 </when>
92 </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)">
80 <option value="manual">manual</option> 94 <option value="manual">manual</option>
81 <option value="max" selected="true">max</option> 95 <option value="max" selected="true">max</option>
82 <option value="min">min</option> 96 <option value="min">min</option>
83 <option value="mean">mean</option> 97 <option value="mean">mean</option>
84 <option value="sum">sum</option> 98 <option value="sum">sum</option>
85 <expand macro="list_string_san"/> 99 <expand macro="list_string_san" name="retention_time_summarization_method"/>
86 </param> 100 </param>
87 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 101 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
88 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 102 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
89 <expand macro="list_string_san"/> 103 <expand macro="list_string_san" name="test"/>
90 </param> 104 </param>
91 </expand> 105 </expand>
92 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 106 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
93 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 107 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
94 </param> 108 </param>
97 <data name="out" label="${tool.name} on ${on_string}: out" format="csv"/> 111 <data name="out" label="${tool.name} on ${on_string}: out" format="csv"/>
98 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 112 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
99 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 113 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
100 </data> 114 </data>
101 </outputs> 115 </outputs>
102 <tests> 116 <tests><!-- TOPP_MSstatsConverter_1 -->
103 <expand macro="autotest_MSstatsConverter"/> 117 <test expect_num_outputs="2">
104 <expand macro="manutest_MSstatsConverter"/> 118 <section name="adv_opts">
119 <param name="retention_time_summarization_method" value="max"/>
120 <param name="force" value="false"/>
121 <param name="test" value="true"/>
122 </section>
123 <param name="in" value="MSstatsConverter_1_in.consensusXML"/>
124 <param name="in_design" value="MSstatsConverter_1_design.tsv" ftype="tabular"/>
125 <param name="method" value="LFQ"/>
126 <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/>
127 <param name="msstats_condition" value="MSstats_Condition"/>
128 <param name="msstats_mixture" value="MSstats_Mixture"/>
129 <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"/>
131 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
132 <output name="ctd_out" ftype="xml">
133 <assert_contents>
134 <is_valid_xml/>
135 </assert_contents>
136 </output>
137 </test>
138 <!-- TOPP_MSstatsConverter_2 -->
139 <test expect_num_outputs="2">
140 <section name="adv_opts">
141 <param name="retention_time_summarization_method" value="manual"/>
142 <param name="force" value="false"/>
143 <param name="test" value="true"/>
144 </section>
145 <param name="in" value="MSstatsConverter_2_in.consensusXML"/>
146 <param name="in_design" value="MSstatsConverter_2_design.tsv" ftype="tabular"/>
147 <param name="method" value="ISO"/>
148 <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/>
149 <param name="msstats_condition" value="MSstats_Condition"/>
150 <param name="msstats_mixture" value="MSstats_Mixture"/>
151 <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"/>
153 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
154 <output name="ctd_out" ftype="xml">
155 <assert_contents>
156 <is_valid_xml/>
157 </assert_contents>
158 </output>
159 </test>
160 <!-- TOPP_MSstatsConverter_3 -->
161 <test expect_num_outputs="2">
162 <section name="adv_opts">
163 <param name="retention_time_summarization_method" value="manual"/>
164 <param name="force" value="false"/>
165 <param name="test" value="true"/>
166 </section>
167 <param name="in" value="MSstatsConverter_3_in.consensusXML"/>
168 <param name="in_design" value="MSstatsConverter_3_design.tsv" ftype="tabular"/>
169 <param name="method" value="ISO"/>
170 <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/>
171 <param name="msstats_condition" value="MSstats_Condition"/>
172 <param name="msstats_mixture" value="MSstats_Mixture"/>
173 <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"/>
175 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
176 <output name="ctd_out" ftype="xml">
177 <assert_contents>
178 <is_valid_xml/>
179 </assert_contents>
180 </output>
181 </test>
105 </tests> 182 </tests>
106 <help><![CDATA[Converter to input for MSstats 183 <help><![CDATA[Converter to input for MSstats
107 184
108 185
109 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MSstatsConverter.html]]></help> 186 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MSstatsConverter.html]]></help>
110 <expand macro="references"/> 187 <expand macro="references"/>
111 </tool> 188 </tool>