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comparison EICExtractor.xml @ 16:c0f39306c687 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 21:40:11 +0000
parents f253d41d9170
children
comparison
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15:f253d41d9170 16:c0f39306c687
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: [Quantitation]--> 2 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="EICExtractor" name="EICExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="EICExtractor" name="EICExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Extracts intensities from dedicates positions in a LC/MS map</description> 4 <description>Extracts intensities from dedicates positions in a LC/MS map</description>
6 <macros> 5 <macros>
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 #if $in_header_cond.in_header: 23 #if $in_header_cond.in_header:
25 mkdir in_header_cond.in_header && 24 mkdir in_header_cond.in_header &&
26 #if $in_header_cond.in_header_select == "no" 25 #if $in_header_cond.in_header_select == "no"
27 mkdir ${' '.join(["'in_header_cond.in_header/%s'" % (i) for i, f in enumerate($in_header_cond.in_header) if f])} && 26 mkdir ${' '.join(["'in_header_cond.in_header/%s'" % (i) for i, f in enumerate($in_header_cond.in_header) if f])} &&
28 ${' '.join(["ln -s '%s' 'in_header_cond.in_header/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_header_cond.in_header) if f])} 27 ${' '.join(["cp '%s' 'in_header_cond.in_header/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_header_cond.in_header) if f])}
29 #else 28 #else
30 ln -s '$in_header_cond.in_header' 'in_header_cond.in_header/${re.sub("[^\w\-_]", "_", $in_header_cond.in_header.element_identifier)}.$gxy2omsext($in_header_cond.in_header.ext)' && 29 cp '$in_header_cond.in_header' 'in_header_cond.in_header/${re.sub("[^\w\-_]", "_", $in_header_cond.in_header.element_identifier)}.$gxy2omsext($in_header_cond.in_header.ext)' &&
31 #end if 30 #end if
32 #end if 31 #end if
33 mkdir pos && 32 mkdir pos &&
34 ln -s '$pos' 'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)' && 33 cp '$pos' 'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)' &&
35 mkdir out && 34 mkdir out &&
36 #if "out_debug_TIC_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 35 #if "out_debug_TIC_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
37 mkdir auto_rt_out_debug_TIC && 36 mkdir auto_rt_out_debug_TIC &&
38 #end if 37 #end if
39 38
86 <param name="in_select" type="select" label="Run tool in batch mode for -in"> 85 <param name="in_select" type="select" label="Run tool in batch mode for -in">
87 <option value="no">No: process all datasets jointly</option> 86 <option value="no">No: process all datasets jointly</option>
88 <option value="yes">Yes: process each dataset in an independent job</option> 87 <option value="yes">Yes: process each dataset in an independent job</option>
89 </param> 88 </param>
90 <when value="no"> 89 <when value="no">
91 <param argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input raw data file" help=" select mzml data sets(s)"/> 90 <param argument="-in" type="data" format="mzml" multiple="true" label="Input raw data file" help=" select mzml data sets(s)"/>
92 </when> 91 </when>
93 <when value="yes"> 92 <when value="yes">
94 <param argument="-in" type="data" format="mzml" multiple="false" optional="false" label="Input raw data file" help=" select mzml data sets(s)"/> 93 <param argument="-in" type="data" format="mzml" label="Input raw data file" help=" select mzml data sets(s)"/>
95 </when> 94 </when>
96 </conditional> 95 </conditional>
97 <conditional name="in_header_cond"> 96 <conditional name="in_header_cond">
98 <param name="in_header_select" type="select" label="Run tool in batch mode for -in_header"> 97 <param name="in_header_select" type="select" label="Run tool in batch mode for -in_header">
99 <option value="no">No: process all datasets jointly</option> 98 <option value="no">No: process all datasets jointly</option>
101 </param> 100 </param>
102 <when value="no"> 101 <when value="no">
103 <param argument="-in_header" type="data" format="txt" multiple="true" optional="true" label="[for Waters data only] Read additional information from _HEADER.TXT" help="Provide one for each raw input file select txt data sets(s)"/> 102 <param argument="-in_header" type="data" format="txt" multiple="true" optional="true" label="[for Waters data only] Read additional information from _HEADER.TXT" help="Provide one for each raw input file select txt data sets(s)"/>
104 </when> 103 </when>
105 <when value="yes"> 104 <when value="yes">
106 <param argument="-in_header" type="data" format="txt" multiple="false" optional="true" label="[for Waters data only] Read additional information from _HEADER.TXT" help="Provide one for each raw input file select txt data sets(s)"/> 105 <param argument="-in_header" type="data" format="txt" optional="true" label="[for Waters data only] Read additional information from _HEADER.TXT" help="Provide one for each raw input file select txt data sets(s)"/>
107 </when> 106 </when>
108 </conditional> 107 </conditional>
109 <param argument="-pos" type="data" format="edta" optional="false" label="Input config file stating where to find signal" help=" select edta data sets(s)"/> 108 <param argument="-pos" type="data" format="edta" label="Input config file stating where to find signal" help=" select edta data sets(s)"/>
110 <param argument="-rt_tol" type="float" optional="true" value="3.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help=""/> 109 <param argument="-rt_tol" type="float" value="3.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help=""/>
111 <param argument="-mz_tol" type="float" optional="true" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help=""/> 110 <param argument="-mz_tol" type="float" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help=""/>
112 <param argument="-rt_collect" type="integer" optional="true" value="1" label="# of scans up &amp; down in RT from highest point for ppm estimation in result" help=""/> 111 <param argument="-rt_collect" type="integer" value="1" label="# of scans up &amp; down in RT from highest point for ppm estimation in result" help=""/>
113 <section name="auto_rt" title="Parameters for automatic detection of injection RT peaks (no need to specify them in 'pos' input file)" help="" expanded="false"> 112 <section name="auto_rt" title="Parameters for automatic detection of injection RT peaks (no need to specify them in 'pos' input file)" help="" expanded="false">
114 <param name="enabled" argument="-auto_rt:enabled" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Automatically detect injection peaks from TIC and quantify all m/z x RT combinations" help=""/> 113 <param name="enabled" argument="-auto_rt:enabled" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Automatically detect injection peaks from TIC and quantify all m/z x RT combinations" help=""/>
115 <param name="FHWM" argument="-auto_rt:FHWM" type="float" optional="true" value="5.0" label="Expected full width at half-maximum of each raw RT peak in [s]" help="Gaussian smoothing filter with this width is applied to TIC"/> 114 <param name="FHWM" argument="-auto_rt:FHWM" type="float" value="5.0" label="Expected full width at half-maximum of each raw RT peak in [s]" help="Gaussian smoothing filter with this width is applied to TIC"/>
116 <param name="SNThreshold" argument="-auto_rt:SNThreshold" type="float" optional="true" value="5.0" label="S/N threshold for a smoothed raw peak to pass peak picking" help="Higher thesholds will result in less peaks"/> 115 <param name="SNThreshold" argument="-auto_rt:SNThreshold" type="float" value="5.0" label="S/N threshold for a smoothed raw peak to pass peak picking" help="Higher thesholds will result in less peaks"/>
117 </section> 116 </section>
118 <expand macro="adv_opts_macro"> 117 <expand macro="adv_opts_macro">
119 <param argument="-out_separator" type="text" optional="true" value="," label="Separator character for output CSV file" help=""> 118 <param argument="-out_separator" type="text" value="," label="Separator character for output CSV file" help="">
120 <expand macro="list_string_san" name="out_separator"/> 119 <expand macro="list_string_san" name="out_separator"/>
121 </param> 120 </param>
122 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 121 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
123 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 122 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
124 <expand macro="list_string_san" name="test"/> 123 <expand macro="list_string_san" name="test"/>
125 </param> 124 </param>
126 </expand> 125 </expand>
127 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 126 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
128 <option value="out_debug_TIC_FLAG">out_debug_TIC (Optional output file (for first input) containing the smoothed TIC, S/N levels and picked RT positions)</option> 127 <option value="out_debug_TIC_FLAG">out_debug_TIC (Optional output file (for first input) containing the smoothed TIC, S/N levels and picked RT positions)</option>
136 </data> 135 </data>
137 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 136 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
138 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 137 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
139 </data> 138 </data>
140 </outputs> 139 </outputs>
141 <tests><test expect_num_outputs="1"><!-- just using some random test data --> 140 <tests>
142 <param name="adv_opts|test" value="true"/> 141 <test expect_num_outputs="1">
143 <param name="in" value="spectra.mzML"/> 142 <!-- just using some random test data -->
144 <param name="pos" ftype="edta" value="FileConverter_10_input.edta"/> 143 <param name="adv_opts|test" value="true"/>
145 <output name="out" ftype="csv" value="EICExtractor.csv" lines_diff="2"/> 144 <param name="in" value="spectra.mzML"/>
146 </test> 145 <param name="pos" ftype="edta" value="FileConverter_10_input.edta"/>
147 </tests> 146 <output name="out" ftype="csv" value="EICExtractor.csv" lines_diff="2"/>
147 </test>
148 </tests>
148 <help><![CDATA[Extracts intensities from dedicates positions in a LC/MS map 149 <help><![CDATA[Extracts intensities from dedicates positions in a LC/MS map
149 150
150 151
151 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_EICExtractor.html]]></help> 152 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_EICExtractor.html]]></help>
152 <expand macro="references"/> 153 <expand macro="references"/>
153 </tool> 154 </tool>