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comparison EICExtractor.xml @ 15:f253d41d9170 draft default tip

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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 19:23:24 +0000
parents 0546885ddaf9
children
comparison
equal deleted inserted replaced
14:3cedbe742c68 15:f253d41d9170
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: [Quantitation]--> 3 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="EICExtractor" name="EICExtractor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <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> 5 <description>Extracts intensities from dedicates positions in a LC/MS map</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">EICExtractor</token> 7 <token name="@EXECUTABLE@">EICExtractor</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@
16 #import re 14 #import re
17 15
18 ## Preprocessing 16 ## Preprocessing
19 mkdir in && 17 mkdir in_cond.in &&
20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } 18 #if $in_cond.in_select == "no"
21 #if $in_header: 19 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
22 mkdir in_header && 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])}
23 ${ ' '.join(["ln -s '%s' 'in_header/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_header if _]) } 21 #else
22 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
23 #end if
24 #if $in_header_cond.in_header:
25 mkdir in_header_cond.in_header &&
26 #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])} &&
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])}
29 #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($in_header_cond.in_header.ext)' &&
31 #end if
24 #end if 32 #end if
25 mkdir pos && 33 mkdir pos &&
26 ln -s '$pos' 'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)' && 34 ln -s '$pos' 'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)' &&
27 mkdir out && 35 mkdir out &&
28 #if "out_debug_TIC_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 36 #if "out_debug_TIC_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
34 set -o pipefail && 42 set -o pipefail &&
35 @EXECUTABLE@ -write_ctd ./ && 43 @EXECUTABLE@ -write_ctd ./ &&
36 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 44 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
37 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 45 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
38 -in 46 -in
39 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} 47 #if $in_cond.in_select == "no"
40 #if $in_header: 48 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
49 #else
50 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
51 #end if
52 #if $in_header_cond.in_header:
41 -in_header 53 -in_header
42 ${' '.join(["'in_header/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_header if _])} 54 #if $in_header_cond.in_header_select == "no"
55 ${' '.join(["'in_header_cond.in_header/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_header_cond.in_header) if f])}
56 #else
57 'in_header_cond.in_header/${re.sub("[^\w\-_]", "_", $in_header_cond.in_header.element_identifier)}.$gxy2omsext($in_header_cond.in_header.ext)'
58 #end if
43 #end if 59 #end if
44 -pos 60 -pos
45 'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)' 61 'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)'
46 -out 62 -out
47 'out/output.${gxy2omsext("csv")}' 63 'out/output.${gxy2omsext("csv")}'
64 <configfiles> 80 <configfiles>
65 <inputs name="args_json" data_style="paths"/> 81 <inputs name="args_json" data_style="paths"/>
66 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 82 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
67 </configfiles> 83 </configfiles>
68 <inputs> 84 <inputs>
69 <param name="in" argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input raw data file" help=" select mzml data sets(s)"/> 85 <conditional name="in_cond">
70 <param name="in_header" 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)"/> 86 <param name="in_select" type="select" label="Run tool in batch mode for -in">
71 <param name="pos" argument="-pos" type="data" format="edta" optional="false" label="Input config file stating where to find signal" help=" select edta data sets(s)"/> 87 <option value="no">No: process all datasets jointly</option>
72 <param name="rt_tol" 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=""/> 88 <option value="yes">Yes: process each dataset in an independent job</option>
73 <param name="mz_tol" argument="-mz_tol" type="float" optional="true" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help=""/> 89 </param>
74 <param name="rt_collect" 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=""/> 90 <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)"/>
92 </when>
93 <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)"/>
95 </when>
96 </conditional>
97 <conditional name="in_header_cond">
98 <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>
100 <option value="yes">Yes: process each dataset in an independent job</option>
101 </param>
102 <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)"/>
104 </when>
105 <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)"/>
107 </when>
108 </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)"/>
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=""/>
111 <param argument="-mz_tol" type="float" optional="true" 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=""/>
75 <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"> 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">
76 <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=""/> 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=""/>
77 <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"/> 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"/>
78 <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"/> 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"/>
79 </section> 117 </section>
80 <expand macro="adv_opts_macro"> 118 <expand macro="adv_opts_macro">
81 <param name="out_separator" argument="-out_separator" type="text" optional="true" value="," label="Separator character for output CSV file" help=""> 119 <param argument="-out_separator" type="text" optional="true" value="," label="Separator character for output CSV file" help="">
82 <expand macro="list_string_san"/> 120 <expand macro="list_string_san" name="out_separator"/>
83 </param> 121 </param>
84 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 122 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
85 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 123 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
86 <expand macro="list_string_san"/> 124 <expand macro="list_string_san" name="test"/>
87 </param> 125 </param>
88 </expand> 126 </expand>
89 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 127 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
90 <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> 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>
91 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 129 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
98 </data> 136 </data>
99 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 137 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
100 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 138 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
101 </data> 139 </data>
102 </outputs> 140 </outputs>
103 <tests> 141 <tests><test expect_num_outputs="1"><!-- just using some random test data -->
104 <expand macro="autotest_EICExtractor"/> 142 <param name="adv_opts|test" value="true"/>
105 <expand macro="manutest_EICExtractor"/> 143 <param name="in" value="spectra.mzML"/>
106 </tests> 144 <param name="pos" ftype="edta" value="FileConverter_10_input.edta"/>
145 <output name="out" ftype="csv" value="EICExtractor.csv" lines_diff="2"/>
146 </test>
147 </tests>
107 <help><![CDATA[Extracts intensities from dedicates positions in a LC/MS map 148 <help><![CDATA[Extracts intensities from dedicates positions in a LC/MS map
108 149
109 150
110 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_EICExtractor.html]]></help> 151 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_EICExtractor.html]]></help>
111 <expand macro="references"/> 152 <expand macro="references"/>
112 </tool> 153 </tool>