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comparison EICExtractor.xml @ 11:2bd3c83eed94 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 12:58:22 +0000
parents e8a9dc186db5
children 0546885ddaf9
comparison
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10:2258e1813440 11:2bd3c83eed94
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="2.3.0"> 4 <tool id="EICExtractor" name="EICExtractor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[EICExtractor 15 @EXT_FOO@
16 #import re
14 17
18 ## Preprocessing
19 mkdir in &&
20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
21 #if $in_header:
22 mkdir in_header &&
23 ${ ' '.join(["ln -s '%s' 'in_header/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_header if _]) }
24 #end if
25 mkdir pos &&
26 ln -s '$pos' 'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)' &&
27 mkdir out &&
28 #if "out_debug_TIC_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
29 mkdir auto_rt_out_debug_TIC &&
30 #end if
31
32 ## Main program call
33
34 set -o pipefail &&
35 @EXECUTABLE@ -write_ctd ./ &&
36 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
37 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
15 -in 38 -in
16 #for token in $param_in: 39 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
17 $token 40 #if $in_header:
18 #end for 41 -in_header
19 -in_header 42 ${' '.join(["'in_header/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_header if _])}
20 #for token in $param_in_header:
21 $token
22 #end for
23 #if $param_pos:
24 -pos $param_pos
25 #end if 43 #end if
26 #if $param_rt_tol: 44 -pos
27 -rt_tol $param_rt_tol 45 'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)'
46 -out
47 'out/output.${gxy2omsext("csv")}'
48 #if "out_debug_TIC_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
49 -auto_rt:out_debug_TIC
50 'auto_rt_out_debug_TIC/output.${gxy2omsext("mzml")}'
28 #end if 51 #end if
29 #if $param_mz_tol: 52 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
30 -mz_tol $param_mz_tol 53 | tee '$stdout'
31 #end if 54 #end if
32 #if $param_rt_collect: 55
33 -rt_collect $param_rt_collect 56 ## Postprocessing
57 && mv 'out/output.${gxy2omsext("csv")}' '$out'
58 #if "out_debug_TIC_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
59 && mv 'auto_rt_out_debug_TIC/output.${gxy2omsext("mzml")}' '$auto_rt_out_debug_TIC'
34 #end if 60 #end if
35 #if $param_out: 61 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
36 -out $param_out 62 && mv '@EXECUTABLE@.ctd' '$ctd_out'
37 #end if 63 #end if]]></command>
38 #if $param_auto_rt_enabled: 64 <configfiles>
39 -auto_rt:enabled 65 <inputs name="args_json" data_style="paths"/>
40 #end if 66 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
41 #if $param_auto_rt_out_debug_TIC: 67 </configfiles>
42 -auto_rt:out_debug_TIC $param_auto_rt_out_debug_TIC
43 #end if
44 #if $adv_opts.adv_opts_selector=='advanced':
45 #if $adv_opts.param_out_separator:
46 -out_separator "$adv_opts.param_out_separator"
47 #end if
48 #if $adv_opts.param_force:
49 -force
50 #end if
51 #if $adv_opts.param_auto_rt_FHWM:
52 -auto_rt:FHWM $adv_opts.param_auto_rt_FHWM
53 #end if
54 #if $adv_opts.param_auto_rt_SNThreshold:
55 -auto_rt:SNThreshold $adv_opts.param_auto_rt_SNThreshold
56 #end if
57 #end if
58 ]]></command>
59 <inputs> 68 <inputs>
60 <param name="param_in" type="data" format="mzml" multiple="true" optional="False" size="30" label="Input raw data file" help="(-in) "> 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)"/>
61 <sanitizer> 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)"/>
62 <valid initial="string.printable"> 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)"/>
63 <remove value="'"/> 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=""/>
64 <remove value="&quot;"/> 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=""/>
65 </valid> 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=""/>
66 </sanitizer> 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">
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=""/>
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"/>
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"/>
79 </section>
80 <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="">
82 <expand macro="list_string_san"/>
83 </param>
84 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite 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="">
86 <expand macro="list_string_san"/>
87 </param>
88 </expand>
89 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
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>
91 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
67 </param> 92 </param>
68 <param name="param_in_header" type="data" format="txt" multiple="true" optional="True" size="30" label="[for Waters data only] Read additional information from _HEADER.TXT" help="(-in_header) Provide one for each raw input file">
69 <sanitizer>
70 <valid initial="string.printable">
71 <remove value="'"/>
72 <remove value="&quot;"/>
73 </valid>
74 </sanitizer>
75 </param>
76 <param name="param_pos" type="data" format="tabular" optional="False" label="Input config file stating where to find signal" help="(-pos) "/>
77 <param name="param_rt_tol" type="float" value="3.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help="(-rt_tol) "/>
78 <param name="param_mz_tol" type="float" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help="(-mz_tol) "/>
79 <param name="param_rt_collect" type="integer" value="1" label="# of scans up &amp; down in RT from highest point for ppm estimation in result" help="(-rt_collect) "/>
80 <param name="param_auto_rt_enabled" display="radio" type="boolean" truevalue="-auto_rt:enabled" falsevalue="" checked="false" optional="True" label="Automatically detect injection peaks from TIC and quantify all m/z x RT combinations" help="(-enabled) "/>
81 <expand macro="advanced_options">
82 <param name="param_out_separator" type="text" size="30" value="," label="Separator character for output CSV file" help="(-out_separator) ">
83 <sanitizer>
84 <valid initial="string.printable">
85 <remove value="'"/>
86 <remove value="&quot;"/>
87 </valid>
88 </sanitizer>
89 </param>
90 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
91 <param name="param_auto_rt_FHWM" type="float" value="5.0" label="Expected full width at half-maximum of each raw RT peak in [s]" help="(-FHWM) Gaussian smoothing filter with this width is applied to TIC"/>
92 <param name="param_auto_rt_SNThreshold" type="float" value="5.0" label="S/N threshold for a smoothed raw peak to pass peak picking" help="(-SNThreshold) Higher thesholds will result in less peaks"/>
93 </expand>
94 </inputs> 93 </inputs>
95 <outputs> 94 <outputs>
96 <data name="param_out" format="tabular"/> 95 <data name="out" label="${tool.name} on ${on_string}: out" format="csv"/>
97 <data name="param_auto_rt_out_debug_TIC" format="mzml"/> 96 <data name="auto_rt_out_debug_TIC" label="${tool.name} on ${on_string}: auto_rt:out_debug_TIC" format="mzml">
97 <filter>OPTIONAL_OUTPUTS is not None and "out_debug_TIC_FLAG" in OPTIONAL_OUTPUTS</filter>
98 </data>
99 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
100 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
101 </data>
98 </outputs> 102 </outputs>
99 <help>Extracts intensities from dedicates positions in a LC/MS map 103 <tests>
104 <expand macro="autotest_EICExtractor"/>
105 <expand macro="manutest_EICExtractor"/>
106 </tests>
107 <help><![CDATA[Extracts intensities from dedicates positions in a LC/MS map
100 108
101 109
102 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_EICExtractor.html</help> 110 For more information, visit http://www.openms.de/documentation/TOPP_EICExtractor.html]]></help>
111 <expand macro="references"/>
103 </tool> 112 </tool>