Mercurial > repos > galaxyp > openms_openswathchromatogramextractor

comparison OpenSwathChromatogramExtractor.xml @ 9:e9c148b32f87 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 20:03:02 +0000
parents 24cfe1d7137e
children 71555764c24a
comparison
equal deleted inserted replaced
8:0b2a3b05a9b4 9:e9c148b32f87
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: [Targeted Experiments]--> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <tool id="OpenSwathChromatogramExtractor" name="OpenSwathChromatogramExtractor" version="2.3.0"> 4 <tool id="OpenSwathChromatogramExtractor" name="OpenSwathChromatogramExtractor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Extract chromatograms (XIC) from a MS2 map file.</description> 5 <description>Extract chromatograms (XIC) from a MS2 map file.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathChromatogramExtractor</token> 7 <token name="@EXECUTABLE@">OpenSwathChromatogramExtractor</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[OpenSwathChromatogramExtractor 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 $in if _]) }
21 mkdir tr &&
22 ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
23 #if $rt_norm:
24 mkdir rt_norm &&
25 ln -s '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' &&
26 #end if
27 mkdir out &&
28
29 ## Main program call
30
31 set -o pipefail &&
32 @EXECUTABLE@ -write_ctd ./ &&
33 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
34 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
15 -in 35 -in
16 #for token in $param_in: 36 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
17 $token 37 -tr
18 #end for 38 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)'
19 #if $param_tr: 39 #if $rt_norm:
20 -tr $param_tr 40 -rt_norm
41 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)'
21 #end if 42 #end if
22 #if $param_rt_norm: 43 -out
23 -rt_norm $param_rt_norm 44 'out/output.${gxy2omsext("mzml")}'
24 #end if 45
25 #if $param_out: 46 ## Postprocessing
26 -out $param_out 47 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
27 #end if 48 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
28 #if $param_min_upper_edge_dist: 49 && mv '@EXECUTABLE@.ctd' '$ctd_out'
29 -min_upper_edge_dist $param_min_upper_edge_dist 50 #end if]]></command>
30 #end if 51 <configfiles>
31 #if $param_mz_window: 52 <inputs name="args_json" data_style="paths"/>
32 -mz_window $param_mz_window 53 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
33 #end if 54 </configfiles>
34 #if $param_rt_window:
35 -rt_window $param_rt_window
36 #end if
37 #if $param_is_swath:
38 -is_swath
39 #end if
40 #if $param_ppm:
41 -ppm
42 #end if
43 #if $param_extract_MS1:
44 -extract_MS1
45 #end if
46 #if $param_extraction_function:
47 -extraction_function
48 #if " " in str($param_extraction_function):
49 "$param_extraction_function"
50 #else
51 $param_extraction_function
52 #end if
53 #end if
54 #if $param_model_type:
55 -model:type
56 #if " " in str($param_model_type):
57 "$param_model_type"
58 #else
59 $param_model_type
60 #end if
61 #end if
62 #if $param_model_symmetric_regression:
63 -model:symmetric_regression
64 #end if
65 #if $adv_opts.adv_opts_selector=='advanced':
66 #if $adv_opts.param_force:
67 -force
68 #end if
69 #end if
70 ]]></command>
71 <inputs> 55 <inputs>
72 <param name="param_in" type="data" format="mzml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) "> 56 <param name="in" argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input files separated by blank" help=" select mzml data sets(s)"/>
73 <sanitizer> 57 <param name="tr" argument="-tr" type="data" format="csv,traml" optional="false" label="transition file ('TraML' or 'csv')" help=" select csv,traml data sets(s)"/>
74 <valid initial="string.printable"> 58 <param name="rt_norm" argument="-rt_norm" type="data" format="trafoxml" optional="true" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help=" select trafoxml data sets(s)"/>
75 <remove value="'"/> 59 <param name="min_upper_edge_dist" argument="-min_upper_edge_dist" type="float" optional="true" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson" help=""/>
76 <remove value="&quot;"/> 60 <param name="rt_window" argument="-rt_window" type="float" optional="true" value="-1.0" label="Extraction window in RT dimension (-1 means extract over the whole range)" help="This is the full window size, e.g. a value of 1000 seconds would extract 500 seconds on either side"/>
77 </valid> 61 <param name="ion_mobility_window" argument="-ion_mobility_window" type="float" optional="true" value="-1.0" label="Extraction window in ion mobility dimension (in milliseconds)" help="This is the full window size, e.g. a value of 10 milliseconds would extract 5 milliseconds on either side"/>
78 </sanitizer> 62 <param name="mz_window" argument="-mz_window" type="float" optional="true" min="0.0" value="0.05" label="Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag)" help="This is the full window size, e.g. 100 ppm would extract 50 ppm on either side"/>
63 <param name="ppm" argument="-ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="m/z extraction_window is in ppm" help=""/>
64 <param name="is_swath" argument="-is_swath" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if the data is SWATH data" help=""/>
65 <param name="extract_MS1" argument="-extract_MS1" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Extract the MS1 transitions based on the precursor values in the TraML file (useful for extracting MS1 XIC)" help=""/>
66 <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false">
67 <param name="type" argument="-model:type" display="radio" type="select" optional="false" label="Type of model" help="">
68 <option value="linear" selected="true">linear</option>
69 <option value="b_spline">b_spline</option>
70 <option value="interpolated">interpolated</option>
71 <option value="lowess">lowess</option>
72 <expand macro="list_string_san"/>
73 </param>
74 <param name="symmetric_regression" argument="-model:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/>
75 </section>
76 <expand macro="adv_opts_macro">
77 <param name="extraction_function" argument="-extraction_function" display="radio" type="select" optional="false" label="Function used to extract the signal" help="">
78 <option value="tophat" selected="true">tophat</option>
79 <option value="bartlett">bartlett</option>
80 <expand macro="list_string_san"/>
81 </param>
82 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
83 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
84 <expand macro="list_string_san"/>
85 </param>
86 </expand>
87 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
88 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
79 </param> 89 </param>
80 <param name="param_tr" type="data" format="tabular,traml" optional="False" label="transition file ('TraML' or 'csv')" help="(-tr) "/>
81 <param name="param_rt_norm" type="data" format="trafoxml" optional="True" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help="(-rt_norm) "/>
82 <param name="param_min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson" help="(-min_upper_edge_dist) "/>
83 <param name="param_mz_window" type="float" min="0.0" optional="True" value="0.05" label="Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag). This is the full window size," help="(-mz_window) e.g. 100 ppm would extract 50 ppm on either side"/>
84 <param name="param_rt_window" type="float" value="-1.0" label="Extraction window in RT dimension (-1 means extract over the whole range). This is the full window size," help="(-rt_window) e.g. a value of 1000 seconds would extract 500 seconds on either side"/>
85 <param name="param_is_swath" display="radio" type="boolean" truevalue="-is_swath" falsevalue="" checked="false" optional="True" label="Set this flag if the data is SWATH data" help="(-is_swath) "/>
86 <param name="param_ppm" display="radio" type="boolean" truevalue="-ppm" falsevalue="" checked="false" optional="True" label="m/z extraction_window is in ppm" help="(-ppm) "/>
87 <param name="param_extract_MS1" display="radio" type="boolean" truevalue="-extract_MS1" falsevalue="" checked="false" optional="True" label="Extract the MS1 transitions based on the precursor values in the TraML file" help="(-extract_MS1) "/>
88 <param name="param_extraction_function" display="radio" type="select" optional="False" value="tophat" label="Function used to extract the signal" help="(-extraction_function) ">
89 <option value="tophat" selected="true">tophat</option>
90 <option value="bartlett">bartlett</option>
91 </param>
92 <param name="param_model_type" display="radio" type="select" optional="False" value="linear" label="Type of model" help="(-type) ">
93 <option value="linear" selected="true">linear</option>
94 <option value="b_spline">b_spline</option>
95 <option value="interpolated">interpolated</option>
96 <option value="lowess">lowess</option>
97 </param>
98 <param name="param_model_symmetric_regression" display="radio" type="boolean" truevalue="-model:symmetric_regression" falsevalue="" checked="false" optional="True" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'"/>
99 <expand macro="advanced_options">
100 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
101 </expand>
102 </inputs> 90 </inputs>
103 <outputs> 91 <outputs>
104 <data name="param_out" format="mzml"/> 92 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
93 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
94 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
95 </data>
105 </outputs> 96 </outputs>
106 <help>Extract chromatograms (XIC) from a MS2 map file. 97 <tests>
98 <expand macro="autotest_OpenSwathChromatogramExtractor"/>
99 <expand macro="manutest_OpenSwathChromatogramExtractor"/>
100 </tests>
101 <help><![CDATA[Extract chromatograms (XIC) from a MS2 map file.
107 102
108 103
109 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_OpenSwathChromatogramExtractor.html</help> 104 For more information, visit http://www.openms.de/documentation/TOPP_OpenSwathChromatogramExtractor.html]]></help>
105 <expand macro="references"/>
110 </tool> 106 </tool>