Mercurial > repos > galaxyp > openms_featurefindermetaboident

comparison FeatureFinderMetaboIdent.xml @ 0:539b683e9752 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 19:59:38 +0000
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children 7e29bf457263
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-1:000000000000 0:539b683e9752
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.-->
3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="FeatureFinderMetaboIdent" name="FeatureFinderMetaboIdent" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Detects features in MS1 data based on metabolite identifications.</description>
6 <macros>
7 <token name="@EXECUTABLE@">FeatureFinderMetaboIdent</token>
8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros>
12 <expand macro="requirements"/>
13 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@
16 #import re
17
18 ## Preprocessing
19 mkdir in &&
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
21 mkdir id &&
22 ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
23 mkdir out &&
24 #if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
25 mkdir lib_out &&
26 #end if
27 #if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
28 mkdir chrom_out &&
29 #end if
30 #if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
31 mkdir candidates_out &&
32 #end if
33 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
34 mkdir trafo_out &&
35 #end if
36
37 ## Main program call
38
39 set -o pipefail &&
40 @EXECUTABLE@ -write_ctd ./ &&
41 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
42 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
43 -in
44 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
45 -id
46 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)'
47 -out
48 'out/output.${gxy2omsext("featurexml")}'
49 #if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
50 -lib_out
51 'lib_out/output.${gxy2omsext("traml")}'
52 #end if
53 #if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
54 -chrom_out
55 'chrom_out/output.${gxy2omsext("mzml")}'
56 #end if
57 #if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
58 -candidates_out
59 'candidates_out/output.${gxy2omsext("featurexml")}'
60 #end if
61 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
62 -trafo_out
63 'trafo_out/output.${gxy2omsext("trafoxml")}'
64 #end if
65 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
66 | tee '$stdout'
67 #end if
68
69 ## Postprocessing
70 && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
71 #if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
72 && mv 'lib_out/output.${gxy2omsext("traml")}' '$lib_out'
73 #end if
74 #if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
75 && mv 'chrom_out/output.${gxy2omsext("mzml")}' '$chrom_out'
76 #end if
77 #if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
78 && mv 'candidates_out/output.${gxy2omsext("featurexml")}' '$candidates_out'
79 #end if
80 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
81 && mv 'trafo_out/output.${gxy2omsext("trafoxml")}' '$trafo_out'
82 #end if
83 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
84 && mv '@EXECUTABLE@.ctd' '$ctd_out'
85 #end if]]></command>
86 <configfiles>
87 <inputs name="args_json" data_style="paths"/>
88 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
89 </configfiles>
90 <inputs>
91 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input file: LC-MS raw data" help=" select mzml data sets(s)"/>
92 <param name="id" argument="-id" type="data" format="tabular" optional="false" label="Input file: Metabolite identifications" help=" select tabular data sets(s)"/>
93 <section name="extract" title="Parameters for ion chromatogram extraction" help="" expanded="false">
94 <param name="mz_window" argument="-extract:mz_window" type="float" optional="true" min="0.0" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help=""/>
95 <param name="n_isotopes" argument="-extract:n_isotopes" type="integer" optional="true" min="2" value="2" label="Number of isotopes to include in each assay" help=""/>
96 <param name="isotope_pmin" argument="-extract:isotope_pmin" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Minimum probability for an isotope to be included in the assay for a compound" help="If set, this parameter takes precedence over 'extract:n_isotopes'"/>
97 <param name="rt_window" argument="-extract:rt_window" type="float" optional="true" min="0.0" value="0.0" label="RT window size (in sec.) for chromatogram extraction" help="If zero, calculated based on 'detect:peak_width'"/>
98 </section>
99 <section name="detect" title="Parameters for detecting features in extracted ion chromatograms" help="" expanded="false">
100 <param name="peak_width" argument="-detect:peak_width" type="float" optional="true" min="0.0" value="5.0" label="Expected elution peak width in seconds, for smoothing (Gauss filter)" help="Also determines the RT extration window, unless set explicitly via 'extract:rt_window'"/>
101 <param name="min_peak_width" argument="-detect:min_peak_width" type="float" optional="true" min="0.0" value="0.2" label="Minimum elution peak width" help="Absolute value in seconds if 1 or greater, else relative to 'peak_width'"/>
102 <param name="signal_to_noise" argument="-detect:signal_to_noise" type="float" optional="true" min="0.1" value="0.8" label="Signal-to-noise threshold for OpenSWATH feature detection" help=""/>
103 </section>
104 <section name="model" title="Parameters for fitting elution models to features" help="" expanded="false">
105 <param name="type" argument="-model:type" display="radio" type="select" optional="false" label="Type of elution model to fit to features" help="">
106 <option value="symmetric" selected="true">symmetric</option>
107 <option value="asymmetric">asymmetric</option>
108 <option value="none">none</option>
109 <expand macro="list_string_san"/>
110 </param>
111 <param name="add_zeros" argument="-model:add_zeros" type="float" optional="true" min="0.0" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="This parameter sets the weight given to these points during model fitting; '0' to disable"/>
112 <param name="unweighted_fit" argument="-model:unweighted_fit" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress weighting of mass traces according to theoretical intensities when fitting elution models" help=""/>
113 <param name="no_imputation" argument="-model:no_imputation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimate" help=""/>
114 <section name="check" title="Parameters for checking the validity of elution models (and rejecting them if necessary)" help="" expanded="false">
115 <param name="min_area" argument="-model:check:min_area" type="float" optional="true" min="0.0" value="1.0" label="Lower bound for the area under the curve of a valid elution model" help=""/>
116 <param name="boundaries" argument="-model:check:boundaries" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting" help=""/>
117 <param name="width" argument="-model:check:width" type="float" optional="true" min="0.0" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores; '0' to disable" help=""/>
118 <param name="asymmetry" argument="-model:check:asymmetry" type="float" optional="true" min="0.0" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable" help=""/>
119 </section>
120 </section>
121 <expand macro="adv_opts_macro">
122 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
123 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
124 <expand macro="list_string_san"/>
125 </param>
126 </expand>
127 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
128 <option value="lib_out_FLAG">lib_out (Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable)</option>
129 <option value="chrom_out_FLAG">chrom_out (Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable)</option>
130 <option value="candidates_out_FLAG">candidates_out (Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable)</option>
131 <option value="trafo_out_FLAG">trafo_out (Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable)</option>
132 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
133 </param>
134 </inputs>
135 <outputs>
136 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
137 <data name="lib_out" label="${tool.name} on ${on_string}: lib_out" format="traml">
138 <filter>OPTIONAL_OUTPUTS is not None and "lib_out_FLAG" in OPTIONAL_OUTPUTS</filter>
139 </data>
140 <data name="chrom_out" label="${tool.name} on ${on_string}: chrom_out" format="mzml">
141 <filter>OPTIONAL_OUTPUTS is not None and "chrom_out_FLAG" in OPTIONAL_OUTPUTS</filter>
142 </data>
143 <data name="candidates_out" label="${tool.name} on ${on_string}: candidates_out" format="featurexml">
144 <filter>OPTIONAL_OUTPUTS is not None and "candidates_out_FLAG" in OPTIONAL_OUTPUTS</filter>
145 </data>
146 <data name="trafo_out" label="${tool.name} on ${on_string}: trafo_out" format="trafoxml">
147 <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter>
148 </data>
149 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
150 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
151 </data>
152 </outputs>
153 <tests>
154 <expand macro="autotest_FeatureFinderMetaboIdent"/>
155 <expand macro="manutest_FeatureFinderMetaboIdent"/>
156 </tests>
157 <help><![CDATA[Detects features in MS1 data based on metabolite identifications.
158
159
160 For more information, visit http://www.openms.de/documentation/UTILS_FeatureFinderMetaboIdent.html]]></help>
161 <expand macro="references"/>
162 </tool>