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comparison SiriusAdapter.xml @ 4:01731de4b735 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 12:48:58 +0000
parents 8a3a17bbcb63
children ac6f09817679
comparison
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3:4af2c942c879 4:01731de4b735
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: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="SiriusAdapter" name="SiriusAdapter" version="2.3.0"> 4 <tool id="SiriusAdapter" name="SiriusAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Tool for metabolite identification using single and tandem mass spectrometry</description> 5 <description>Tool for metabolite identification using single and tandem mass spectrometry</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">SiriusAdapter</token> 7 <token name="@EXECUTABLE@">SiriusAdapter</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[SiriusAdapter 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 mkdir in &&
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
21 #if $in_featureinfo:
22 mkdir in_featureinfo &&
23 ln -s '$in_featureinfo' 'in_featureinfo/${re.sub("[^\w\-_]", "_", $in_featureinfo.element_identifier)}.$gxy2omsext($in_featureinfo.ext)' &&
17 #end if 24 #end if
18 #if $param_out_sirius: 25 #if "out_sirius_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
19 -out_sirius $param_out_sirius 26 mkdir out_sirius &&
20 #end if 27 #end if
21 #if $param_out_fingerid: 28 #if "out_fingerid_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
22 -out_fingerid $param_out_fingerid 29 mkdir out_fingerid &&
23 #end if 30 #end if
24 #if $param_profile: 31 #if "out_ms_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
25 -profile 32 mkdir out_ms &&
26 #if " " in str($param_profile):
27 "$param_profile"
28 #else
29 $param_profile
30 #end if
31 #end if 33 #end if
32 #if $param_candidates: 34
33 -candidates $param_candidates 35 ## Main program call
36
37 set -o pipefail &&
38 @EXECUTABLE@ -write_ctd ./ &&
39 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
40 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
41 -in
42 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
43 #if $in_featureinfo:
44 -in_featureinfo
45 'in_featureinfo/${re.sub("[^\w\-_]", "_", $in_featureinfo.element_identifier)}.$gxy2omsext($in_featureinfo.ext)'
34 #end if 46 #end if
35 #if $param_database: 47 #if "out_sirius_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
36 -database 48 -out_sirius
37 #if " " in str($param_database): 49 'out_sirius/output.${gxy2omsext("mztab")}'
38 "$param_database"
39 #else
40 $param_database
41 #end if
42 #end if 50 #end if
43 #if $param_noise: 51 #if "out_fingerid_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
44 -noise $param_noise 52 -out_fingerid
53 'out_fingerid/output.${gxy2omsext("mztab")}'
45 #end if 54 #end if
46 #if $param_ppm_max: 55 #if "out_ms_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
47 -ppm_max $param_ppm_max 56 -out_ms
57 'out_ms/output.${gxy2omsext("sirius.ms")}'
48 #end if 58 #end if
49 #if $param_isotope: 59 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
50 -isotope 60 | tee '$stdout'
51 #if " " in str($param_isotope):
52 "$param_isotope"
53 #else
54 $param_isotope
55 #end if
56 #end if 61 #end if
57 #if $param_elements: 62
58 -elements "$param_elements" 63 ## Postprocessing
64 #if "out_sirius_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
65 && mv 'out_sirius/output.${gxy2omsext("mztab")}' '$out_sirius'
59 #end if 66 #end if
60 #if $param_number: 67 #if "out_fingerid_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
61 -number $param_number 68 && mv 'out_fingerid/output.${gxy2omsext("mztab")}' '$out_fingerid'
62 #end if 69 #end if
63 #if $param_auto_charge: 70 #if "out_ms_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
64 -auto_charge 71 && mv 'out_ms/output.${gxy2omsext("sirius.ms")}' '$out_ms'
65 #end if 72 #end if
66 #if $param_iontree: 73 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
67 -iontree 74 && mv '@EXECUTABLE@.ctd' '$ctd_out'
68 #end if 75 #end if]]></command>
69 #if $param_no_recalibration: 76 <configfiles>
70 -no_recalibration 77 <inputs name="args_json" data_style="paths"/>
71 #end if 78 <configfile name="hardcoded_json"><![CDATA[{"executable": "\$(which sirius)", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
72 #if $adv_opts.adv_opts_selector=='advanced': 79 </configfiles>
73 #if $adv_opts.param_force:
74 -force
75 #end if
76 #end if
77 ]]></command>
78 <inputs> 80 <inputs>
79 <param name="param_in" type="data" format="mzml" optional="False" label="MzML Input file" help="(-in) "/> 81 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="MzML Input file" help=" select mzml data sets(s)"/>
80 <param name="param_profile" display="radio" type="select" optional="False" value="qtof" label="Specify the used analysis profile" help="(-profile) "> 82 <param name="in_featureinfo" argument="-in_featureinfo" type="data" format="featurexml" optional="true" label="FeatureXML input with feature and adduct information" help=" select featurexml data sets(s)"/>
81 <option value="qtof" selected="true">qtof</option> 83 <param name="out_workspace_directory" argument="-out_workspace_directory" type="text" optional="true" value="" label="Output directory for SIRIUS workspace" help="">
82 <option value="orbitrap">orbitrap</option> 84 <expand macro="list_string_san"/>
83 <option value="fticr">fticr</option>
84 </param> 85 </param>
85 <param name="param_candidates" type="integer" value="5" label="The number of candidates in the output" help="(-candidates) Default 5 best candidates"/> 86 <section name="preprocessing" title="Preprocessing" help="" expanded="false">
86 <param name="param_database" type="select" optional="False" value="all" label="search formulas in given database" help="(-database) "> 87 <param name="filter_by_num_masstraces" argument="-preprocessing:filter_by_num_masstraces" type="integer" optional="true" min="1" value="1" label="Features have to have at least x MassTraces" help="To use this parameter feature_only is neccessary"/>
87 <option value="all" selected="true">all</option> 88 <param name="precursor_mz_tolerance" argument="-preprocessing:precursor_mz_tolerance" type="float" optional="true" value="0.005" label="Tolerance window for precursor selection (Feature selection in regard to the precursor)" help=""/>
88 <option value="chebi">chebi</option> 89 <param name="precursor_mz_tolerance_unit" argument="-preprocessing:precursor_mz_tolerance_unit" display="radio" type="select" optional="false" label="Unit of the precursor_mz_tolerance" help="">
89 <option value="custom">custom</option> 90 <option value="Da" selected="true">Da</option>
90 <option value="kegg">kegg</option> 91 <option value="ppm">ppm</option>
91 <option value="bio">bio</option> 92 <expand macro="list_string_san"/>
92 <option value="natural products">natural products</option> 93 </param>
93 <option value="pubmed">pubmed</option> 94 <param name="precursor_rt_tolerance" argument="-preprocessing:precursor_rt_tolerance" type="integer" optional="true" value="5" label="Tolerance window (left and right) for precursor selection [seconds]" help=""/>
94 <option value="hmdb">hmdb</option> 95 <param name="isotope_pattern_iterations" argument="-preprocessing:isotope_pattern_iterations" type="integer" optional="true" value="3" label="Number of iterations that should be performed to extract the C13 isotope pattern" help="If no peak is found (C13 distance) the function will abort. Be careful with noisy data - since this can lead to wrong isotope patterns"/>
95 <option value="biocyc">biocyc</option> 96 <param name="feature_only" argument="-preprocessing:feature_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Uses the feature information from in_featureinfo to reduce the search space to MS2 associated with a feature" help=""/>
96 <option value="hsdb">hsdb</option> 97 <param name="no_masstrace_info_isotope_pattern" argument="-preprocessing:no_masstrace_info_isotope_pattern" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag if the masstrace information from a feature should be discarded and the isotope_pattern_iterations should be used instead" help=""/>
97 <option value="knapsack">knapsack</option> 98 </section>
98 <option value="biological">biological</option> 99 <section name="sirius" title="Parameters for SIRIUS and CSI:FingerID" help="" expanded="false">
99 <option value="zinc bio">zinc bio</option> 100 <param name="profile" argument="-sirius:profile" display="radio" type="select" optional="false" label="Specify the used analysis profile" help="">
100 <option value="gnps">gnps</option> 101 <option value="qtof" selected="true">qtof</option>
101 <option value="pubchem">pubchem</option> 102 <option value="orbitrap">orbitrap</option>
102 <option value="mesh">mesh</option> 103 <option value="fticr">fticr</option>
103 <option value="maconda">maconda</option> 104 <expand macro="list_string_san"/>
105 </param>
106 <param name="candidates" argument="-sirius:candidates" type="integer" optional="true" min="1" value="5" label="The number of candidates in the SIRIUS output" help=""/>
107 <param name="database" argument="-sirius:database" type="select" optional="false" label="search formulas in given database" help="">
108 <option value="all" selected="true">all</option>
109 <option value="chebi">chebi</option>
110 <option value="custom">custom</option>
111 <option value="kegg">kegg</option>
112 <option value="bio">bio</option>
113 <option value="natural products">natural products</option>
114 <option value="pubmed">pubmed</option>
115 <option value="hmdb">hmdb</option>
116 <option value="biocyc">biocyc</option>
117 <option value="hsdb">hsdb</option>
118 <option value="knapsack">knapsack</option>
119 <option value="biological">biological</option>
120 <option value="zinc bio">zinc bio</option>
121 <option value="gnps">gnps</option>
122 <option value="pubchem">pubchem</option>
123 <option value="mesh">mesh</option>
124 <option value="maconda">maconda</option>
125 <expand macro="list_string_san"/>
126 </param>
127 <param name="noise" argument="-sirius:noise" type="integer" optional="true" min="0" value="0" label="median intensity of noise peaks" help=""/>
128 <param name="ppm_max" argument="-sirius:ppm_max" type="integer" optional="true" value="10" label="allowed ppm for decomposing masses" help=""/>
129 <param name="isotope" argument="-sirius:isotope" display="radio" type="select" optional="false" label="how to handle isotope pattern data" help="Use 'score' to use them for ranking or 'filter' if you just want to remove candidates with bad isotope pattern. With 'both' you can use isotopes for filtering and scoring. Use 'omit' to ignore isotope pattern">
130 <option value="score">score</option>
131 <option value="filter">filter</option>
132 <option value="both" selected="true">both</option>
133 <option value="omit">omit</option>
134 <expand macro="list_string_san"/>
135 </param>
136 <param name="elements" argument="-sirius:elements" type="text" optional="true" value="CHNOP[5]S[8]Cl[1]" label="The allowed elements" help="Write CHNOPSCl to allow the elements C, H, N, O, P, S and Cl. Add numbers in brackets to restrict the maximal allowed occurrence of these elements: CHNOP[5]S[8]Cl[1]">
137 <expand macro="list_string_san"/>
138 </param>
139 <param name="compound_timeout" argument="-sirius:compound_timeout" type="integer" optional="true" min="0" value="10" label="Time out in seconds per compound" help="To disable the timeout set the value to 0"/>
140 <param name="tree_timeout" argument="-sirius:tree_timeout" type="integer" optional="true" min="0" value="0" label="Time out in seconds per fragmentation tree computation" help=""/>
141 <param name="top_n_hits" argument="-sirius:top_n_hits" type="integer" optional="true" min="1" value="10" label="The number of top hits for each compound written to the CSI:FingerID output" help=""/>
142 <param name="cores" argument="-sirius:cores" type="integer" optional="true" min="1" value="1" label="The number of cores SIRIUS is allowed to use on the system" help=""/>
143 <param name="auto_charge" argument="-sirius:auto_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this option if the charge of your compounds is unknown and you do not want to assume [M+H]+ as default" help="With the auto charge option SIRIUS will not care about charges and allow arbitrary adducts for the precursor peak"/>
144 <param name="ion_tree" argument="-sirius:ion_tree" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Print molecular formulas and node labels with the ion formula instead of the neutral formula" help=""/>
145 <param name="no_recalibration" argument="-sirius:no_recalibration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this option is set, SIRIUS will not recalibrate the spectrum during the analysis" help=""/>
146 <param name="most_intense_ms2" argument="-sirius:most_intense_ms2" type="boolean" truevalue="true" falsevalue="false" checked="false" label="SIRIUS uses the fragmentation spectrum with the most intense precursor peak (for each spectrum)" help=""/>
147 </section>
148 <expand macro="adv_opts_macro">
149 <param name="converter_mode" argument="-converter_mode" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag in combination with the out_ms file to only convert the input mzML and featureXML to an .ms file" help="Without further SIRIUS processing"/>
150 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
151 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
152 <expand macro="list_string_san"/>
153 </param>
154 </expand>
155 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false">
156 <option value="out_sirius_FLAG">out_sirius (SIRIUS uses the fragmentation spectrum with the most intense precursor peak (for each spectrum))</option>
157 <option value="out_fingerid_FLAG">out_fingerid (SIRIUS uses the fragmentation spectrum with the most intense precursor peak (for each spectrum))</option>
158 <option value="out_ms_FLAG">out_ms (SIRIUS uses the fragmentation spectrum with the most intense precursor peak (for each spectrum))</option>
159 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
104 </param> 160 </param>
105 <param name="param_noise" type="integer" value="0" label="median intensity of noise peaks" help="(-noise) "/>
106 <param name="param_ppm_max" type="integer" value="10" label="allowed ppm for decomposing masses" help="(-ppm_max) "/>
107 <param name="param_isotope" display="radio" type="select" optional="False" value="both" label="how to handle isotope pattern data" help="(-isotope) Use 'score' to use them for ranking or 'filter' if you just want to remove candidates with bad isotope pattern. With 'both' you can use isotopes for filtering and scoring (default). Use 'omit' to ignore isotope pattern">
108 <option value="score">score</option>
109 <option value="filter">filter</option>
110 <option value="both" selected="true">both</option>
111 <option value="omit">omit</option>
112 </param>
113 <param name="param_elements" type="text" size="30" value="CHNOP[5]S" label="The allowed elements" help="(-elements) Write CHNOPSCl to allow the elements C, H, N, O, P, S and Cl. Add numbers in brackets to restrict the maximal allowed occurence of these elements: CHNOP[5]S[8]Cl[1]. By default CHNOP[5]S is used">
114 <sanitizer>
115 <valid initial="string.printable">
116 <remove value="'"/>
117 <remove value="&quot;"/>
118 </valid>
119 </sanitizer>
120 </param>
121 <param name="param_number" type="integer" value="10" label="The number of compounds used in the output" help="(-number) "/>
122 <param name="param_auto_charge" display="radio" type="boolean" truevalue="-auto_charge" falsevalue="" checked="false" optional="True" label="Use this option if the charge of your compounds is unknown and you do not want to assume [M+H]+ as default" help="(-auto_charge) With the auto charge option SIRIUS will not care about charges and allow arbitrary adducts for the precursor peak"/>
123 <param name="param_iontree" display="radio" type="boolean" truevalue="-iontree" falsevalue="" checked="false" optional="True" label="Print molecular formulas and node labels with the ion formula instead of the neutral formula" help="(-iontree) "/>
124 <param name="param_no_recalibration" display="radio" type="boolean" truevalue="-no_recalibration" falsevalue="" checked="false" optional="True" label="If this option is set, SIRIUS will not recalibrate the spectrum during the analysis" help="(-no_recalibration) "/>
125 <expand macro="advanced_options">
126 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
127 </expand>
128 </inputs> 161 </inputs>
129 <outputs> 162 <outputs>
130 <data name="param_out_sirius" format="tabular"/> 163 <data name="out_sirius" label="${tool.name} on ${on_string}: out_sirius" format="mztab">
131 <data name="param_out_fingerid" format="tabular"/> 164 <filter>OPTIONAL_OUTPUTS is not None and "out_sirius_FLAG" in OPTIONAL_OUTPUTS</filter>
165 </data>
166 <data name="out_fingerid" label="${tool.name} on ${on_string}: out_fingerid" format="mztab">
167 <filter>OPTIONAL_OUTPUTS is not None and "out_fingerid_FLAG" in OPTIONAL_OUTPUTS</filter>
168 </data>
169 <data name="out_ms" label="${tool.name} on ${on_string}: out_ms" format="sirius.ms">
170 <filter>OPTIONAL_OUTPUTS is not None and "out_ms_FLAG" in OPTIONAL_OUTPUTS</filter>
171 </data>
172 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
173 <filter>OPTIONAL_OUTPUTS is None</filter>
174 </data>
175 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
176 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
177 </data>
132 </outputs> 178 </outputs>
133 <help>Tool for metabolite identification using single and tandem mass spectrometry 179 <tests>
180 <expand macro="autotest_SiriusAdapter"/>
181 <expand macro="manutest_SiriusAdapter"/>
182 </tests>
183 <help><![CDATA[Tool for metabolite identification using single and tandem mass spectrometry
134 184
135 185
136 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_SiriusAdapter.html</help> 186 For more information, visit http://www.openms.de/documentation/UTILS_SiriusAdapter.html]]></help>
187 <expand macro="references"/>
137 </tool> 188 </tool>