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comparison mzmine_batch.xml @ 1:90d60c9da21e draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
author iuc
date Fri, 10 Nov 2023 14:20:45 +0000
parents 02e802817d48
children
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0:02e802817d48 1:90d60c9da21e
1 <tool id="mzmine_batch" name="MZMine batch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 1 <tool id="mzmine_batch" name="MZMine batch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <macros> 2 <macros>
3 <token name="@TOOL_VERSION@">3.6.0</token> 3 <token name="@TOOL_VERSION@">3.9.0</token>
4 <token name="@VERSION_SUFFIX@">0</token> 4 <token name="@VERSION_SUFFIX@">0</token>
5 </macros> 5 </macros>
6 <xrefs> 6 <xrefs>
7 <xref type="bio.tools">mzmine</xref> 7 <xref type="bio.tools">mzmine</xref>
8 </xrefs> 8 </xrefs>
9 <requirements> 9 <requirements>
10 <requirement type="package" version="@TOOL_VERSION@">mzmine</requirement> 10 <requirement type="package" version="@TOOL_VERSION@">mzmine</requirement>
11 <requirement type="package" version="3.11">python</requirement>
11 </requirements> 12 </requirements>
12 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
13 #import re 14 #import re
14 15
15 mkdir -p input && 16 mkdir -p input &&
28 #end for 29 #end for
29 #end if 30 #end if
30 ## modify output paths in batch XML to relative path 31 ## modify output paths in batch XML to relative path
31 ## - any output will be redirected to ./output/BASENAME 32 ## - any output will be redirected to ./output/BASENAME
32 mkdir -p output/ && 33 mkdir -p output/ &&
33 34 python '$__tool_directory__/set_path.py'
34 sed -e 's@<current_file>.*[\\\/]\([^\\\/]\+\)</current_file>@<current_file>./output/\1</current_file>@' '$batch' > batch.xml && 35 --input '$batch'
36 --output batch.xml
37 #if $localdb
38 --localdb '$localdb'
39 #end if
40 &&
35 41
42 ## https://github.com/mzmine/mzmine3/issues/1534
43 JAVA_OPTS="-XX:ActiveProcessorCount=\${GALAXY_SLOTS:-1}"
36 mzmine 44 mzmine
37 --batch 'batch.xml' 45 --batch 'batch.xml'
38 --input 'input.txt' 46 --input 'input.txt'
39 #if $libraries 47 #if $libraries
40 --libraries 'libraries.txt' 48 --libraries 'libraries.txt'
52 ]]></command> 60 ]]></command>
53 <inputs> 61 <inputs>
54 <param argument="--batch" type="data" format="xml" label="MZMine batch file" help="XML batch file (ideally created with version @TOOL_VERSION@)"/> 62 <param argument="--batch" type="data" format="xml" label="MZMine batch file" help="XML batch file (ideally created with version @TOOL_VERSION@)"/>
55 <param argument="--input" type="data" format="mzml,mzxml,csv" multiple="true" label="Spectra (mzml)"/> 63 <param argument="--input" type="data" format="mzml,mzxml,csv" multiple="true" label="Spectra (mzml)"/>
56 <param argument="--libraries" type="data" format="json,mgf,msp" multiple="true" optional="true" label="Spectral libraries"/> 64 <param argument="--libraries" type="data" format="json,mgf,msp" multiple="true" optional="true" label="Spectral libraries"/>
65 <param name="localdb" type="data" format="csv,tsv,tabular,txt" optional="true" label="Local database" help="For 'Custom database search'"/>
57 </inputs> 66 </inputs>
58 <outputs> 67 <outputs>
59 <collection name="output" type="list"> 68 <collection name="output" type="list">
60 <discover_datasets pattern="__name_and_ext__" directory="output"/> 69 <discover_datasets pattern="__name_and_ext__" directory="output"/>
61 </collection> 70 </collection>
62 </outputs> 71 </outputs>
63 <tests> 72 <tests>
64 <test> 73 <!-- <test>
65 <param name="batch" value="test_small.xml" ftype="xml"/> 74 <param name="batch" value="test_small.xml" ftype="xml"/>
66 <param name="input" value="DOM_a.mzML,DOM_b.mzXML"/> 75 <param name="input" location="https://raw.githubusercontent.com/mzmine/mzmine3/v@TOOL_VERSION@/src/test/resources/rawdatafiles/DOM_a.mzML,https://raw.githubusercontent.com/mzmine/mzmine3/v@TOOL_VERSION@/src/test/resources/rawdatafiles/DOM_b.mzXML"/>
67 <param name="libraries" value="GNPS-FAULKNERLEGACY.json" ftype="json"/> 76 <param name="libraries" value="GNPS-FAULKNERLEGACY.json" ftype="json"/>
68 <!-- <param name="input" location="https://raw.githubusercontent.com/mzmine/mzmine3/master/src/test/resources/rawdatafiles/DOM_a.mzML"/> -->
69 <!-- <param name="input" location="https://raw.githubusercontent.com/mzmine/mzmine3/master/src/test/resources/rawdatafiles/DOM_a.mzML,https://raw.githubusercontent.com/mzmine/mzmine3/master/src/test/resources/rawdatafiles/DOM_b.mzXML"/>
70 <param name="libraries" location="https://external.gnps2.org/gnpslibrary/GNPS-FAULKNERLEGACY.json" ftype="json"/> -->
71 <output_collection name="output" count="3" type="list"> 77 <output_collection name="output" count="3" type="list">
72 <element name="test2_iimn_gnps" ftype="mgf"> 78 <element name="test2_iimn_gnps" ftype="mgf">
73 <assert_contents> 79 <assert_contents>
74 <has_n_lines n="2103"/> 80 <has_n_lines n="2103"/>
75 <has_text text="BEGIN IONS"/> 81 <has_text text="BEGIN IONS"/>
86 <has_n_lines n="54406"/> 92 <has_n_lines n="54406"/>
87 <has_text text="BEGIN IONS"/> 93 <has_text text="BEGIN IONS"/>
88 </assert_contents> 94 </assert_contents>
89 </element> 95 </element>
90 </output_collection> 96 </output_collection>
91 </test> 97 <assert_stderr>
98 <has_text text="INFO: Starting processing of task Local CSV identification using database" negate="true"/>
99 <has_text text="INFO: Finished a batch of 11 steps"/>
100 </assert_stderr>
101 </test> -->
102 <!-- test with localdb -->
103 <!-- <test>
104 <param name="batch" value="test_localdatabase.xml" ftype="xml"/>
105 <param name="input" location="https://raw.githubusercontent.com/mzmine/mzmine3/v@TOOL_VERSION@/src/test/resources/rawdatafiles/DOM_a.mzML,https://raw.githubusercontent.com/mzmine/mzmine3/v@TOOL_VERSION@/src/test/resources/rawdatafiles/DOM_b.mzXML"/>
106 <param name="libraries" value="GNPS-FAULKNERLEGACY.json" ftype="json"/>
107 <param name="localdb" value="local_database.csv" ftype="csv"/>
108 <output_collection name="output" count="3" type="list">
109 <element name="test2_iimn_gnps" ftype="mgf">
110 <assert_contents>
111 <has_n_lines n="2103"/>
112 <has_text text="BEGIN IONS"/>
113 </assert_contents>
114 </element>
115 <element name="test2_iimn_gnps_quant" ftype="csv">
116 <assert_contents>
117 <has_n_lines n="34"/>
118 <has_n_columns sep="," n="16"/>
119 </assert_contents>
120 </element>
121 <element name="test2_sirius" ftype="mgf">
122 <assert_contents>
123 <has_n_lines n="54406"/>
124 <has_text text="BEGIN IONS"/>
125 </assert_contents>
126 </element>
127 </output_collection>
128 <assert_stderr>
129 <has_text text="INFO: Starting processing of task Local CSV identification using database"/>
130 <has_text text="INFO: Finished a batch of 12 steps"/>
131 </assert_stderr>
132 </test> -->
133 <!-- test with localdb in batch, but user does not provide one-->
134 <!-- <test expect_failure="true" expect_exit_code="1">
135 <param name="batch" value="test_localdatabase.xml" ftype="xml"/>
136 <param name="input" location="https://raw.githubusercontent.com/mzmine/mzmine3/v@TOOL_VERSION@/src/test/resources/rawdatafiles/DOM_a.mzML,https://raw.githubusercontent.com/mzmine/mzmine3/v@TOOL_VERSION@/src/test/resources/rawdatafiles/DOM_b.mzXML"/>
137 <param name="libraries" value="GNPS-FAULKNERLEGACY.json" ftype="json"/>
138 <assert_stderr>
139 <has_text text="Batch file contains LocalCSVDatabaseSearchModule but no local DB CSV file given"/>
140 </assert_stderr>
141 </test> -->
92 </tests> 142 </tests>
93 <help><![CDATA[ 143 <help><![CDATA[
94 MZmine 3 is an open-source software for mass-spectrometry data processing, with the main focus on LC-MS data. 144 MZmine 3 is an open-source software for mass-spectrometry data processing, with the main focus on LC-MS data.
95 145
96 This Galaxy tool allows to execute MZmine batches. That is you can create MZmine batch (XML) files thatdescribe the parameters of a MZmine analysis using the MZmine GUI 146 This Galaxy tool allows to execute MZmine batches. That is you can create MZmine batch (XML) files thatdescribe the parameters of a MZmine analysis using the MZmine GUI
99 **Inputs** 149 **Inputs**
100 150
101 - MZMine batch file in XML format. This file describes the parameters for a MZmine batch analysis. It can be generated with the MZmine GUI (preferentiall with a matching version, i.e. @TOOL_VERSION@). 151 - MZMine batch file in XML format. This file describes the parameters for a MZmine batch analysis. It can be generated with the MZmine GUI (preferentiall with a matching version, i.e. @TOOL_VERSION@).
102 - Input spectra in mzml format 152 - Input spectra in mzml format
103 - Spectra libraries in mgf or json format (optional) 153 - Spectra libraries in mgf or json format (optional)
154
155 If the batch file contains steps requiring input data sets these need to be provided
156 via the optional inputs. Currently this is:
157
158 - 'Local database' for a 'Custom database search' (LocalCSVDatabaseSearchModule) step
159
160 Please open an issue if inputs for other steps are needed: https://github.com/galaxyproject/tools-iuc/issues/new
104 161
105 **Outputs** 162 **Outputs**
106 163
107 Galaxy will store all outputs of MZMine in a single collection. When specifying the batch XML 164 Galaxy will store all outputs of MZMine in a single collection. When specifying the batch XML
108 file one should pay attention to use file extensions that correspond to Galaxy datatypes 165 file one should pay attention to use file extensions that correspond to Galaxy datatypes