Mercurial > repos > tomnl > create_sqlite_db

comparison create_sqlite_db.xml @ 4:ff61a6fb23bf draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
author tomnl
date Wed, 04 Apr 2018 17:08:30 -0400
parents 2766f2a85997
children 9ab472c5714c
comparison
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3:2766f2a85997 4:ff61a6fb23bf
1 <tool id="create_sqlite_db" name="create_sqlite_db" version="0.0.3"> 1 <tool id="create_sqlite_db" name="create_sqlite_db" version="0.0.4">
2 <description>
3 Create SQLite database of an XCMS-CAMERA dataset
4 </description>
5
6
2 <macros> 7 <macros>
3 <import>macros.xml</import> 8 <import>macros.xml</import>
4 </macros> 9 </macros>
5 10
6 <expand macro="requirements"> 11 <expand macro="requirements">
7 <!-- would ideally have xcms 3.0.0 but not available in bioconda at the point of tool creation--> 12
8 </expand> 13 </expand>
9 14
10 <description> 15
11 Create SQLite database of an XCMS-CAMERA dataset
12 </description>
13 <stdio> 16 <stdio>
14 <exit_code range="1:" /> 17 <exit_code range="1:" />
15 </stdio> 18 </stdio>
16 <command interpreter="Rscript"><![CDATA[ 19 <command interpreter="Rscript"><![CDATA[
17 create_sqlite_db.R 20 create_sqlite_db.R
70 <expand macro="fileload" /> 73 <expand macro="fileload" />
71 74
72 </inputs> 75 </inputs>
73 <outputs> 76 <outputs>
74 <data name="lcms_data_sqlite" format="sqlite" label="${tool.name} on ${on_string}: LC-MS(/MS) data SQLite db" 77 <data name="lcms_data_sqlite" format="sqlite" label="${tool.name} on ${on_string}: LC-MS(/MS) data SQLite db"
75 from_work_dir="lcms_data.sqlite" visible="true"/> 78 from_work_dir="lcms_data.sqlite" />
76 <data name="cpeakgroup_msms" format="sqlite" label="${tool.name} on ${on_string}: c-peak-group-msms" 79 <data name="cpeakgroup_msms" format="sqlite" label="${tool.name} on ${on_string}: c-peak-group-msms"
77 from_work_dir="cpeakgroup_msms.tsv" visible="true"/> 80 from_work_dir="cpeakgroup_msms.tsv" />
78 81
79 </outputs> 82 </outputs>
80 <tests> 83 <tests>
81 <test> 84 <test>
82 <conditional name="file_load_conditional"> 85 <conditional name="file_load_conditional">
95 <param name="pa" value="frag4feature.rdata"/> 98 <param name="pa" value="frag4feature.rdata"/>
96 <output name="cpeakgroup_msms" value="cpeakgroup_msms.tsv" > 99 <output name="cpeakgroup_msms" value="cpeakgroup_msms.tsv" >
97 </output> 100 </output>
98 </test> 101 </test>
99 </tests> 102 </tests>
100 <expand macro="citations" /> 103
101 <help><![CDATA[ 104 <help><![CDATA[
102 ============================================================= 105 =============================================================
103 Create SQLite database for LC-MS(/MS) dataset 106 Create SQLite database for LC-MS(/MS) dataset
104 ============================================================= 107 =============================================================
105 Create an SQLite database for the msPurity and XCMS (CAMERA) outputs. The SQLite database created can 108 Create an SQLite database for the msPurity and XCMS (CAMERA) outputs. The SQLite database created can
112 ----------- 115 -----------
113 * lcms_sqlite: An SQLite database of the LC-MS(/MS) data (including fragmentation scans) 116 * lcms_sqlite: An SQLite database of the LC-MS(/MS) data (including fragmentation scans)
114 * cpeakgroup_msms: A csv file for all grouped features that have associated fragmentation spectra 117 * cpeakgroup_msms: A csv file for all grouped features that have associated fragmentation spectra
115 118
116 ]]></help> 119 ]]></help>
117 120 <expand macro="citations" />
118 </tool> 121 </tool>