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comparison createDatabase.xml @ 0:7dc0cde206d8 draft default tip

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
author computational-metabolomics
date Thu, 04 Mar 2021 12:14:02 +0000
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-1:000000000000 0:7dc0cde206d8
1 <tool id="mspurity_createdatabase" name="msPurity.createDatabase" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
2 <description>Create and SQLite database of an LC-MS(/MS) experiment</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 Rscript '$__tool_directory__/createDatabase.R'
9 --outDir=.
10 --xset_xa='$xset_xa'
11 --pa='$pa'
12 --xcms_camera_option=$camera_xcms
13 --cores=\${GALAXY_SLOTS:-4}
14 #if $file_load_conditional.file_load_select=="yes"
15 --mzML_files='
16 #for $i in $file_load_conditional.input
17 $i,
18 #end for
19 '
20 --galaxy_names='
21 #for $i in $file_load_conditional.input
22 $i.name,
23 #end for
24 '
25 #end if
26
27 #if $eic
28 --eic
29 #end if
30
31 #if $grp_peaklist_opt.grp_peaklist_opt=="yes"
32 --grpPeaklist='$grp_peaklist'
33 #end if
34
35 ]]></command>
36 <inputs>
37 <param argument="--xset_xa" type="data" label="xcmsSet or CAMERA object"
38 help="Either xcmsSet object saved as 'xset' or CAMERA 'xa' object in an RData file.
39 Please specify which to use below"
40 format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata"/>
41 <expand macro="camera_xcms" />
42 <param argument="--pa" type="data" label="purityA object (frag4feature output)" format="rdata"
43 help="purityA object saved as 'pa' in a RData file (output from frag4feature)"/>
44 <param argument="--eic" type="boolean" label="Include EIC data?"
45 help="The Extracted Ion Chromatogram can be calculated for each peak and stored in
46 the database. Note, this will take considerable time for large datasets and
47 the resulting SQLite database can be large"/>
48 <expand macro="grp_peaklist" />
49 <expand macro="fileload" />
50 </inputs>
51 <outputs>
52 <data name="createDatabase_output_sqlite" format="sqlite"
53 label="${tool.name} on ${on_string}: LC-MS(/MS) data SQLite db"
54 from_work_dir="createDatabase_output.sqlite" />
55
56 </outputs>
57 <tests>
58 <test>
59 <conditional name="file_load_conditional">
60 <param name="file_load_select" value="yes"/>
61 <param name="input" >
62 <collection type="list">
63 <element name="LCMS_1.mzML" value="LCMS_1.mzML"/>
64 <element name="LCMS_2.mzML" value="LCMS_2.mzML"/>
65 <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
66 <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/>
67 </collection>
68 </param>
69 </conditional>
70 <param name="camera_xcms" value="xcms"/>
71 <param name="xset_xa" value="xset_group_LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.RData"/>
72 <param name="pa" value="averageFragSpectra_output_all.RData"/>
73 <output name="createDatabase_output_sqlite" value="createDatabase_output.sqlite" ftype="sqlite" compare="sim_size"/>
74 </test>
75
76 <test>
77 <conditional name="file_load_conditional">
78 <param name="file_load_select" value="yes"/>
79 <param name="input" >
80 <collection type="list">
81 <element name="LCMS_1.mzML" value="LCMS_1.mzML"/>
82 <element name="LCMS_2.mzML" value="LCMS_2.mzML"/>
83 <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
84 <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/>
85 </collection>
86 </param>
87 </conditional>
88 <param name="camera_xcms" value="xcms"/>
89 <param name="eic" value="true"/>
90 <param name="xset_xa" value="xset_group_LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.RData"/>
91 <param name="pa" value="averageFragSpectra_output_all.RData"/>
92 <output name="createDatabase_output_sqlite" value="createDatabase_output_eic.sqlite" ftype="sqlite" compare="sim_size"/>
93 </test>
94 </tests>
95
96 <help><![CDATA[
97 =============================================================
98 Create SQLite database for LC-MS(/MS) dataset
99 =============================================================
100 ** General **
101
102 Create and SQLite database of an LC-MS(/MS) experiment (replaces the create_database function).
103
104 Schema details can be found [here](https://www.bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-database-vignette.html).
105
106 **Example LC-MS/MS processing workflow**
107
108 * Purity assessments
109 + (mzML files) -> purityA -> (pa)
110 * XCMS processing
111 + (mzML files) -> xcms.xcmsSet -> xcms.merge -> xcms.group -> xcms.retcor -> xcms.group -> (xset)
112 * Fragmentation processing
113 + (xset, pa) -> frag4feature -> filterFragSpectra -> averageAllFragSpectra -> **createDatabase** -> spectralMatching -> (sqlite spectral database)
114
115
116 -----------
117 Output
118 -----------
119 * lcms_sqlite: An SQLite database of the LC-MS(/MS) data (including fragmentation scans)
120
121 ]]></help>
122 <expand macro="citations" />
123 </tool>