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comparison create_sqlite_db.xml @ 0:fe7d7cc95ca5 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
author tomnl
date Tue, 27 Mar 2018 06:03:50 -0400
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children 3a3aab720f52
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1 <tool id="create_sqlite_db" name="create_sqlite_db" version="0.0.1">
2 <macros>
3 <import>macros.xml</import>
4 </macros>
5
6 <expand macro="requirements">
7 <!-- would ideally have xcms 3.0.0 but not available in bioconda at the point of tool creation-->
8 </expand>
9
10 <description>
11 Create SQLite database of an XCMS-CAMERA dataset
12 </description>
13 <stdio>
14 <exit_code range="1:" />
15 </stdio>
16 <command interpreter="Rscript"><![CDATA[
17 create_sqlite_db.R
18 --out_dir=.
19 --xset_xa=$xset_xa
20 --pa=$pa
21 --xcms_camera_option=$camera_xcms
22 --cores=\${GALAXY_SLOTS:-4}
23 #if $file_load_conditional.file_load_select=="yes"
24 --mzML_files='
25 #for $i in $file_load_conditional.input
26 $i,
27 #end for
28 '
29 --galaxy_names='
30 #for $i in $file_load_conditional.input
31 $i.name,
32 #end for
33 '
34 #end if
35
36 #if $eic
37 --eic
38 #end if
39 #if $raw_rt_columns
40 --raw_rt_columns
41 #end if
42 #if $grp_peaklist_opt.grp_peaklist_opt=="yes"
43 --grp_peaklist=$grp_peaklist
44 #end if
45
46 ]]></command>
47 <inputs>
48
49
50 <param type="data" name="xset_xa" label="xcmsSet or CAMERA object"
51 help="Either xcmsSet object saved as 'xset' or CAMERA 'xa' object in an RData file. Please
52 specify which to use below" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata"/>
53 <expand macro="camera_xcms" />
54
55 <param type="data" name="pa" label="purityA object" format="rdata"
56 help="purityA object saved as 'pa' in a RData file (output from assess_purity_msms)"/>
57
58 <param name="eic" type="boolean" label="Include EIC data?"
59 help="The Extracted Ion Chromatogram can be calculated for each peak and stored in
60 the database. Note, this will take considerable time for large datasets and
61 the resulting SQLite database can be large"/>
62
63 <param name="raw_rt_columns" type="boolean" label="Use user defined Raw RT columns?"
64 help="Only use if the track_rt_raw tool has been used"/>
65
66
67 <expand macro="grp_peaklist" />
68
69
70 <expand macro="fileload" />
71
72 </inputs>
73 <outputs>
74 <data name="lcms_data_sqlite" format="sqlite" label="${tool.name} on ${on_string}: LC-MS(/MS) data SQLite db"
75 from_work_dir="lcms_data.sqlite" visible="true"/>
76 <data name="cpeakgroup_msms" format="sqlite" label="${tool.name} on ${on_string}: c-peak-group-msms"
77 from_work_dir="cpeakgroup_msms.tsv" visible="true"/>
78
79 </outputs>
80 <tests>
81 <test>
82 <conditional name="file_load_conditional">
83 <param name="file_load_select" value="yes"/>
84 <param name="input" >
85 <collection type="list">
86 <element name="LCMS_1.mzML" value="LCMS_1.mzML"/>
87 <element name="LCMS_2.mzML" value="LCMS_2.mzML"/>
88 <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
89 <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/>
90 </collection>
91 </param>
92 </conditional>
93 <param name="camera_xcms" value="xcms"/>
94 <param name="xset_xa" value="LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.xset.group.rdata"/>
95 <param name="pa" value="frag4feature.rdata"/>
96 <output name="cpeakgroup_msms" value="cpeakgroup_msms.tsv" >
97 </output>
98 </test>
99 </tests>
100 <expand macro="citations" />
101 <help><![CDATA[
102 =============================================================
103 Create SQLite database for LC-MS(/MS) dataset
104 =============================================================
105 Create an SQLite database for the msPurity and XCMS (CAMERA) outputs. The SQLite database created can
106 be used as input to the spectral_matching tool.
107
108 Please note that getting the extracted ion chromatograms can take a long time if the dataset has a large number of files and peaks.
109
110 -----------
111 Output
112 -----------
113 * 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
115
116 ]]></help>
117
118 </tool>