Mercurial > repos > tomnl > create_sqlite_db

annotate create_sqlite_db.xml @ 13:4acad02faf32 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
author tomnl
date Fri, 11 May 2018 06:08:10 -0400
parents c59965822dc8
children 69d5cb5a8e90
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
13
4acad02faf32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
tomnl
parents: 11
diff changeset
1 <tool id="create_sqlite_db" name="create_sqlite_db" version="0.0.9">
4
ff61a6fb23bf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 3
diff changeset
2 <description>
ff61a6fb23bf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 3
diff changeset
3 Create SQLite database of an XCMS-CAMERA dataset
ff61a6fb23bf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 3
diff changeset
4 </description>
ff61a6fb23bf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 3
diff changeset
5
ff61a6fb23bf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 3
diff changeset
6
0
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
7 <macros>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
8 <import>macros.xml</import>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
9 </macros>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
10
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
11 <expand macro="requirements">
4
ff61a6fb23bf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 3
diff changeset
12
0
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
13 </expand>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
14
4
ff61a6fb23bf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 3
diff changeset
15
0
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
16 <stdio>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
17 <exit_code range="1:" />
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
18 </stdio>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
19 <command interpreter="Rscript"><![CDATA[
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
20 create_sqlite_db.R
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
21 --out_dir=.
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
22 --xset_xa=$xset_xa
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
23 --pa=$pa
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
24 --xcms_camera_option=$camera_xcms
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
25 --cores=\${GALAXY_SLOTS:-4}
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
26 #if $file_load_conditional.file_load_select=="yes"
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
27 --mzML_files='
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
28 #for $i in $file_load_conditional.input
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
29 $i,
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
30 #end for
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
31 '
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
32 --galaxy_names='
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
33 #for $i in $file_load_conditional.input
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
34 $i.name,
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
35 #end for
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
36 '
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
37 #end if
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
38
11
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
39
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
40 #if $metfrag_conditional.metfrag_select=="yes"
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
41 --metfrag_result=$metfrag_result
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
42 #end if
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
43
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
44 #if $sirius_csifingerid_conditional.sirius_csifingerid_select=="yes"
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
45 --sirius_csifingerid_result=$sirius_csifingerid_result
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
46 #end if
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
47
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
48 #if $probmetab_conditional.probmetab_select=="yes"
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
49 --probmetab_result=$probmetab_result
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
50 #end if
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
51
0
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
52 #if $eic
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
53 --eic
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
54 #end if
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
55 #if $raw_rt_columns
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
56 --raw_rt_columns
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
57 #end if
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
58 #if $grp_peaklist_opt.grp_peaklist_opt=="yes"
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
59 --grp_peaklist=$grp_peaklist
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
60 #end if
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
61
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
62 ]]></command>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
63 <inputs>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
64
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
65
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
66 <param type="data" name="xset_xa" label="xcmsSet or CAMERA object"
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
67 help="Either xcmsSet object saved as 'xset' or CAMERA 'xa' object in an RData file. Please
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
68 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"/>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
69 <expand macro="camera_xcms" />
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
70
13
4acad02faf32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
tomnl
parents: 11
diff changeset
71 <param type="data" name="pa" label="purityA object (frag4feature output)" format="rdata"
4acad02faf32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
tomnl
parents: 11
diff changeset
72 help="purityA object saved as 'pa' in a RData file (output from frag4feature)"/>
0
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
73
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
74 <param name="eic" type="boolean" label="Include EIC data?"
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
75 help="The Extracted Ion Chromatogram can be calculated for each peak and stored in
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
76 the database. Note, this will take considerable time for large datasets and
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
77 the resulting SQLite database can be large"/>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
78
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
79 <param name="raw_rt_columns" type="boolean" label="Use user defined Raw RT columns?"
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
80 help="Only use if the track_rt_raw tool has been used"/>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
81
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
82
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
83 <expand macro="grp_peaklist" />
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
84
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
85
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
86 <expand macro="fileload" />
11
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
87 <conditional name="metfrag_conditional">
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
88 <param name="metfrag_select" type="select" label="Include MetFrag results?">
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
89 <option value="no" >no</option>
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
90 <option value="yes" >yes</option>
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
91 </param>
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
92 <when value="no">
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
93 </when>
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
94 <when value="yes">
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
95 <param type="data" name="metfrag_result" label="MetFrag result" format="tsv,tabular"
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
96 help="MetFrag result from corresponding dataset"/>
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
97 </when>
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
98 </conditional>
0
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
99
11
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
100 <conditional name="sirius_csifingerid_conditional">
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
101 <param name="sirius_csifingerid_select" type="select" label="Include Sirius CSI-FingerID results?">
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
102 <option value="no" >no</option>
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
103 <option value="yes" >yes</option>
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
104 </param>
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
105 <when value="no">
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
106 </when>
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
107 <when value="yes">
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
108 <param type="data" name="sirius_csifingerid_result" label="Sirius CSI-FingerID result" format="tsv,tabular"
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
109 help="Sirius CSI-FingerID result from corresponding dataset"/>
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
110 </when>
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
111 </conditional>
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
112
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
113
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
114 <conditional name="probmetab_conditional">
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
115 <param name="probmetab_select" type="select" label="Include ProbMetab results?">
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
116 <option value="no" >no</option>
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
117 <option value="yes" >yes</option>
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
118 </param>
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
119 <when value="no">
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
120 </when>
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
121 <when value="yes">
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
122 <param type="data" name="probmetab_result" label="ProbMetab result" format="tsv,tabular"
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
123 help="ProbMetab result from corresponding dataset"/>
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
124 </when>
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
125 </conditional>
c59965822dc8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4116082655a03d3007a49e4a4b00fc6ad4698412-dirty
tomnl
parents: 5
diff changeset
126
0
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
127 </inputs>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
128 <outputs>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
129 <data name="lcms_data_sqlite" format="sqlite" label="${tool.name} on ${on_string}: LC-MS(/MS) data SQLite db"
4
ff61a6fb23bf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 3
diff changeset
130 from_work_dir="lcms_data.sqlite" />
5
9ab472c5714c planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit afee93a926072b534bb3541e1524f1ad6a7decb9
tomnl
parents: 4
diff changeset
131 <data name="cpeakgroup_msms" format="tsv" label="${tool.name} on ${on_string}: c-peak-group-msms"
4
ff61a6fb23bf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 3
diff changeset
132 from_work_dir="cpeakgroup_msms.tsv" />
0
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
133
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
134 </outputs>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
135 <tests>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
136 <test>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
137 <conditional name="file_load_conditional">
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
138 <param name="file_load_select" value="yes"/>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
139 <param name="input" >
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
140 <collection type="list">
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
141 <element name="LCMS_1.mzML" value="LCMS_1.mzML"/>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
142 <element name="LCMS_2.mzML" value="LCMS_2.mzML"/>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
143 <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
144 <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
145 </collection>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
146 </param>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
147 </conditional>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
148 <param name="camera_xcms" value="xcms"/>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
149 <param name="xset_xa" value="LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.xset.group.rdata"/>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
150 <param name="pa" value="frag4feature.rdata"/>
13
4acad02faf32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
tomnl
parents: 11
diff changeset
151
0
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
152 <output name="cpeakgroup_msms" value="cpeakgroup_msms.tsv" >
13
4acad02faf32 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
tomnl
parents: 11
diff changeset
153
5
9ab472c5714c planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit afee93a926072b534bb3541e1524f1ad6a7decb9
tomnl
parents: 4
diff changeset
154
0
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
155 </output>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
156 </test>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
157 </tests>
4
ff61a6fb23bf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 3
diff changeset
158
0
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
159 <help><![CDATA[
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
160 =============================================================
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
161 Create SQLite database for LC-MS(/MS) dataset
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
162 =============================================================
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
163 Create an SQLite database for the msPurity and XCMS (CAMERA) outputs. The SQLite database created can
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
164 be used as input to the spectral_matching tool.
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
165
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
166 Please note that getting the extracted ion chromatograms can take a long time if the dataset has a large number of files and peaks.
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
167
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
168 -----------
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
169 Output
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
170 -----------
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
171 * lcms_sqlite: An SQLite database of the LC-MS(/MS) data (including fragmentation scans)
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
172 * cpeakgroup_msms: A csv file for all grouped features that have associated fragmentation spectra
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
173
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
174 ]]></help>
4
ff61a6fb23bf planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 3
diff changeset
175 <expand macro="citations" />
0
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
176 </tool>