Mercurial > repos > tomnl > frag4feature

annotate frag4feature.xml @ 29:15228fa5b475 draft default tip

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 1800a3818988f21ef129e500818c9a087fce5875
author tomnl
date Wed, 18 Jul 2018 06:01:53 -0400
parents 07e3b8fb7c14
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
28
07e3b8fb7c14 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit a598583947118bd50cfe5ae12d955c20d6e502a6
tomnl
parents: 21
diff changeset
1 <tool id="frag4feature" name="frag4feature" version="0.0.20">
6
e94ce372d03d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 5
diff changeset
2 <description>
e94ce372d03d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 5
diff changeset
3 Assign fragmentation spectra to XCMS features using msPurity
e94ce372d03d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 5
diff changeset
4 </description>
e94ce372d03d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 5
diff changeset
5
0
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
6 <macros>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
7 <import>macros.xml</import>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
8 </macros>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
9
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
10 <expand macro="requirements">
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
11 <!-- would ideally have xcms 3.0.0 but not available in bioconda at the point of tool creation-->
1
c55e06ccf670 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
12 <!-- <requirement type="package" version="1.46.0" >bioconductor-xcms</requirement>-->
0
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
13 </expand>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
14
6
e94ce372d03d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 5
diff changeset
15
0
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
16 <stdio>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
17 <exit_code range="1:" />
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
18 </stdio>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
19 <command interpreter="Rscript"><![CDATA[
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
20 frag4feature.R
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
21 --out_dir=.
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
22 --xset=$xset
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
23 --pa=$pa
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
24 --cores=\${GALAXY_SLOTS:-4}
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
25 #if $file_load_conditional.file_load_select=="yes"
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
26 --mzML_files='
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
27 #for $i in $file_load_conditional.input
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
28 $i,
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
29 #end for
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
30 '
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
31 --galaxy_names='
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
32 #for $i in $file_load_conditional.input
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
33 $i.name,
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
34 #end for
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
35 '
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
36 #end if
28
07e3b8fb7c14 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit a598583947118bd50cfe5ae12d955c20d6e502a6
tomnl
parents: 21
diff changeset
37 #if $use_group
07e3b8fb7c14 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit a598583947118bd50cfe5ae12d955c20d6e502a6
tomnl
parents: 21
diff changeset
38 --use_group
07e3b8fb7c14 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit a598583947118bd50cfe5ae12d955c20d6e502a6
tomnl
parents: 21
diff changeset
39 #end if
07e3b8fb7c14 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit a598583947118bd50cfe5ae12d955c20d6e502a6
tomnl
parents: 21
diff changeset
40
0
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
41 --ppm=$ppm_f4f
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
42 --plim=$plim_f4f
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
43 #if $mostIntense_f4f
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
44 --mostIntense
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
45 #end if
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
46 #if $convert2RawRT_f4f
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
47 --convert2RawRT
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
48 #end if
28
07e3b8fb7c14 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit a598583947118bd50cfe5ae12d955c20d6e502a6
tomnl
parents: 21
diff changeset
49 #if $createDB
1
c55e06ccf670 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
50 --createDB
c55e06ccf670 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
51 #end if
c55e06ccf670 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
52
0
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
53 #if $grp_peaklist_opt.grp_peaklist_opt=="yes"
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
54 --grp_peaklist=$grp_peaklist
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
55 #end if
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
56
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
57 ]]></command>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
58 <inputs>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
59
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
60 <param type="data" name="xset" label="xcmsSet object"
5
2365c3b350fa planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 4
diff changeset
61 help="grouped xcmsSet object saved as 'xset' in an RData file" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata"/>
0
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
62 <param type="data" name="pa" label="purityA object" format="rdata"
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
63 help="purityA object saved as 'pa' in a RData file (output from assess_purity_msms)"/>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
64
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
65 <param name="mostIntense_f4f" type="boolean" checked="true" label="For matching fragmentation to a feature,
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
66 use most intense peak within isolation window for precursor?"/>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
67
28
07e3b8fb7c14 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit a598583947118bd50cfe5ae12d955c20d6e502a6
tomnl
parents: 21
diff changeset
68 <param name="use_group" type="boolean" checked="false" label="For matching fragmentation to a feature,
07e3b8fb7c14 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit a598583947118bd50cfe5ae12d955c20d6e502a6
tomnl
parents: 21
diff changeset
69 use the grouped feature range" help="If the MS1 and MS2 are in different files this is option has to be set to true"
07e3b8fb7c14 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit a598583947118bd50cfe5ae12d955c20d6e502a6
tomnl
parents: 21
diff changeset
70 />
07e3b8fb7c14 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit a598583947118bd50cfe5ae12d955c20d6e502a6
tomnl
parents: 21
diff changeset
71
0
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
72 <param name="convert2RawRT_f4f" type="boolean" checked="false" label="Was retention time correction used?"
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
73 help="If retention time correction has been used in XCMS set this to yes"/>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
74
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
75 <param name="ppm_f4f" type="float" label="ppm" value="10"
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
76 help="ppm tolerance between precursor mz and feature mz"/>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
77
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
78 <param name="plim_f4f" type="float" label="plim" value="0" max="1" min="0"
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
79 help="min purity of precursor to be included"/>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
80
1
c55e06ccf670 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
81 <param name="createDB" type="boolean" checked="true" label="Create SQLite database of spcetra?"/>
c55e06ccf670 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
82
c55e06ccf670 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
83 <expand macro="grp_peaklist" />
0
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
84
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
85 <expand macro="fileload" />
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
86
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
87 </inputs>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
88 <outputs>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
89 <data name="frag4feature_grouped_msms" format="tsv" label="${tool.name} on ${on_string}: tsv"
6
e94ce372d03d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 5
diff changeset
90 from_work_dir="frag4feature.tsv" />
0
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
91 <data name="frag4feature_rdata" format="rdata" label="${tool.name} on ${on_string}: RData"
6
e94ce372d03d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 5
diff changeset
92 from_work_dir="frag4feature.RData" />
0
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
93 <data name="frag4feature_sqlite" format="sqlite" label="${tool.name} on ${on_string}: Sqlite"
6
e94ce372d03d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 5
diff changeset
94 from_work_dir="alldata.sqlite" />
0
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
95 </outputs>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
96 <tests>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
97 <test>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
98 <conditional name="file_load_conditional">
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
99 <param name="file_load_select" value="yes"/>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
100 <param name="input" >
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
101 <collection type="list">
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
102 <element name="LCMS_1.mzML" value="LCMS_1.mzML"/>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
103 <element name="LCMS_2.mzML" value="LCMS_2.mzML"/>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
104 <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
105 <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
106 </collection>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
107 </param>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
108 </conditional>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
109 <param name="xset" value="LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.xset.group.rdata"/>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
110 <param name="pa" value="LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.assess_purity.rdata"/>
1
c55e06ccf670 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 0
diff changeset
111 <output name="frag4feature_grouped_msms" value="frag4feature_output.tsv" >
7
9501e9b13b48 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit afee93a926072b534bb3541e1524f1ad6a7decb9
tomnl
parents: 6
diff changeset
112
0
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
113 </output>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
114 </test>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
115 </tests>
6
e94ce372d03d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 5
diff changeset
116
0
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
117 <help><![CDATA[
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
118 =============================================================
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
119 Link fragmentation spectra to XCMS features
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
120 =============================================================
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
121 -----------
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
122 Description
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
123 -----------
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
124
5
2365c3b350fa planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 4
diff changeset
125 Tool to link XCMS features to fragmentation spectra and create an SQLite database of all the data and connections.
2365c3b350fa planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 4
diff changeset
126
2365c3b350fa planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 4
diff changeset
127 Please note that the xcmsSet object needs to have been grouped.
0
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
128
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
129 The data inputs are:
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
130
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
131 * A purityA object (generated from assess_purity_msms) saved in an rdata file.
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
132 * A xcmsSet grouped object (generated from xcms_group) saved in an rdata file
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
133 * [optional] a dataset collection of the mzML files to resubmit
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
134
5
2365c3b350fa planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents: 4
diff changeset
135 See Bioconductor documentation for more details, function msPurity::frag4feature()
0
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
136
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
137 -----------
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
138 Outputs
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
139 -----------
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
140 * frag4feature_rdata: An updated purityA object saved as rdata file with fragmentation-feature links added
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
141 * frag4feature_grouped_msms: A flat file of all the XCMS peaks for each grouped feature and the corresponding fragmentation scans
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
142 * frag4feature_sqlite: An SQLite database of the data (including fragmentation scans)
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
143
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
144
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
145
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
146 ]]></help>
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
147
6
e94ce372d03d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 5
diff changeset
148 <expand macro="citations" />
e94ce372d03d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
tomnl
parents: 5
diff changeset
149
0
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
tomnl
parents:
diff changeset
150 </tool>