Mercurial > repos > tomnl > cameradims
annotate cameradims.xml @ 3:11597f112979 draft
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit d4159f1962ef3fe37dd4f3047e4050afe013c15a-dirty
author | tomnl |
---|---|
date | Thu, 03 May 2018 05:27:48 -0400 |
parents | 1965e2b5a3d0 |
children | ba45716d676d |
rev | line source |
---|---|
3
11597f112979
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit d4159f1962ef3fe37dd4f3047e4050afe013c15a-dirty
tomnl
parents:
2
diff
changeset
|
1 <tool id="cameradims" name="CAMERA_DIMS" version="0.1.15"> |
0
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
2 <description>Modification of the R package CAMERA to work on DIMS data</description> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
3 <requirements> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
4 <requirement type="package" version="3.4.1">R</requirement> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
5 <requirement type="package" version="0.2.4">r-cameradims</requirement> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
6 <requirement type="package" version="1.4.4" >r-optparse</requirement> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
7 </requirements> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
8 <stdio> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
9 <exit_code range="1:" /> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
10 </stdio> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
11 <command interpreter="Rscript"><![CDATA[ |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
12 cameradims.R --in_file $peaks_file |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
13 --out_dir . |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
14 --ppm_adduct $ppm_adduct |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
15 --ppm_iso $ppm_iso |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
16 --mzabs_adduct $mzabs_adduct |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
17 --mzabs_iso $mzabs_iso |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
18 --maxiso $maxiso |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
19 --maxcharge $maxcharge |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
20 --maxmol $maxmol |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
21 --polarity $polarity |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
22 --rule_type $ruleset.ruleset |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
23 #if $ruleset.ruleset == 'user' |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
24 --rule_path $ruleset.rulesfile |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
25 #end if |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
26 #if $export_ruleset |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
27 --export_ruleset |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
28 #end if |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
29 --intensity_filter=$intensity_filter |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
30 ]]></command> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
31 |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
32 <inputs> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
33 <param type="data" name="peaks_file" format="tabular,tsv" |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
34 help="tsv or tabular file with mz and intensity columns"/> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
35 <param name="ppm_adduct" type="float" label="ppm (adduct)" value="5" |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
36 help="general ppm error (adduct)"/> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
37 <param name="ppm_iso" type="float" label="ppm (iso)" value="5" |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
38 help="general ppm error (iso)"/> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
39 <param name="mzabs_adduct" type="float" label="mzabs (adduct)" value="0.015" |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
40 help="general absolute error in m/z"/> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
41 <param name="mzabs_iso" type="float" label="mzabs (iso)" value="0.015" |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
42 help="general absolute error in m/z"/> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
43 <param name="maxmol" type="integer" label="maxmol" value="3" |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
44 help="highest number(n) of allowed clusterion [nM+ion] (argument called multiplier in findAdducts())"/> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
45 <param name="maxiso" type="integer" label="maxiso" value="4" |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
46 help="max number of expected isotopes"/> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
47 <param name="maxcharge" type="integer" label="maxcharge" value="3" |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
48 help="max ion charge for finding isotopes"/> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
49 <param name="polarity" type="select" label="polarity" help="Which polarity mode was used for measuring of the ms sample" > |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
50 <option value="pos" selected="true">positive</option> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
51 <option value="neg">negative</option> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
52 </param> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
53 |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
54 <param name="intensity_filter" type="float" label="Intensity filter" value="5000" |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
55 help="Filter out any peaks that have intensity less than this value. (Adduct calculation may take |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
56 a very long time if peaks are not filtered before hand) "/> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
57 |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
58 <conditional name="ruleset"> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
59 <param name="ruleset" type="select" label="Rules for adducts" > |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
60 <option value="primary adducts" >Primary adducts ([M+Na]+, [M+K]+ and [M+NH4]+")</option> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
61 <option value="extended" selected="true" >Extended adducts</option> |
3
11597f112979
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit d4159f1962ef3fe37dd4f3047e4050afe013c15a-dirty
tomnl
parents:
2
diff
changeset
|
62 <option value="extended_large" >Extended adducts (large)</option> |
0
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
63 <option value="user" >Provide a csv file of the rules to use</option> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
64 </param> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
65 <when value="user"> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
66 <param type="data" name="rulesfile" format="tsv, tabular" |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
67 help="User supplied rules file used to to calculate adducts, should contain the following |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
68 columns name,nmol,charge,massdiff,oidscore,quasi,ips. |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
69 If using the adducts to guide fragmentation then the frag_score column should be included. Where |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
70 a score of 1 indicates the adduct is the best adduct form to fragment"/> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
71 </when> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
72 <when value="extended"> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
73 </when> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
74 <when value="primary adducts"> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
75 </when> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
76 </conditional> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
77 <param name="export_ruleset" type="boolean" label="Export the adduct ruleset used?" help=""/> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
78 </inputs> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
79 <outputs> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
80 <data name="camera_annotated_map" format="tsv" label="${tool.name} on ${on_string}: map" |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
81 from_work_dir="camera_annotated_map.txt" /> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
82 <data name="camera_annotated_peaklist" label="${tool.name} on ${on_string}: peaklist" |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
83 from_work_dir="camera_annotated_peaklist.txt" format="tsv"/> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
84 <data name="ruleset" label="${tool.name} on ${on_string}: ruleset" |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
85 from_work_dir="ruleset.txt" format="tsv"> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
86 <filter>export_ruleset is True</filter> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
87 </data> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
88 |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
89 |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
90 |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
91 </outputs> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
92 <tests> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
93 <test> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
94 <param name="peaks_file" value="peaklist_in.tsv" ftype="tsv"/> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
95 <output name="camera_annotated_peaklist" value="camera_annotated_peaklist.txt"/> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
96 <output name="camera_annotated_map" value="camera_annotated_map.txt"/> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
97 </test> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
98 </tests> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
99 <help><![CDATA[ |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
100 cameraDIMS |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
101 |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
102 ]]></help> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
103 <citations> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
104 <citation type="doi">10.1021/ac202450g</citation> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
105 </citations> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
changeset
|
106 </tool> |