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ProbMetab For Galaxy

Home Page: http://workflow4metabolomics.org/

R 99.48% Shell 0.52%

metabolomics lc-ms galaxy-project workflow4metabolomics usegalaxy

probmetab's Issues

Add functional test

using planemo

Need sections

To clarify which arguments are used by which part of the tool

Need to deal with single file as xcms

Since probmetab need the raw data somewhere.
It also need to deal with the single file used by xcms.xcmsSet

workflow4metabolomics/tools-metabolomics#2

So some fix must be done to accept outputs from xcms tools from 2.1.0 (currently in beta in tne testtoolshed)

test-data: two acquisition mode

@workflow4metabolomics/ms

It seems that the two acquisition mode was not enough tested.
I want to add a functional test with 2 RData from CAMERA for Negative and Positive modes

Is anybody have 2 very small datasets for this purpose?
The job must process within 15 min.

Many thanks

build.database.kegg("ath") Fail

rsilvabioinfo/ProbMetab#3

Some modifications were done.
So I need to update the conda package and update the ProbMetab version in the wrapper

create.reactionM

Using a test-data generate from faahKO_reduce.zip:

> reactionM = create.reactionM(DB, ionAnnot, ppm.tol=listArguments[["ppm_tol"]])
There were 50 or more warnings (use warnings() to see the first 50)

> warnings()
Warning messages:
1: In f.extract(formula) : Invalid formula:C2H4NO2R(C2H2NOR)n
2: In f.extract(formula) : Invalid formula:C2H4NO2R(C2H2NOR)n
3: In f.extract(formula) : Invalid formula:C10H17O8PR2(C5H8O5PR)n
4: In f.extract(formula) : Invalid formula:C10H17O8PR2(C5H8O5PR)n
5: In formula2mass(as.character(x)) : Invalid formula:C22H35N7O17P3SR
6: In formula2mass(as.character(x)) : Invalid formula:C2H4NO2R
7: In f.extract(formula) : Invalid formula:C10H18O13P2R2(C5H8O6PR)n
8: In f.extract(formula) : Invalid formula:C10H18O13P2R2(C5H8O6PR)n
9: In formula2mass(as.character(x)) : Invalid formula:CO2R
10: In f.extract(formula) : Invalid formula:C10H17O10PR2(C5H8O6PR)n
11: In f.extract(formula) : Invalid formula:C10H17O10PR2(C5H8O6PR)n
12: In formula2mass(as.character(x)) : Invalid formula:HOR
13: In formula2mass(as.character(x)) : Invalid formula:CHOR
14: In f.extract(formula) : Invalid formula:C2H4NO2R(C2H2NOR)n
15: In formula2mass(as.character(x)) : Invalid formula:C4H6N2O3R2
16: In f.extract(formula) : Invalid formula:C20H37O4P(C5H8)n
17: In f.extract(formula) : Invalid formula:C20H37O4P(C5H8)n
18: In formula2mass(as.character(x)) : Invalid formula:C42H44FeN8O8S2R4
19: In formula2mass(as.character(x)) : Invalid formula:C42H44FeN8O8S2R4
20: In formula2mass(as.character(x)) : Invalid formula:HSR
21: In formula2mass(as.character(x)) : Invalid formula:C2H4NO2R
22: In formula2mass(as.character(x)) : Invalid formula:C10H18NO8PR2
23: In formula2mass(as.character(x)) : Invalid formula:C2HO3R
24: In formula2mass(as.character(x)) : Invalid formula:CHO2R
25: In formula2mass(as.character(x)) : Invalid formula:C5H6O5R2
26: In formula2mass(as.character(x)) : Invalid formula:C5H10O7PR
27: In f.extract(formula) : Invalid formula:C10H19O16P3R2(C5H8O6PR)n
28: In f.extract(formula) : Invalid formula:C10H19O16P3R2(C5H8O6PR)n
29: In formula2mass(as.character(x)) : Invalid formula:C3H4OSR2
30: In formula2mass(as.character(x)) : Invalid formula:C12H9N4O2R
31: In formula2mass(as.character(x)) : Invalid formula:C19H36NO3R
32: In f.extract(formula) : Invalid formula:C13H11N2. CH3SO4
33: In f.extract(formula) : Invalid formula:C13H11N2. CH3SO4
34: In formula2mass(as.character(x)) : Invalid formula:C5H12O13P3R
35: In f.extract(formula) : Invalid formula:C53H79CoN11O14P(R1)(R2)
36: In f.extract(formula) : Invalid formula:C4H6N2O3R2(C7H9N2O2R)n
37: In f.extract(formula) : Invalid formula:C4H6N2O3R2(C7H9N2O2R)n
38: In f.extract(formula) : Invalid formula:C16H18N3S. Cl
39: In f.extract(formula) : Invalid formula:C12H14N2. 2Cl
40: In formula2mass(as.character(x)) : Invalid formula:CH3OR
41: In formula2mass(as.character(x)) : Invalid formula:HSR
42: In formula2mass(as.character(x)) : Invalid formula:C15H25O16P2R3
43: In formula2mass(as.character(x)) : Invalid formula:CH2NOR
44: In formula2mass(as.character(x)) : Invalid formula:C24H37N7O18P3SR
45: In formula2mass(as.character(x)) : Invalid formula:C14H19N3O15P2R2
46: In formula2mass(as.character(x)) : Invalid formula:SR2
47: In f.extract(formula) : Invalid formula:C18H33N3O10(R1)(R2)
48: In formula2mass(as.character(x)) : Invalid formula:CH3OR
49: In formula2mass(as.character(x)) : Invalid formula:C10H14N4O4S2R4
50: In formula2mass(as.character(x)) : Invalid formula:C10H12N4O4S2R4

conda install not working

Hi @lecorguille and W4M team,

Are there any plans to address the current problem of installing the probmetab tool?

Currently the tool can't install and hangs at the solving environment stage due to problems with the conda install (see bioconda issue ).

The issue can be fixed by being more explicit to R version in the dependencies in the XML of the Galaxy tool (see).

However, I notice the branch "update_deps" has been setup to update to new dependencies but this branch is currently failing planemo-travis testing.

Is more work planned on this branch? Or, do you think we could merge the fork I have made and push to the test-toolshed. The fork is currently passing the planemo testing on travis.

This would be useful as I need the Probmetab tool for the analysis I am performing, and it will be very beneficial to have a working tool in a public toolshed.

FYI: @RJMW

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