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  • Jan 31 2019 17:58
    jorgemachucav starred galaxyproject/tools-iuc
  • Jan 31 2019 17:45
    bebatut opened #2270
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    bernt-matthias review_requested #2269
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  • Jan 31 2019 12:13
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  • Jan 30 2019 18:36
    bgruening commented #2268
  • Jan 30 2019 15:23
    nsoranzo commented #2268
  • Jan 30 2019 15:23
    nsoranzo commented #2267
martenson
@martenson:matrix.org
[m]
It looks a bit like the file was written by multiple writers or so.
pvanheusden
@pvanheusden:matrix.org
[m]
yep. and I can't seem to find a cached version of the file anywhere.
martenson
@martenson:matrix.org
[m]
but it wasn't mangled, just some sections copied over and over
pvanheusden
@pvanheusden:matrix.org
[m]
mine had a <sniffer>...</sniffer></datatypes><datatype> in it - so bad XML
martenson
@martenson:matrix.org
[m]
mine was invalid xml for sure too, what I meant is that it was a bit too organized for a rogue writer theory
pvanheusden
@pvanheusden:matrix.org
[m]
yes, agreed.
Yvan Le Bras
@yvanlebras
Hi everyone
hope all is ok on your sides !
Just see that we have an issue trying to manage a binary file (with datatype not known from Galaxy) in our cheetah code on the XML tool file.... it seems that Galaxy ""don't see"" the file so we can't copy or use it
If we change the input datatype from "binary" to "binary,txt" and that we provide a txt file, "Galaxy see" the file (on the command line generated by Galaxy, we see the file name)
bgruening
@bgruening:matrix.org
[m]
do you have some code?
what does mean "not see"? in the UI?
Yvan Le Bras
@yvanlebras
no
;) sorry for the not precise questoin ;)
in the command line (when with planemo we execute the tool, then look at the job "information" and the "command line"), we have "nothing" where we put the $input (name of the input parameter)
when the file is binary
when the fle is txt, we have for example input_file.txt
bgruening
@bgruening:matrix.org
[m]
mh, that sounds strange
can you point us to some code?
Yvan Le Bras
@yvanlebras
maybe a security thing for binary files who are not specified in the Galaxy datatypes ?
Marie Jossé
@Marie59
cp $input_raster ${input_raster.element_identifier} &&
        cp $input_header ${input_header.element_identifier} &&
        Rscript
            '$__tool_directory__/data_reading.r'
            '$input_raster.element_identifier'
            '$input_header.element_identifier'
            '$output_shannon'
            '$output_alpha'
            '$output_beta'
            '$plots'
        ]]>
    </command>
    <inputs>
        <param name="input_raster" type="data" format="binary,txt" label="Input raster"/>
        <param name="input_header" type="data" format="txt" label="Input raster header"/>
    </inputs>
Yvan Le Bras
@yvanlebras
Thjank you MArie for copy pasting the xml code ;)
so here is the code wonder Björn
Marie Jossé
@Marie59
cp  L2A_T38QKM_A035839_20220503T074203_Refl && cp /tmp/tmp44kveofp/files/000/dataset_138.dat L2A_T38QKM_A035839_20220503T074203_Refl.hdr && Rscript '/home/pndb-cr/Documents/GitHub/Data_explo_tools/test_planemo/data_reading.r' 'L2A_T38QKM_A035839_20220503T074203_Refl' 'L2A_T38QKM_A035839_20220503T074203_Refl.hdr' '/tmp/tmp44kveofp/files/000/dataset_255.dat' '/tmp/tmp44kveofp/files/000/dataset_256.dat' '/tmp/tmp44kveofp/files/000/dataset_257.dat' '<galaxy.tools.wrappers.DatasetCollectionWrapper object at 0x7f5e027c4790>'
Yvan Le Bras
@yvanlebras
and here is the stdout from Galaxy side
where we don't have the file /tmp.... for L2A_T38QKM_A035839_20220503T074203_Reflelement_identifier
when the file in input_raster is binary
BUT when this is not a binary file BUT a txt one (in input_raster)
:
(roulement de tambour ;) )
Marie Jossé
@Marie59
cp /tmp/tmp44kveofp/files/000/dataset_130.dat S2A_Subset.hdr && cp /tmp/tmp44kveofp/files/000/dataset_138.dat L2A_T38QKM_A035839_20220503T074203_Refl.hdr && Rscript '/home/pndb-cr/Documents/GitHub/Data_explo_tools/test_planemo/data_reading.r' 'S2A_Subset.hdr' 'L2A_T38QKM_A035839_20220503T074203_Refl.hdr' '/tmp/tmp44kveofp/files/000/dataset_258.dat' '/tmp/tmp44kveofp/files/000/dataset_259.dat' '/tmp/tmp44kveofp/files/000/dataset_260.dat' '<galaxy.tools.wrappers.DatasetCollectionWrapper object at 0x7f5e020742d0>'
bgruening
@bgruening:matrix.org
[m]
you test this with planemo test
or planemo serve?
single-quotes are missing around the filenames?
What kind of format is that?
Yvan Le Bras
@yvanlebras
but this work "fine" with txt file
planemo serve
bgruening
@bgruening:matrix.org
[m]
yes, its strange
Yvan Le Bras
@yvanlebras
hey hey ;)
bgruening
@bgruening:matrix.org
[m]
can you see the binary as uploaded file in Galaxy, with filesize and a path?
Yvan Le Bras
@yvanlebras
I think we will try to add the datatype to see
name and filesize are ok
path is not an info of the "dataset information" isn't it ?
bgruening
@bgruening:matrix.org
[m]
it is but only for admins I think
Yvan Le Bras
@yvanlebras
she is
Can we test the creation of a datatype using planemo ???
bgruening
@bgruening:matrix.org
[m]
if you use a local galaxy instance, for example with planemo test --galaxy_root /home/yvan/galaxy
you can simply add the datatype to this local galaxy instance
Yvan Le Bras
@yvanlebras
ok
bgruening
@bgruening:matrix.org
[m]
e.g. by editing the datatypes_conf.xml file