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update proteinortho v6.2.3 and some changes to the xml #5184

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merged 27 commits into from
Jun 16, 2023
Merged

update proteinortho v6.2.3 and some changes to the xml #5184

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2c48f81
Updating tools/proteinortho from version 6.1.5 to 6.1.6
Dec 19, 2022
274f47c
Updating tools/proteinortho from version 6.1.6 to 6.1.7
Jan 20, 2023
c15bae7
update 6.2.0
Mar 10, 2023
ab3b5f2
test
Mar 11, 2023
b09844f
update test block with sections
Mar 11, 2023
4a50b12
added diamond as p option for test1-3
Mar 11, 2023
5a820db
update diamond
Mar 11, 2023
fab286e
test wo C.faa
Mar 11, 2023
e5176d6
another test
Mar 11, 2023
dbf7ee6
w/o C2 diamond test
Mar 11, 2023
f6547f6
resolved the TODO
Mar 12, 2023
6a4198f
resolved the TODO
Mar 12, 2023
d7f03fd
added column_names metadata
Mar 13, 2023
db4cf99
additional data tag xml
Mar 13, 2023
327ec1e
test metadata
Mar 13, 2023
0b5050f
trigger recalculation of test
Mar 13, 2023
2e8c048
remove the test metadata again
Mar 13, 2023
e87ac1f
adding the test metadata again now in the test macro
Mar 13, 2023
9f75c38
without proteinortho.tsv test metadata
Mar 13, 2023
c2f99c2
test metadata proteinortho.tsv
Mar 14, 2023
7875829
forgot the new parameter -core
Mar 14, 2023
6b74efa
typos and some improvements to the help
Mar 14, 2023
1ac41c6
order of fasta matters
Mar 14, 2023
8648d00
thanks bernt-matthias
Mar 14, 2023
b155c21
new version 6.2.2
Mar 23, 2023
cbdff6b
6.2.3
Mar 30, 2023
48c7407
trigger test
Apr 2, 2023
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31 changes: 28 additions & 3 deletions tools/proteinortho/proteinortho.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -129,9 +129,34 @@
</conditional>
</inputs>
<outputs>
<data name="blastgraph" format="tabular" label="${tool.name} on ${on_string}: RBH graph" from_work_dir="result.blast-graph"/>
<data name="proteinortho" format="tabular" label="${tool.name} on ${on_string}: orthology-groups" from_work_dir="result.proteinortho.tsv"/>
<data name="proteinorthograph" format="tabular" label="${tool.name} on ${on_string}: orthology-pairs" from_work_dir="result.proteinortho-graph"/>
<data name="blastgraph"
format="tabular"
label="${tool.name} on ${on_string}: RBH graph"
from_work_dir="result.blast-graph">
<actions>
<action name="column_names" type="metadata"
default="seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba"/>
</actions>
</data>
<data name="proteinortho"
format="tabular"
label="${tool.name} on ${on_string}: orthology-groups"
from_work_dir="result.proteinortho.tsv">
<actions>
<action name="column_names" type="metadata"
default="species,genes,alg.-conn.,${','.join([ f.element_identifier for f in $input_files ])}"/>
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Lets see if this works. You should certainly check with planemo serve if this works out as expected. Maybe also include it in the tests https://docs.galaxyproject.org/en/master/dev/schema.html#tool-tests-test-output-metadata

There are even more advanced techniques for setting output metadata. For instance you can deposit a file galaxy.json in the working directory. That describes all sorts of output properties. Unfortunately this is largely undocumented https://planemo.readthedocs.io/en/latest/writing_advanced.html?highlight=galaxy.json#tool-provided-metadata

</actions>
</data>
<data name="proteinorthograph"
format="tabular"
label="${tool.name} on ${on_string}: orthology-pairs"
from_work_dir="result.proteinortho-graph">
<actions>
<action name="column_names" type="metadata"
default="seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba"/>
</actions>
</data>
</data>
</outputs>
<tests>
<test expect_num_outputs="3"> <!-- test normal -->
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