Add tracegroomer tool #5898

bdartigues · 2024-03-21T14:18:09Z

FOR CONTRIBUTOR:

I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
License permits unrestricted use (educational + commercial)
This PR adds a new tool or tool collection
This PR updates an existing tool or tool collection
This PR does something else (explain below)

switched to configfile and general wrapper updates

compatibility with tracegroomer 0.1.3

bgruening · 2024-03-25T19:54:48Z

tools/tracegroomer/tracegroomer.xml

+    <command detect_errors="exit_code"><![CDATA[
+        mkdir -p config &&
+        #if $sample_metadata_path:
+            ln -s $sample_metadata_path ./sample_metadata.csv &&


Suggested change

ln -s $sample_metadata_path ./sample_metadata.csv &&

ln -s '$sample_metadata_path' ./sample_metadata.csv &&

bgruening · 2024-03-25T19:55:26Z

tools/tracegroomer/tracegroomer.xml

+        #end if
+        #if $type_of_file.type_of_file_selector == "rule_tsv":
+            #if $variable_metadata_path:
+                ln -s $variable_metadata_path ./variableMetadata.tsv &&


Suggested change

ln -s $variable_metadata_path ./variableMetadata.tsv &&

ln -s '$variable_metadata_path' ./variableMetadata.tsv &&

bgruening · 2024-03-25T19:55:37Z

tools/tracegroomer/tracegroomer.xml

+                ln -s $variable_metadata_path ./variableMetadata.tsv &&
+            #end if
+        #end if
+        ln -s $param_file config/config.yaml &&


Suggested change

ln -s $param_file config/config.yaml &&

ln -s '$param_file' config/config.yaml &&

bgruening · 2024-03-25T19:55:48Z

tools/tracegroomer/tracegroomer.xml

+            #end if
+        #end if
+        ln -s $param_file config/config.yaml &&
+        cat config/config.yaml &&


is this needed?

bgruening · 2024-03-25T19:56:11Z

tools/tracegroomer/tracegroomer.xml

+            -lm '${labeled_metabo_file}'
+            -tf '${type_of_file_selector}'
+            #if $amount_material:
+                --amountMaterial_path ${amount_material}


single quote for all paths and text parameters

bgruening · 2024-03-25T19:56:56Z

tools/tracegroomer/tracegroomer.xml

+            </section>
+            <output file="isotopologuesCorrValues.tsv" name="isotopologuesCorrValues" ftype="tabular"/>
+        </test>
+<!--        <test expect_num_outputs="3">-->


what the problem with this test?

It was the same problem we encoutered with DIMet when there are too many decimals in output test file. So i modified the input file for this test and it should works now

bgruening · 2024-03-25T19:58:12Z

tools/tracegroomer/macros.xml

+        <section name="advanced_options" title="Advanced options" expanded="false">
+            <param name="alternative_div_amount_material" type="boolean" value="true" label="add strip plot on abundance bar" help="When dividing values by the amount of material, also multiplies by mean(amountMaterial) to stay in abundance units"/>
+            <param name="div_isotopologues_by_amount_material" type="boolean" value="true" label="isotopologues by amount material" help="Apply normalization by the amount of material, at the level of isotopologue absolute values. After this, re-computes all derived metrics. If False, only total abundances are normalized"/>
+            <param name="use_internal_standard" type="text" optional="true" help="Internal Standard for performing the division: abundances/internal_standard, example: --use_internal_standard Myristic_acid_d27. By default is not performed." label="internal standard" />


I don't understand this parameter.

i added some explanation in help section and there is also a link to the wiki in the help section.

bgruening · 2024-03-27T12:21:45Z

tools/tracegroomer/tracegroomer.xml

@@ -0,0 +1,327 @@
+<tool id="tracegroomer" name="@TOOL_LABEL@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
+    <description>
+        TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool.


This should be shorter. It will be used in the tool panel and the tool bar, so as short as possible.

Done in last commit

hello @bdartigues , if not too late, please make this short description to be: Format and normalise files for DIMet tool

bgruening · 2024-03-27T12:22:16Z

tools/tracegroomer/tracegroomer.xml

+        TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool.
+    </description>
+    <macros>
+        <token name="@TOOL_LABEL@">tracegroomer</token>


TOOL_LABEL is only used one time, isn't it? Maybe that an overuse of macros :)

Done in last commit

bgruening · 2024-03-27T12:23:51Z

tools/tracegroomer/macros.xml

+    </xml>
+    <xml name="advanced_options">
+        <section name="advanced_options" title="Advanced options" expanded="false">
+            <param name="alternative_div_amount_material" type="boolean" value="true" label="alternative isotopologues division by amount material" help="In the normalisation by the amount of material, not only the division of the given absolute values by these amounts is performed, but also the product of the resulting quotients and the averaged amount of material is computed"/>


this is a boolean, you should use truevalue="--alternative_div_amount_material" falsvalue="" this will simplify the param here but also the command section (no if clause needed).

You can also use argument="--alternative_div_amount_material" here I think

https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#booleans

Done in last commit

bgruening · 2024-03-27T12:26:01Z

tools/tracegroomer/tracegroomer.xml

+                cp -rf '${MeanEnrichment13C}.tsv' '${MeanEnrichment13C}' &&
+                cp -rf '${IsotopologuesProp}.tsv' '${IsotopologuesProp}' &&
+                cp -rf '${IsotopologuesAbs}.tsv' '${IsotopologuesAbs}'
+            #end if


if else if?

Done in last commit

…n truevalue,falsevalue and argument attributes + repalce multiple if by if else

johaGL · 2024-03-27T20:04:43Z

a last revision of the short description in course.

tools/tracegroomer/.shed.yml

bgruening · 2024-03-28T13:05:55Z

Thanks @bdartigues and @johaGL!

bdartigues and others added 27 commits March 12, 2024 16:46

first commit to add tracegroomer

e54ea7c

add test-data files

aebe9a9

switched to configfile and general wrapper updates

11a8c30

updated version

5d8d592

Merge pull request #1 from hechth/hh_tracegroomer

86e6ada

switched to configfile and general wrapper updates

compatibility with tracegroomer 0.1.3

b73e893

fixed linting and removed unused parameters

9b3211c

Merge pull request #2 from hechth/hh_tracegroomer

d0093c7

compatibility with tracegroomer 0.1.3

replace with helge code

c7ff168

add tracegroomer tool prequel of DIMet

f7f322a

add tracegroomer tool prequel of DIMet

8556ab3

repair conflict

462f01d

add tracegroomer tool prequel of DIMet

3e96315

Merge branch 'galaxyproject:main' into add_tracegroomer_tool

79f51ce

escape < in macros.xml

b1aa566

remove unescaped < in macros.xml

3491bbb

repair malformed table reStructuredText

4d17213

replace cp command by ln

f6454a4

replace cp command by ln

7d7591e

replace cp command by ln

af368ec

repair config file metadata entry

9d8f61f

add other modes for different input format

bcb9727

add other modes for different input format

4715e0e

add title for section

0bd115a

repair test2 failed cause of bad isotopologue file

0b021ca

remove title for section in help

0e4837b

repair linting error due to duplicated labels

3e87479

bgruening reviewed Mar 25, 2024

View reviewed changes

bdartigues added 2 commits March 26, 2024 11:55

add quote for path and fix test 4

e6893bd

add missing test files

5e95ed4

complete help ds

c668fa9

bdartigues requested a review from bgruening March 27, 2024 11:38

bgruening reviewed Mar 27, 2024

View reviewed changes

bdartigues added 2 commits March 27, 2024 16:11

remove TOOLS_LABEL macro + Shorten tool description text + use boolea…

142b9de

…n truevalue,falsevalue and argument attributes + repalce multiple if by if else

remove argument attribute redudant with the name attribute

a2b63f1

bdartigues requested a review from bgruening March 27, 2024 15:40

bdartigues and others added 2 commits March 28, 2024 10:05

remove argument attribute redudant with the name attribute

d9b0b31

Update tracegroomer.xml

29844c8

bgruening reviewed Mar 28, 2024

View reviewed changes

tools/tracegroomer/.shed.yml Outdated Show resolved Hide resolved

bgruening and others added 2 commits March 28, 2024 11:39

Update tools/tracegroomer/.shed.yml

3b2ef9e

Merge branch 'galaxyproject:main' into add_tracegroomer_tool

b459c41

bgruening approved these changes Mar 28, 2024

View reviewed changes

bgruening merged commit 6a049d6 into galaxyproject:main Mar 28, 2024
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SaimMomin12 mentioned this pull request Apr 30, 2024

add Tracegroomer tool #5818

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Add tracegroomer tool #5898

Add tracegroomer tool #5898

bdartigues commented Mar 21, 2024 •

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johaGL commented Mar 27, 2024

bgruening commented Mar 28, 2024

	ln -s $sample_metadata_path ./sample_metadata.csv &&
	ln -s '$sample_metadata_path' ./sample_metadata.csv &&

	ln -s $variable_metadata_path ./variableMetadata.tsv &&
	ln -s '$variable_metadata_path' ./variableMetadata.tsv &&

	ln -s $param_file config/config.yaml &&
	ln -s '$param_file' config/config.yaml &&

Add tracegroomer tool #5898

Add tracegroomer tool #5898

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bdartigues commented Mar 21, 2024 • edited Loading

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johaGL commented Mar 27, 2024

bgruening commented Mar 28, 2024

bdartigues commented Mar 21, 2024 •

edited

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