add ChewBBACA #5899

nilchia · 2024-03-21T14:41:06Z

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)

bgruening · 2024-03-25T16:18:50Z

tools/chewbbaca/AlleleCall.xml

+        mkdir ./input &&
+        mkdir ./schema &&
+        #for $file in $input_file
+        cp $file ./input/${file.element_identifier} &&


please single-quote all file-path

bgruening · 2024-03-25T16:20:02Z

tools/chewbbaca/CreateSchema.xml

+    <command detect_errors="exit_code"><![CDATA[
+        mkdir ./input &&
+        #for $file in $input_file
+        cp $file ./input/${file.element_identifier} &&


is

Suggested change

cp $file ./input/${file.element_identifier} &&

ln -sf '$file' './input/${file.element_identifier}' &&

working instead of copying?

bgruening · 2024-03-25T16:20:59Z

tools/chewbbaca/CreateSchema.xml

+        </test>
+    </tests>
+    <help><![CDATA[
+chewBBACA version: 3.3.3


Please create a useful help section, the parameters are already explained in the form, here you can describe the tool, the functionality and maybe where you can get the zip file from.

bgruening · 2024-03-25T16:21:17Z

tools/chewbbaca/PrepExternalSchema.xml

+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir ./schema &&
+        unzip $input_schema -d ./schema &&


Suggested change

unzip $input_schema -d ./schema &&

unzip '$input_schema' -d ./schema &&

bgruening · 2024-03-25T16:22:06Z

tools/chewbbaca/macros.xml

+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">


why not citing here the real publication? 10.1099/mgen.0.000166

tools/chewbbaca/CreateSchema.xml

bgruening · 2024-04-10T16:25:38Z

tools/chewbbaca/CreateSchema.xml

+        <test expect_num_outputs="1">
+            <param name="input_file" value="CDS_Str_agalactiae.fasta"/>
+            <param name="cds_input" value="true"/>
+            <output name="schema" file="Str_agalactiae_cds.zip" compare="sim_size"/>


Instead of comparing the sim_size you can check for members in the archive: https://docs.galaxyproject.org/en/latest/dev/schema.html#has-archive-member

Thanks! Yes that makes more sense. I have added it.

bgruening · 2024-04-10T16:27:17Z

tools/chewbbaca/DownloadSchema.xml

+            <assert_stdout>
+                <has_text text="Schema is now available at"/>
+                <has_text text="Finished at"/>
+            </assert_stdout>


same here you can test the zip file content

bgruening · 2024-04-10T16:28:06Z

tools/chewbbaca/JoinProfiles.xml

+        <param argument="--common" type="boolean" truevalue="--common" falsevalue="" checked="false" label="Common" optional="true" help="Create file with profiles for the set of common loci" />
+    </inputs>
+    <outputs>
+        <data format="tsv" name="JoinedProfile" from_work_dir="JoinedProfile.tsv" label="${tool.name} on ${on_string}: Joined profiles"/>


Can you use format="tabular" here?

Yes, I updated it. But isn't it same?

bgruening · 2024-04-10T16:28:27Z

tools/chewbbaca/JoinProfiles.xml

+    <tests>
+        <test>
+            <param name="input1" value="results_alleles.tsv,results_alleles2.tsv"/>
+            <output name="JoinedProfile" file="JoinedProfile.tsv" compare="sim_size"/>


Why sim_size here and not comparing by diff? Or using asserts?

Updated it with compare="diff"

bgruening · 2024-04-10T16:29:16Z

tools/chewbbaca/NSStats.xml

+    <tests>
+        <test>
+            <param name="mode" value="species" />
+            <output name="NSStats" file="NSStats.txt" compare="sim_size" />


sim_size is not a good test, its the least stringent test that we have and we should do better whenever we can ... please use diff or asserts

Updated in any tool that has sim_size as test

bgruening · 2024-04-10T16:30:12Z

tools/chewbbaca/PrepExternalSchema.xml

+    <inputs>
+        <param format="zip" name="input_schema" type="data" multiple="true" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and a folder named 'short' that contains the FASTA files with the loci representative alleles."/>
+        <section name="advanced" title="Advanced options">
+            <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" />


format binary is strange? What is this file?

bgruening · 2024-04-10T16:30:39Z

tools/chewbbaca/PrepExternalSchema.xml

+        <test expect_num_outputs="1">
+            <param name="input_schema" value="GCA_000007265.1_ASM726v1_schema_seed.zip"/>
+            <param name="size_filter" value="false"/>
+            <output name="schema" file="GCA_000007265.1_ASM726v1_PExternalschema_seed.zip" compare="sim_size"/>


please use assserts here: https://docs.galaxyproject.org/en/latest/dev/schema.html#has-archive-member

Co-authored-by: Björn Grüning <[email protected]>

nilchia · 2024-04-11T11:33:38Z

@bgruening the binary file is a file with ".trn" extention (called Prodigal training file). I tried to open it in VSCode and it says: The file is not displayed in the text editor because it is either binary or uses an unsupported text encoding.

I googled the file and got this:
Prodigal (PROkaryotic DynamIc programming Genefinding ALgorithm) is an open source lightweight microbial genefinding program developed at University of Tennessee and Oak Ridge National Laboratory.

the prodigal package provides 3 output formats GFF3, GenBank and Sequin table format.
But in chewBBACA it is a .trn file

bgruening · 2024-04-12T05:07:54Z

tools/chewbbaca/test-data/NSStats.txt

@@ -8,7 +8,7 @@ Contacts: [email protected]
 =======================
  chewBBACA - NSStats
 =======================
-Started at: 2024-04-03T10:24:19
+Started at: 2024-04-11T17:01:56


updating the time will not help much, if you have time in your diffs ... you need to allow for certain lines of difference with lines_diff

tools-iuc/tools/lofreq/lofreq_filter.xml

Line 210 in 26fe7d2

<output name="outvcf" file="call-out1.vcf" lines_diff="6" />

Thanks.
I added line_diff="4" and it passed the planemo test but here it got error, I put assert_contents for the test.

bgruening · 2024-04-13T15:52:20Z

Thanks, @nilchia for your first contribution! Great work - it was a complicated tool!

nilchia · 2024-04-13T18:20:00Z

Hooray 😃 ,
Thank you so much, @bgruening and @pavanvidem for your invaluable help and guidance. I've learned a lot and I couldn't have done this without you both! 🌷

add ChewBBACA

0d90128

nilchia marked this pull request as draft March 21, 2024 14:41

nilchia added 8 commits March 21, 2024 16:58

update macros

e31b5f9

add compare by sim_size for zip files

9c403c7

3rd tool PrepExternalSchema

1c22e19

Change to min value of --l

b38e5c7

Add PrepExternalSchema tool from chewbbaca

f1b2d85

Some minor adjustment to xmls. create output of allelecall in test-data

d22ff0c

update test-data

87386a9

update test-data

22e2901

bgruening reviewed Mar 25, 2024

View reviewed changes

nilchia added 2 commits March 25, 2024 17:57

add prepareexternalschema

698b1fd

removing uploaded wrong files

cbc4c70

nilchia force-pushed the chewbbaca branch from bc4a59a to cbc4c70 Compare March 25, 2024 17:02

nilchia and others added 16 commits March 25, 2024 19:05

aading DownloadSchema tool

5b94ea1

aading DownloadSchema tool

cef81ad

Add AlleleCallEvaluator

7468524

update alleleCallEvaluator

933f5fd

Add FastTree requirement to macros

b7dc7c0

add AlleleCallEvaluator

67a7f4c

update AlleleCall.xml to write cds_coordinates as output

ad1b55a

Update AllelCallEvluator

0256df7

update test.data

0ca96db

update test-data

1092358

add ExtractCgMLST.xml

0bd6e4f

Merge branch 'galaxyproject:main' into chewbbaca

58bd441

add NSStats.xml

422a8a2

add JoinProfiles.xml

9d1dc78

updata test-data

d867846

final NSStats.xml

7fe39d5

nilchia added 4 commits April 10, 2024 15:34

added test for annotation file in AlleleCallEvaluator.xml

6203ca7

updateed help for AlleleCall.xml ExtractCgMLST.xml

788e640

update the name of test2 output

1c51e77

update on 2nd test of AlleleCallEvaluator

28219f5

bgruening reviewed Apr 10, 2024

View reviewed changes

Update tools/chewbbaca/CreateSchema.xml

4b45c8f

Co-authored-by: Björn Grüning <[email protected]>

nilchia added 12 commits April 11, 2024 16:42

changed test of CreateSchema to check the archive members

b669c99

changed test of DownloadSchema to check the archive members

1772a31

changed format=tsv to =tabular in CreateSchema

4be4711

changed format=tsv to =tabular in JoinProfile

a0e8b31

compare diff in JoinProfile

0f0cc2d

compare diff in AlleleCallEvaluator

c50ca26

compare diff and assert_contents in NSSTATS

3a94dc7

test checks archive members in PrepExternalSchema

72259d6

sim_size to diff in AlleleCall

52195a5

deleted unnecessary test data

9224590

update test check in NSSTAT

2a8c54c

update test data

969e98b

bgruening reviewed Apr 12, 2024

View reviewed changes

nilchia and others added 5 commits April 12, 2024 11:11

updated test for NSSTATS. line_diff

bfd3a5d

Update line_diff

dcda29d

update line_diff

e306bfb

update on NSSTATS test

47ed2ac

Merge branch 'galaxyproject:main' into chewbbaca

3810705

bgruening approved these changes Apr 13, 2024

View reviewed changes

bgruening merged commit 8722918 into galaxyproject:main Apr 13, 2024
14 checks passed

nilchia deleted the chewbbaca branch April 13, 2024 22:34

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add ChewBBACA #5899

add ChewBBACA #5899

nilchia commented Mar 21, 2024

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nilchia Apr 11, 2024 •

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nilchia commented Apr 11, 2024

bgruening Apr 12, 2024

nilchia Apr 12, 2024

bgruening commented Apr 13, 2024

nilchia commented Apr 13, 2024

	cp $file ./input/${file.element_identifier} &&
	ln -sf '$file' './input/${file.element_identifier}' &&

	unzip $input_schema -d ./schema &&
	unzip '$input_schema' -d ./schema &&

add ChewBBACA #5899

add ChewBBACA #5899

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nilchia commented Mar 21, 2024

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nilchia Apr 11, 2024 • edited Loading

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nilchia commented Apr 11, 2024

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bgruening commented Apr 13, 2024

nilchia commented Apr 13, 2024

nilchia Apr 11, 2024 •

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