Migrate fastx toolkit from tools-devteam, condafy. #1413

davebx · 2017-07-10T16:00:14Z

No description provided.

martenson · 2017-07-10T16:14:31Z

Please also open the corresponding PR to move the tools in the devteam repo to legacy folder. There is also a WIP PR opened against these tools from @bgruening

Unfortunately tests are missing

-Q 33 is the default, but it needs to be set to -Q 64 for fastqillumina and fastqsolexa.

… wrapper versions.

bgruening

@davebx tests are still failing, unfortunately :(

bgruening · 2017-07-14T05:56:56Z

tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml

+    </macros>
+    <command><![CDATA[
+        command -v perl5.22.0 &&
+        perl5.22.0 `command -v fasta_clipping_histogram.pl` '$input' '$outfile' ||


Anyone know why we do this here?

I have no idea, and it doesn't seem like something we would need to do.

davebx · 2017-07-14T13:50:41Z

@bgruening yeah, there seem to be some issues with the readline dependency, not sure what's breaking it yet.

bgruening · 2017-08-05T13:56:26Z

I tried to pin the libwebp library here: conda-forge/libgd-feedstock#17
@davebx do we already have push access to these repositories?

davebx · 2017-08-07T13:33:39Z

@bgruening we did not, we do now.

nsoranzo · 2018-04-27T13:56:47Z

tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml

+            <param name="SKIPN" value="no"/>
+            <param name="RENAMESEQ" value="yes"/>
+            <output name="output" file="fastq_to_fasta1b.out" />
+        </test>


We should a test using fastqsanger input format.

This tool now has three tests.

nsoranzo · 2018-05-03T18:50:25Z

tool_collections/fastx_toolkit/fasta_clipping_histogram/.shed.yml

+homepage_url: http://hannonlab.cshl.edu/fastx_toolkit/
+name: fasta_clipping_histogram
+owner: devteam
+remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram


s/tools-devteam/tools-iuc/

for all tools' remote_repository_url

Fixed, will push once the tests complete, just in case I need to make some changes based on the results.

nsoranzo · 2018-05-03T19:11:32Z

tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml

+]]>
+    </command>
+    <inputs>
+        <param format="fasta" name="input" type="data" label="Library to re-format" />


Maybe add fasta.gz to format, otherwise using zcat in the command doesn't make much sense.

Similarly for the other tools using zcat.

Yeah, I was chewing on that myself, don't know why they used zcat in the first place, since these tools were wrapped long before we supported fastx.gz filetypes.

nsoranzo · 2018-05-04T14:30:18Z

tool_collections/fastx_toolkit/macros.xml

+<macros>
+    <token name="@FQQUAL@">
+        <![CDATA[
+            #if $input.ext == "fastqsanger":


#if $input.is_of_type("fastqsanger", "fastqsanger.gz"):

nsoranzo · 2018-05-04T15:12:44Z

tool_collections/fastx_toolkit/macros.xml

+        <![CDATA[
+            #if $input.ext == "fastqsanger":
+                -Q 33
+            #else:


#elif $input.is_of_type("fastqsolexa", "fastqsolexa.gz", "fastqillumina", "fastqillumina.gz"):

Quality encoding doesn't make sense for FASTA datasets (even if it doesn't make the tool fail probably).

- Add support for fasta.bz2 - Only add quality offset flag on fastq files - Tokenize the cat command and make it dependent on input format

bgruening · 2018-05-04T20:46:36Z

tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml

@@ -0,0 +1,73 @@
+<tool id="cshl_fastx_renamer" name="Rename sequences" version="@VERSION@+galaxy0" >


have you increased all other tool versions as well?

Also it seems that the @VERSION@ token is not defined.

Increased, yes. The other tools were 1.x.x, so I couldn't set them to 0.0.14

nsoranzo · 2018-05-04T21:49:46Z

tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml

@@ -0,0 +1,65 @@
+<tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot" version="1.0.1">
+	<description></description>


Indentation of this file is not correct.

nsoranzo · 2018-05-04T21:56:11Z

tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml

+            <output name="output" file="fastq_to_fasta-out2.out" />
+        </test>
+	</tests>
+<help>


Indentation of the previous 2 lines.

nsoranzo · 2018-05-04T21:56:58Z

tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml

+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
+</help>


Indentation

nsoranzo · 2018-05-04T22:00:01Z

..._collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml

+            <output name="output" file="fastx_nucleotides_distribution-out1.png" compare="sim_size" delta="512" />
+        </test>
+    </tests>
+<help>


Indentation

nsoranzo · 2018-05-04T22:00:46Z

..._collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml

+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
+
+</help>
+<expand macro="citations" />


Indentation of the previous 2 lines.

nsoranzo · 2018-05-04T22:05:33Z

tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml

@@ -0,0 +1,73 @@
+<tool id="cshl_fastx_renamer" name="Rename sequences" version="@VERSION@+galaxy0" >


Also it seems that the @VERSION@ token is not defined.

Attribute order per IUC style.

nsoranzo · 2018-05-08T13:33:00Z

Thanks @davebx!

nsoranzo · 2018-05-08T14:52:34Z

@davebx Upload to the Test Tool Shed is failing: "Repository contents updated but failed to update metadata for repository 'fasta_clipping_histogram' on the test Tool Shed."

https://travis-ci.org/galaxyproject/tools-iuc/jobs/376368639

davebx · 2018-05-08T15:13:14Z

@nsoranzo yeah, apparently I need to grant repository admin privileges to IUC on TTS. I'll do that and rerun the deploy job.

martenson · 2018-05-08T17:00:06Z

@davebx I think you need to do the same on MTS

davebx added 2 commits July 10, 2017 11:50

Adopt fastx toolkit from devteam.

7153bd3

Upgrade to depend on conda version of fastx.

f84ca38

This was referenced Jul 10, 2017

Move fastx_toolkit to legacy pending adoption by IUC. galaxyproject/tools-devteam#476

Merged

Apply fixes from upstream git repo. bioconda/bioconda-recipes#5178

Merged

WIP: Update and test fastx-tools galaxyproject/tools-devteam#375

Open

bgruening and others added 13 commits July 12, 2017 13:35

Upgrade to newer version of fastx

ddb0f77

Unfortunately tests are missing

Add tests for the remaining fastx tools

1bc6d3b

Explicitly set -Q for all non-cs fastq variants

89e5bb0

-Q 33 is the default, but it needs to be set to -Q 64 for fastqillumina and fastqsolexa.

Close command tag

5f17e09

Fix command tag ... again

02ec6a5

Fix requirements

0c18297

Don't fail with gnuplot warnings

c5a5fc1

Use simsize comparison for png

91d043d

Retab certain fastx tools, remove duplicate macro imports

8b6d2af

Retab more fastx tools

514e9ea

Replace '.ext ==' pattern with is_of_type

7b47f56

Merge in Björn's changes from galaxyproject/tools-devteam#375, update…

7e2048a

… wrapper versions.

Add missing test output.

eb85ba3

bgruening reviewed Jul 14, 2017

View reviewed changes

bgruening closed this Dec 17, 2017

bgruening reopened this Dec 17, 2017

nsoranzo reviewed Apr 27, 2018

View reviewed changes

davebx added 2 commits April 27, 2018 12:49

Adopt Assaf Gordon's fastx_toolkit wrappers.

8269f19

Condafy, fix tests, update to 0.0.14

1a458ea

nsoranzo mentioned this pull request Apr 27, 2018

Fastx Toolkit #1856

Closed

Initial incorporation of Lance's enhancements.

3e6b2f7

davebx added 2 commits May 1, 2018 16:05

Remove command that breaks tests.

2c726fc

Add quotes to input/output files, maybe fix tests.

12ed6a0

nsoranzo reviewed May 3, 2018

View reviewed changes

Fix repository url, bump delta for quality boxplot.

d002263

nsoranzo reviewed May 3, 2018

View reviewed changes

davebx added 2 commits May 4, 2018 09:24

Unify input parameters, add filetype support.

3036e0b

Fix tests for quality converter, add tests for sanger inputs.

9c846dc

nsoranzo reviewed May 4, 2018

View reviewed changes

davebx added 2 commits May 4, 2018 12:59

Fixes per Nicola's advice

bda216e

- Add support for fasta.bz2 - Only add quality offset flag on fastq files - Tokenize the cat command and make it dependent on input format

Support bz2 compressed filetypes that exist.

93a658e

nsoranzo approved these changes May 4, 2018

View reviewed changes

davebx added the enhancement label May 4, 2018

bgruening added 3 commits May 4, 2018 22:39

style changes

9dd5464

quote script name

20f8c8e

style fixes

bba9ee1

bgruening reviewed May 4, 2018

View reviewed changes

small style adjustments

200ea40

bgruening approved these changes May 4, 2018

View reviewed changes

nsoranzo reviewed May 4, 2018

View reviewed changes

davebx and others added 5 commits May 7, 2018 09:30

Tabs to spaces, add @Version@ token.

f9ebaa0

Merge Björn's style adjustments.

43e0171

Fix more indentation.

6cb5c84

Restore URL linting (fixed in Planemo 0.49.0)

f6e1829

More CDATA, indentation fixes. Use element_identifier

60a914f

Attribute order per IUC style.

nsoranzo merged commit bbb2e6b into galaxyproject:master May 8, 2018

bgruening deleted the fastx_migrate branch May 8, 2018 21:45

		@@ -0,0 +1,73 @@
		<tool id="cshl_fastx_renamer" name="Rename sequences" version="@VERSION@+galaxy0" >

		@@ -0,0 +1,65 @@
		<tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot" version="1.0.1">
		<description></description>

Migrate fastx toolkit from tools-devteam, condafy. #1413

Migrate fastx toolkit from tools-devteam, condafy. #1413

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davebx commented Jul 10, 2017

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davebx commented Jul 14, 2017

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nsoranzo commented May 8, 2018

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davebx commented May 8, 2018

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nsoranzo Apr 27, 2018 •

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