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bio_hansel: allow gz input #3639

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merged 2 commits into from
May 6, 2021
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gregvonkuster
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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)

Comment on lines 69 to 82
#if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'):
#if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastqsanger.gz') or $data_type.fastq_input1.is_of_type('fastq') or $data_type.fastq_input1.is_of_type('fastq.gz'):
fast_q_single.fastq
#end if

#if $data_type.fastq_input1.is_of_type('fasta'):
#elif $data_type.fastq_input1.is_of_type('fasta') or $data_type.fastq_input1.is_of_type('fasta.gz'):
fast_a_single.fasta
#end if
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Suggested change
#if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'):
#if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastqsanger.gz') or $data_type.fastq_input1.is_of_type('fastq') or $data_type.fastq_input1.is_of_type('fastq.gz'):
fast_q_single.fastq
#end if
#if $data_type.fastq_input1.is_of_type('fasta'):
#elif $data_type.fastq_input1.is_of_type('fasta') or $data_type.fastq_input1.is_of_type('fasta.gz'):
fast_a_single.fasta
#end if
#if $data_type.fastq_input1.ext.startswith("fastq")
fast_q_single.fastq
#else
fast_a_single.fasta
#end if

Maybe this simplifies also elsewhere.

<xml name="requirements">
<requirements>
<requirement type="package" version="2.6.1">bio_hansel</requirement>
<requirement type="package" version="20.3.0">attrs</requirement>
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Do you know what attrs is doing here?

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@bernt-matthias bernt-matthias left a comment

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Good to go?

@bgruening bgruening merged commit 80309b6 into galaxyproject:master May 6, 2021
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Thanks @gregvonkuster and @bernt-matthias

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3 participants