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Updating tools/rna_tools/ribotaper from version 1.3.1a to 1.3.1 #1825

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Updating tools/rna_tools/ribotaper from version 1.3.1a to 1.3.1 #1825

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121700e
Updating tools/rna_tools/ribotaper from version 1.3.1a to 1.3.1
Mar 30, 2026
8783413
Fix GTF format in annotation file parameters
pavanvidem Apr 20, 2026
c0f9f3e
Change BAM format from uppercase to lowercase
pavanvidem Apr 20, 2026
1c63bc5
set annotation type to tar
pavanvidem Apr 20, 2026
140b64d
Fix typo in annotation_path parameter attribute
pavanvidem Apr 21, 2026
af6fedf
Rename annotation_path.tgz to annotation_path.tar
pavanvidem Apr 21, 2026
5f68944
Fix annotation path in ribotaper_part3_main.xml
pavanvidem Apr 21, 2026
62c72d9
Rename annotation_path.tar to annotation_path.tgz
pavanvidem Apr 21, 2026
75d41eb
revert ftype to tgz
pavanvidem Apr 21, 2026
495616b
revert annotation path file extension
pavanvidem Apr 21, 2026
20ae929
Update tar command for handling tgz files
pavanvidem Apr 23, 2026
2ca3c27
Change annotation path format from tgz to tar.gz
pavanvidem Apr 24, 2026
706d988
add &&
pavanvidem Apr 24, 2026
5af16ee
add another test to see if it runs tar -xvf instead of tar - xvzf
pavanvidem Apr 24, 2026
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8 changes: 4 additions & 4 deletions tools/rna_tools/ribotaper/macros.xml
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Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
<macros>
<token name="@TOOL_VERSION@">1.3.1a</token>
<token name="@VERSION_SUFFIX@">2</token>
<token name="@TOOL_VERSION@">1.3.1</token>
<token name="@VERSION_SUFFIX@">0</token>
<xml name="requirements">
<requirements>
<requirement type="package" version="@TOOL_VERSION@">ribotaper</requirement>
<requirement type="package" version="9.1">coreutils</requirement>
<requirement type="package" version="9.54.0">ghostscript</requirement>
<requirement type="package" version="9.5">coreutils</requirement>
<requirement type="package" version="10.07.0">ghostscript</requirement>

</requirements>
</xml>
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2 changes: 1 addition & 1 deletion tools/rna_tools/ribotaper/ribotaper_part1_create_annotation_files.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@

]]></command>
<inputs>
<param name="gtf" type="data" format="GTF" label="Annotation file"
<param name="gtf" type="data" format="gtf" label="Annotation file"
help="The GTF file should contain: 1) coding and non-coding genes, 2) a 'transcript_id' and a 'gene_id' field for each 'exon' and 'CDS' row."/>
<conditional name="reference_genome">
<param name="source" type="select" label="Source for the genome" help="Built-in references were created using default options.">
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16 changes: 11 additions & 5 deletions tools/rna_tools/ribotaper/ribotaper_part3_main.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,8 +8,8 @@
<exit_code range="1:" />
</stdio>
<command><![CDATA[
#if $annotation_path.is_of_type("tgz")
tar -xzvf '${annotation_path}' &&
#if $annotation_path.is_of_type("tar.gz")
tar -xvzf '${annotation_path}' &&
#else
tar -xvf '${annotation_path}' &&
#end if
Expand All @@ -22,9 +22,9 @@
\${GALAXY_SLOTS:-12}
]]></command>
<inputs>
<param name="annotation_path" type="data" format="tgz,tar" label="Annotation path" help="Please run 'ribotaper part 1' to generate the archive."/>
<param name="ribo_bam" type="data" format="BAM" label="Ribo-seq alignment file" help="Ribo-seq alignment file in BAM format."/>
<param name="rna_bam" type="data" format="BAM" label="RNA-seq alignment file" help="RNA-seq alignment file in BAM format."/>
<param name="annotation_path" type="data" format="tar.gz,tgz,tar" label="Annotation path" help="Please run 'ribotaper part 1' to generate the archive."/>
<param name="ribo_bam" type="data" format="bam" label="Ribo-seq alignment file" help="Ribo-seq alignment file in BAM format."/>
<param name="rna_bam" type="data" format="bam" label="RNA-seq alignment file" help="RNA-seq alignment file in BAM format."/>
<param name="read_lenghts_ribo" type="text" value="26,28,29" label="Read length" help="Read lengths, comma-separated values, which are used for P-site calculation. Example, 26,28,29.
Please run 'ribotaper part 2' to deterimine appropriate values.">
<sanitizer invalid_char="">
Expand Down Expand Up @@ -55,6 +55,12 @@
<data name="output8" format="pdf" from_work_dir="Final_ORF_results.pdf" label="${tool.name} on ${on_string}: ORF categories (length/coverage)"/>
</outputs>
<tests>
<test expect_num_outputs="8">
<param name="annotation_path" value="annotation_path.tgz" ftype="tar.gz"/>
<param name="ribo_bam" value="test_ribo.bam"/>
<param name="rna_bam" value="test_rna.bam"/>
<output name="output2" file="ORFs_genes_found"/>
</test>
<test expect_num_outputs="8">
<param name="annotation_path" value="annotation_path.tgz"/>
<param name="ribo_bam" value="test_ribo.bam"/>
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