| Previous changeset 0:3f438bf5475d (2021-01-03) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit 669dd4d406e86aee7d83e7420dced981c180d805 |
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modified:
canongff3.xml macros.xml |
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| diff -r 3f438bf5475d -r c45c9dd066e2 canongff3.xml --- a/canongff3.xml Sun Jan 03 14:58:31 2021 +0000 +++ b/canongff3.xml Sun Feb 11 11:29:29 2024 +0000 |
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| @@ -1,53 +1,53 @@ -<tool id='aegean_canongff3' name=' AEGeAn CanonGFF3' version='@TOOL_VERSION@' profile='20.01'> +<tool id="aegean_canongff3" name="AEGeAn CanonGFF3" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> <description> pre-process GFF3 files, removing all features not directly related to protein-coding genes</description> <macros> <import>macros.xml</import> </macros> - <expand macro='xrefs'/> - <expand macro='edam_ontology'/> - <expand macro='requirements'/> + <expand macro="edam_ontology"/> + <expand macro="xrefs"/> + <expand macro="requirements"/> <version_command>canon-gff3 --version</version_command> - <command detect_errors='exit_code'> + <command detect_errors="exit_code"> <![CDATA[ - canon-gff3 '$gff3file' + canon-gff3 "$gff3file" $infer #if $source - -s '$source' + -s "$source" #end if - -o '$output' + -o "$output" ]]> </command> <inputs> - <param name='gff3file' type='data' format='gff3' label='GFF3 File' - help="GFF3 annotation file" multiple='true' /> - <param argument='--infer' type='boolean' - truevalue='--infer' falsevalue='' - label='Infer gene feature for transcripts lacking it' - help='For transcript features lacking an explicitly declared gene feature as a parent, create this feature on-they-fly'/> - <param argument='--source' type='text' - value='' optional='true' - label='Reset the source of each feature' - help='Reset the source of each feature to the given value. Source keywords can be a program (e.g. RepeatMasker) or an organization (like TAIR)'> + <param name="gff3file" type="data" format="gff3" label="GFF3 File" + help="GFF3 annotation file" multiple="true" /> + <param argument="--infer" type="boolean" + truevalue="--infer" falsevalue="" + label="Infer gene feature for transcripts lacking it" + help="For transcript features lacking an explicitly declared gene feature as a parent, create this feature on-they-fly"/> + <param argument="--source" type="text" + value="" optional="true" + label="Reset the source of each feature" + help="Reset the source of each feature to the given value. Source keywords can be a program (e.g. RepeatMasker) or an organization (like TAIR)"> <validator type="regex" message="Please only use letters, numbers or underscores in sample label">^[\w]+$</validator> </param> </inputs> <outputs> - <data name='output' format='gff3' /> + <data name="output" format="gff3" /> </outputs> <tests> <test> - <param name='gff3file' value='TAIR10_GFF3_genes.gff'/> - <output name='output' file='canon-output_test1.gff3'/> + <param name="gff3file" value="TAIR10_GFF3_genes.gff" ftype="gff3"/> + <output name="output" file="canon-output_test1.gff3"/> </test> <test> - <param name='gff3file' value='TAIR10_GFF3_genes.gff'/> - <param name='source' value='test_source'/> - <output name='output' file='canon-output_test2.gff3'/> + <param name="gff3file" value="TAIR10_GFF3_genes.gff" ftype="gff3"/> + <param name="source" value="test_source"/> + <output name="output" file="canon-output_test2.gff3"/> </test> <test> - <param name='gff3file' value='TAIR10_GFF3_genes.gff'/> - <param name='infer' value='true'/> - <output name='output' file='canon-output_test3.gff3'/> + <param name="gff3file" value="TAIR10_GFF3_genes.gff" ftype="gff3"/> + <param name="infer" value="true"/> + <output name="output" file="canon-output_test3.gff3"/> </test> </tests> <help> @@ -78,5 +78,5 @@ ]]> </help> - <expand macro='citations'/> + <expand macro="citations"/> </tool> |
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| diff -r 3f438bf5475d -r c45c9dd066e2 macros.xml --- a/macros.xml Sun Jan 03 14:58:31 2021 +0000 +++ b/macros.xml Sun Feb 11 11:29:29 2024 +0000 |
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| @@ -9,12 +9,12 @@ </xml> <xml name="xrefs"> <xrefs> - <xref type='bio.tools'>gaeval</xref> + <xref type="bio.tools">gaeval</xref> </xrefs> </xml> <xml name="requirements"> <requirements> - <requirement type="package" version="0.16.0">aegean</requirement> + <requirement type="package" version="@TOOL_VERSION@">aegean</requirement> </requirements> </xml> <xml name="citations"> @@ -32,5 +32,5 @@ </citations> </xml> <token name="@TOOL_VERSION@">0.16.0</token> - + <token name="@VERSION_SUFFIX@">1</token> </macros> |