Mercurial > repos > devteam > fastx_collapser
changeset 4:07497255281e draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit fd099d17eceaa319fbfe429f4725328d88b18c9f
| author | iuc |
|---|---|
| date | Thu, 10 Aug 2023 06:53:56 +0000 |
| parents | 7ce1891db6f5 |
| children | |
| files | fastx_collapser.xml macros.xml |
| diffstat | 2 files changed, 12 insertions(+), 2 deletions(-) [+] |
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--- a/fastx_collapser.xml Tue May 08 13:27:36 2018 -0400 +++ b/fastx_collapser.xml Thu Aug 10 06:53:56 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="cshl_fastx_collapser" version="1.0.1" name="Collapse"> +<tool id="cshl_fastx_collapser" version="1.0.1+galaxy@VERSION_SUFFIX@" profile="22.05" name="Collapse"> <description>sequences</description> <macros> <import>macros.xml</import>
--- a/macros.xml Tue May 08 13:27:36 2018 -0400 +++ b/macros.xml Thu Aug 10 06:53:56 2023 +0000 @@ -2,7 +2,7 @@ <macros> <token name="@CATS@"> #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'): - zcat -f '$input' | + gunzip -c -f '$input' | #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'): bzcat -f '$input' | #else: @@ -18,6 +18,15 @@ #end if ]]> </token> + <token name="@GZIP@"> + <![CDATA[ + #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'): + | gzip -c + #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'): + | bzip2 -c + #end if + ]]> + </token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">fastx_toolkit</requirement> @@ -25,6 +34,7 @@ </requirements> </xml> <token name="@VERSION@">0.0.14</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@SANGER@">fastqsanger,fastqsanger.gz,fastqsanger.bz2</token> <token name="@SOLEXA@">fastqsolexa,fastqsolexa.gz,fastqsolexa.bz2</token> <token name="@ILLUMINA@">fastqillumina,fastqillumina.gz,fastqillumina.bz2</token>