Mercurial > repos > iuc > ucsc_axtchain
changeset 4:64d732725a73 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain commit 420bba1b6a3ac4747a282f4c183fcd985a1a9075
| author | iuc |
|---|---|
| date | Fri, 24 Oct 2025 17:46:27 +0000 |
| parents | 7e353b95f0b6 |
| children | |
| files | axtchain.xml test-data/hg38.chrM.mm39.chrM.axt.gz |
| diffstat | 2 files changed, 12 insertions(+), 2 deletions(-) [+] |
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--- a/axtchain.xml Mon Jun 30 10:32:16 2025 +0000 +++ b/axtchain.xml Fri Oct 24 17:46:27 2025 +0000 @@ -1,9 +1,10 @@ -<tool id="ucsc_axtchain" name="axtChain" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT"> +<tool id="ucsc_axtchain" name="axtChain" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05" license="MIT"> <description> Chain together axt alignments </description> <macros> <token name="@TOOL_VERSION@">482</token> + <token name="@VERSION_SUFFIX@">1</token> </macros> <xrefs> <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref> @@ -27,7 +28,7 @@ #else -linearGap=$linear_gap_options.linear_gap #end if - '$in_axt' + <(gzip -cdfq '$in_axt') '$in_target' '$in_query' '$out' @@ -66,6 +67,15 @@ </conditional> <output name="out" file="hg38.chrM.mm39.chrM.chain" /> </test> + <test> + <param name="in_axt" value="hg38.chrM.mm39.chrM.axt.gz" /> + <param name="in_target" value="hg38.chrM.fasta" /> + <param name="in_query" value="mm39.chrM.fasta" /> + <conditional name="linear_gap_options"> + <param name="linear_gap" value="medium" /> + </conditional> + <output name="out" file="hg38.chrM.mm39.chrM.chain" /> + </test> </tests> <help><![CDATA[ **What it does**