Mercurial > repos > iuc > ucsc_axtchain

comparison axtchain.xml @ 3:56132e3167a9 draft default tip

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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 17:46:18 +0000
parents 0ad4e20ecce4
children
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2:0ad4e20ecce4 3:56132e3167a9
1 <tool id="ucsc_axtchain" name="axtChain" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT"> 1 <tool id="ucsc_axtchain" name="axtChain" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05" license="MIT">
2 <description> 2 <description>
3 Chain together axt alignments 3 Chain together axt alignments
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <token name="@TOOL_VERSION@">469</token> 6 <token name="@TOOL_VERSION@">482</token>
7 <token name="@VERSION_SUFFIX@">1</token>
7 </macros> 8 </macros>
8 <xrefs> 9 <xrefs>
9 <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref> 10 <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
10 </xrefs> 11 </xrefs>
11 <requirements> 12 <requirements>
25 #if str($linear_gap_options.linear_gap) == "linear_gap_file" 26 #if str($linear_gap_options.linear_gap) == "linear_gap_file"
26 -linearGap='${linear_gap_options.lineargap_input}' 27 -linearGap='${linear_gap_options.lineargap_input}'
27 #else 28 #else
28 -linearGap=$linear_gap_options.linear_gap 29 -linearGap=$linear_gap_options.linear_gap
29 #end if 30 #end if
30 '$in_axt' 31 <(gzip -cdfq '$in_axt')
31 '$in_target' 32 '$in_target'
32 '$in_query' 33 '$in_query'
33 '$out' 34 '$out'
34 ]]></command> 35 ]]></command>
35 <inputs> 36 <inputs>
57 <data name="out" format="chain" /> 58 <data name="out" format="chain" />
58 </outputs> 59 </outputs>
59 <tests> 60 <tests>
60 <test> 61 <test>
61 <param name="in_axt" value="hg38.chrM.mm39.chrM.axt" /> 62 <param name="in_axt" value="hg38.chrM.mm39.chrM.axt" />
63 <param name="in_target" value="hg38.chrM.fasta" />
64 <param name="in_query" value="mm39.chrM.fasta" />
65 <conditional name="linear_gap_options">
66 <param name="linear_gap" value="medium" />
67 </conditional>
68 <output name="out" file="hg38.chrM.mm39.chrM.chain" />
69 </test>
70 <test>
71 <param name="in_axt" value="hg38.chrM.mm39.chrM.axt.gz" />
62 <param name="in_target" value="hg38.chrM.fasta" /> 72 <param name="in_target" value="hg38.chrM.fasta" />
63 <param name="in_query" value="mm39.chrM.fasta" /> 73 <param name="in_query" value="mm39.chrM.fasta" />
64 <conditional name="linear_gap_options"> 74 <conditional name="linear_gap_options">
65 <param name="linear_gap" value="medium" /> 75 <param name="linear_gap" value="medium" />
66 </conditional> 76 </conditional>