Mercurial > repos > iuc > odgi_build
changeset 0:0acf4893bee5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
| author | iuc |
|---|---|
| date | Wed, 08 Apr 2020 12:12:18 -0400 |
| parents | |
| children | 7fb3bb1e221e |
| files | build.xml macros.xml test-data/note5.gfa test-data/note5.png test-data/note5_out.og test-data/t.gfa |
| diffstat | 6 files changed, 136 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build.xml Wed Apr 08 12:12:18 2020 -0400 @@ -0,0 +1,48 @@ +<tool id="odgi_build" name="odgi build" version="@TOOL_VERSION@"> + <description>construct a dynamic succinct variation graph</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +odgi build +-g '$gfa' +-o '$odgi_output' +$sort +#if $to_gfa: + --to-gfa > '$gfa_output' +#end if + ]]></command> + <inputs> + <param argument="--gfa" type="data" format="gfa1" label="Construct the graph from this GFA input file" /> + <param argument="--sort" type="boolean" truevalue="--sort" falsevalue="" checked="false" + label="Topological sort the graph" + help="Apply generalized topological sort to the graph and set node ids to order." /> + <param argument="--to-gfa" type="boolean" truevalue="--to-gfa" falsevalue="" checked="false" + label="Output additional GFA file" + help="" /> + </inputs> + <outputs> + <data name="odgi_output" format="odgi" /> + <data name="gfa_output" format="gfa1"> + <filter>to_gfa</filter> + </data> + </outputs> + <tests> + <test> + <param name="gfa" value="t.gfa" /> + <param name="sort" value="true" /> + <param name="to_gfa" value="true" /> + <output name="odgi_output" file="note5_out.og" /> + <output name="gfa_output" file="note5.gfa" /> + </test> + </tests> + <help><![CDATA[ +optimized dynamic genome/graph implementation (odgi) +---------------------------------------------------- + +Construct a dynamic succinct variation graph (build) + ]]></help> + <expand macro="citations"> + </expand> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Apr 08 12:12:18 2020 -0400 @@ -0,0 +1,14 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">odgi</requirement> + </requirements> + </xml> + <token name="@TOOL_VERSION@">0.3</token> + <xml name="citations"> + <citations> + <yield /> + </citations> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/note5.gfa Wed Apr 08 12:12:18 2020 -0400 @@ -0,0 +1,37 @@ +H VN:Z:1.0 +S 1 CAAATAAG +L 1 + 2 + 0M +L 1 + 3 + 0M +S 2 A +L 2 + 4 + 0M +L 2 + 5 + 0M +S 3 G +L 3 + 4 + 0M +L 3 + 5 + 0M +S 4 T +L 4 + 6 + 0M +S 5 C +L 5 + 6 + 0M +S 6 TTG +L 6 + 7 + 0M +L 6 + 8 + 0M +S 7 A +L 7 + 9 + 0M +S 8 G +L 8 + 9 + 0M +S 9 AAATTTTCTGGAGTTCTAT +L 9 + 10 + 0M +L 9 + 11 + 0M +S 10 A +L 10 + 12 + 0M +S 11 T +L 11 + 12 + 0M +S 12 ATAT +L 12 + 13 + 0M +L 12 + 14 + 0M +S 13 A +L 13 + 15 + 0M +S 14 T +L 14 + 15 + 0M +S 15 CCAACTCTCTG +P x 1+,3+,5+,6+,8+,9+,11+,12+,14+,15+ *,*,*,*,*,*,*,*,*
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/t.gfa Wed Apr 08 12:12:18 2020 -0400 @@ -0,0 +1,37 @@ +H VN:Z:1.0 +S 1 CAAATAAG +S 2 A +S 3 G +S 4 T +S 5 C +S 6 TTG +S 7 A +S 8 G +S 9 AAATTTTCTGGAGTTCTAT +S 10 A +S 11 T +S 12 ATAT +S 13 A +S 14 T +S 15 CCAACTCTCTG +P x 1+,3+,5+,6+,8+,9+,11+,12+,14+,15+ 8M,1M,1M,3M,1M,19M,1M,4M,1M,11M +L 1 + 2 + 0M +L 1 + 3 + 0M +L 2 + 4 + 0M +L 2 + 5 + 0M +L 3 + 4 + 0M +L 3 + 5 + 0M +L 4 + 6 + 0M +L 5 + 6 + 0M +L 6 + 7 + 0M +L 6 + 8 + 0M +L 7 + 9 + 0M +L 8 + 9 + 0M +L 9 + 10 + 0M +L 9 + 11 + 0M +L 10 + 12 + 0M +L 11 + 12 + 0M +L 12 + 13 + 0M +L 12 + 14 + 0M +L 13 + 15 + 0M +L 14 + 15 + 0M