| Next changeset 1:536768de4748 (2020-04-09) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c" |
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added:
macros.xml test-data/note5.gfa test-data/note5.png test-data/note5_out.og test-data/t.gfa vis.xml |
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| diff -r 000000000000 -r eeea2b5a81dd macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Apr 08 12:12:55 2020 -0400 |
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| @@ -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> |
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| diff -r 000000000000 -r eeea2b5a81dd test-data/note5.gfa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/note5.gfa Wed Apr 08 12:12:55 2020 -0400 |
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| @@ -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+ *,*,*,*,*,*,*,*,* |
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| diff -r 000000000000 -r eeea2b5a81dd test-data/note5.png |
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| Binary file test-data/note5.png has changed |
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| diff -r 000000000000 -r eeea2b5a81dd test-data/note5_out.og |
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| Binary file test-data/note5_out.og has changed |
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| diff -r 000000000000 -r eeea2b5a81dd test-data/t.gfa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/t.gfa Wed Apr 08 12:12:55 2020 -0400 |
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| @@ -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 |
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| diff -r 000000000000 -r eeea2b5a81dd vis.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vis.xml Wed Apr 08 12:12:55 2020 -0400 |
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| @@ -0,0 +1,57 @@ +<tool id="odgi_viz" name="odgi viz" version="@TOOL_VERSION@"> + <description>variation graph visualizations</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +odgi viz +-i '$input' +--out='$output' +-x $width +-y $height +#if str($path_height) + --path-height=$path_height +#end if +#if str($path_x_padding) + --path-x-padding=$path_x_padding +#end if +$path_per_row +#if str($link_path_pieces): + --link-path-pieces=$link_path_pieces +#end if +--threads=\${GALAXY_SLOTS:-1} + ]]></command> + <inputs> + <param name="input" type="data" format="odgi" label="odgi input file" /> + + <param argument="--width" type="integer" min="0" value="4000" label="Width in pixels of output image" /> + <param argument="--height" type="integer" min="0" value="500" label="Height in pixels of output image" /> + + <param argument="--path-height" type="integer" min="0" optional="true" label="Path display height" /> + <param argument="--path-x-padding" type="integer" min="0" optional="true" label="Path x padding" /> + <param argument="--path-per-row" type="boolean" truevalue="--path-per-row" falsevalue="" + label="Display a single path per row rather than packing them" /> + + <param argument="--link-path-pieces" type="float" optional="true" + label="Show thin links of this relative width to connect path pieces" /> + </inputs> + <outputs> + <data name="output" format="png" /> + </outputs> + <tests> + <test> + <param name="input" value="note5_out.og" /> + <param name="width" value="4000" /> + <param name="height" value="500" /> + <output name="output" file="note5.png" ftype="png" /> + </test> + </tests> + <help><![CDATA[ +optimized dynamic genome/graph implementation (odgi) +---------------------------------------------------- + +variation graph visualizations (viz) + ]]></help> + <expand macro="citations" /> +</tool> |
