Mercurial > repos > iuc > vg_deconstruct
comparison deconstruct.xml @ 0:d9e1149f48d6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
| author | iuc |
|---|---|
| date | Thu, 09 Apr 2020 08:33:31 +0000 |
| parents | |
| children | f4c7b4c3f46f |
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| -1:000000000000 | 0:d9e1149f48d6 |
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| 1 <tool id="vg_deconstruct" name="vg deconstruct" version="@TOOL_VERSION@"> | |
| 2 <description>construct a dynamic succinct variation graph</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"/> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 ln -s '$infile' ./infile.${infile.ext} && | |
| 9 | |
| 10 vg deconstruct | |
| 11 #if $path: | |
| 12 --path '${','.join([$p for $p in $path])}' | |
| 13 #end if | |
| 14 #if $path_prefix | |
| 15 --path-prefix '${','.join([$p for $p in $path_prefix])}' | |
| 16 #end if | |
| 17 #if $alt_prefix | |
| 18 --alt-prefix '${','.join([$p for $p in $alt_prefix])}' | |
| 19 #end if | |
| 20 #if $snarls: | |
| 21 --snarls '$snarls' | |
| 22 #end if | |
| 23 $path_traversals ## -e | |
| 24 --threads=\${GALAXY_SLOTS:-1} | |
| 25 ./infile.${infile.ext} | |
| 26 | |
| 27 > '$output' | |
| 28 | |
| 29 ]]></command> | |
| 30 <inputs> | |
| 31 <param name="infile" type="data" format="xg,odgi" label="Graph files" /> | |
| 32 <param argument="--path" type="text" value="" label="A reference path to deconstruct against" | |
| 33 help="comma-separated list accepted"> | |
| 34 <sanitizer> | |
| 35 <valid initial="string.printable"> | |
| 36 <remove value="'"/> | |
| 37 </valid> | |
| 38 </sanitizer> | |
| 39 </param> | |
| 40 <param argument="--path-prefix" type="text" value="" label="All paths beginning with this value used as reference" | |
| 41 help="comma-separated list accepted"> | |
| 42 <sanitizer> | |
| 43 <valid initial="string.printable"> | |
| 44 <remove value="'"/> | |
| 45 </valid> | |
| 46 </sanitizer> | |
| 47 </param> | |
| 48 <param argument="--alt-prefix" type="text" value="" label="Non-reference paths beginning with with this value get lumped together to same sample in VCF" | |
| 49 help="comma-separated list accepted"> | |
| 50 <sanitizer> | |
| 51 <valid initial="string.printable"> | |
| 52 <remove value="'"/> | |
| 53 </valid> | |
| 54 </sanitizer> | |
| 55 </param> | |
| 56 <param argument="--snarls" type="data" format="xg,odgi" label="Snarls files" optional="true" | |
| 57 help="from `vg snarls` to avoid recomputing" /> | |
| 58 | |
| 59 <param argument="--path-traversals" type="boolean" truevalue="--path-traversals" falsevalue="" checked="false" | |
| 60 label="Only consider traversals that correspond to paths in the grpah" /> | |
| 61 </inputs> | |
| 62 <outputs> | |
| 63 <data name="output" format="vcf" /> | |
| 64 </outputs> | |
| 65 <tests> | |
| 66 <test> | |
| 67 <param name="infile" value="hla.xg" /> | |
| 68 <param name="path" value="gi|568815592:29791752-29792749" /> | |
| 69 <param name="path_traversals" value="true" /> | |
| 70 <output name="output" file="hla_variants.vcf" /> | |
| 71 </test> | |
| 72 </tests> | |
| 73 <help><![CDATA[ | |
| 74 variation graph (vg) deconstruct module | |
| 75 ----------------------------------- | |
| 76 | |
| 77 Creates VCF records for Snarls present in a graph (relative to a chosen reference path). | |
| 78 | |
| 79 ]]></help> | |
| 80 <expand macro="citations"> | |
| 81 </expand> | |
| 82 </tool> |