Mercurial > repos > gga > chado_phylogeny_load_tree
diff phylogeny_load_tree.xml @ 0:b44be6289549 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
| author | gga |
|---|---|
| date | Thu, 21 Jun 2018 08:42:08 -0400 |
| parents | |
| children | 31f6e0f70e41 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phylogeny_load_tree.xml Thu Jun 21 08:42:08 2018 -0400 @@ -0,0 +1,59 @@ +<?xml version="1.0"?> +<tool id="phylogeny_load_tree" name="Chado load trees" version="@WRAPPER_VERSION@.0"> + <description>for phylogeny module</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <code file="chado.py"/> + <command detect_errors="aggressive"><![CDATA[ +@AUTH@ + +chakin phylogeny load_tree +'$newick' +'$analysis_id' + +#if $name: + --name '$name' +#end if +#if $xref_db: + --xref_db '$xref_db' +#end if +#if $xref_accession: + --xref_accession '$xref_accession' +#end if +#if $match_on_name: + $match_on_name +#end if +#if $prefix: + --prefix '$prefix' +#end if + +| jq -S . > $results + ]]></command> + <inputs> + <!-- arguments --> + <param name="newick" label="Newick" argument="newick" type="data" format="txt" help="Newick file to load (or directory containing multiple newick files to load)" /> + <param argument="--analysis_id" + type="select" + dynamic_options="list_analyses()" + label="Analysis" /> + + <!-- options --> + <param name="name" label="Name" argument="name" type="text" help="The name given to the phylotree entry in the database" /> + <param name="xref_db" label="Xref db" argument="xref_db" value="null" type="text" help="The name of the db to link dbxrefs for the trees" /> + <param name="xref_accession" label="Xref Accession" argument="xref_accession" type="text" help="The accession to use for dbxrefs for the trees (assumed same as name unless otherwise specified)" /> + <param name="match_on_name" label="Match On Name" argument="match_on_name" type="boolean" truevalue="--match_on_name" falsevalue="" help="Match polypeptide features using their name instead of their uniquename" /> + <param name="prefix" label="Prefix" argument="prefix" type="text" help="Comma-separated list of prefix to be removed from identifiers (e.g species prefixes when loading OrthoFinder output)" /> + <expand macro="wait_for"/> + + </inputs> + <outputs> + <data format="json" name="results"/> + </outputs> + <help> +Load a phylogenetic tree (Newick format) into Chado db + +@HELP@ + </help> +</tool>