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

--- /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>