Mercurial > repos > gga > chado_phylogeny_load_tree

changeset 12:4812a8770a8c draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 703eb9ed2bdf6380db14c0af6a7cb1a85fab6d3f
author gga
date Wed, 27 Mar 2019 17:32:01 -0400
parents 8f3b6bb4c05c
children 8d44d72730ed
files phylogeny_load_tree.xml
diffstat 1 files changed, 6 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/phylogeny_load_tree.xml	Tue Mar 05 05:12:24 2019 -0500
+++ b/phylogeny_load_tree.xml	Wed Mar 27 17:32:01 2019 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="phylogeny_load_tree" name="Chado load trees" version="@WRAPPER_VERSION@.0">
+<tool id="phylogeny_load_tree" name="Chado load trees" version="@WRAPPER_VERSION@.1">
     <description>for phylogeny module</description>
 	<macros>
 		<import>macros.xml</import>
@@ -7,13 +7,13 @@
 	<expand macro="requirements"/>
     <code file="chado.py"/>
 	<command detect_errors="aggressive"><![CDATA[
-@AUTH@
-
 #if $input.input_type == "archive":
 	mkdir 'newick_arch/' &&
 	tar -C 'newick_arch/' -xzvf '${input.newick_arch}' > /dev/null &&
 #end if
 
+@AUTH@
+
 chakin phylogeny load_tree
 
 $match_on_name
@@ -26,7 +26,7 @@
   --xref_db '$xref_db'
 #end if
 
-#if $input.input_type == "archive":
+#if $input.input_type == "file":
 	#if $name:
 	  --name '$name'
 	#end if
@@ -40,9 +40,7 @@
 	'newick_arch/'
 #end if
 
-'$analysis_id'
-
-| jq -S . > '$results'
+'$analysis_id' > '$results'
     ]]></command>
 	<inputs>
 		<param argument="analysis_id"
@@ -73,7 +71,7 @@
 
 	</inputs>
 	<outputs>
-		<data format="json" name="results"/>
+		<data format="txt" name="results"/>
 	</outputs>
 	<help>
 Load a phylogenetic tree (Newick format) into Chado db