comparison phylogeny_load_tree.xml @ 12:4812a8770a8c draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 703eb9ed2bdf6380db14c0af6a7cb1a85fab6d3f

11:8f3b6bb4c05c

<?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@

#if $input.input_type == "archive":
	mkdir 'newick_arch/' &&
	tar -C 'newick_arch/' -xzvf '${input.newick_arch}' > /dev/null &&
#end if

chakin phylogeny load_tree

$match_on_name

#if $xref_db:
  --xref_db '$xref_db'
#end if

#if $input.input_type == "archive":
	#if $name:
	  --name '$name'
	#end if

	#if $xref_accession:

	'$newick'
#else
	'newick_arch/'
#end if

'$analysis_id'

| jq -S . > '$results'
    ]]></command>
	<inputs>
		<param argument="analysis_id"
			type="select"
			dynamic_options="list_analyses()"

		<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@

12:4812a8770a8c

<?xml version="1.0"?>
<tool id="phylogeny_load_tree" name="Chado load trees" version="@WRAPPER_VERSION@.1">
    <description>for phylogeny module</description>
	<macros>
		<import>macros.xml</import>
	</macros>
	<expand macro="requirements"/>
    <code file="chado.py"/>
	<command detect_errors="aggressive"><![CDATA[
#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

#if $xref_db:
  --xref_db '$xref_db'
#end if

#if $input.input_type == "file":
	#if $name:
	  --name '$name'
	#end if

	#if $xref_accession:

	'$newick'
#else
	'newick_arch/'
#end if

'$analysis_id' > '$results'
    ]]></command>
	<inputs>
		<param argument="analysis_id"
			type="select"
			dynamic_options="list_analyses()"

		<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="txt" name="results"/>
	</outputs>
	<help>
Load a phylogenetic tree (Newick format) into Chado db

@HELP@