Mercurial > repos > gga > chado_phylogeny_load_tree
changeset 10:2e38005d5205 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
author | gga |
---|---|
date | Mon, 25 Feb 2019 06:04:40 -0500 |
parents | d344316d56b5 |
children | 8f3b6bb4c05c |
files | phylogeny_load_tree.xml |
diffstat | 1 files changed, 41 insertions(+), 17 deletions(-) [+] |
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--- a/phylogeny_load_tree.xml Thu Jan 24 03:15:36 2019 -0500 +++ b/phylogeny_load_tree.xml Mon Feb 25 06:04:40 2019 -0500 @@ -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> @@ -9,19 +9,12 @@ <command detect_errors="aggressive"><![CDATA[ @AUTH@ -chakin phylogeny load_tree -'$newick' -'$analysis_id' - -#if $name: - --name '$name' +#if $input.input_type == "archive": + mkdir 'newick_arch/' && + tar -C 'newick_arch/' -xzvf '${input.newick_arch}' > /dev/null && #end if -#if $xref_db: - --xref_db '$xref_db' -#end if -#if $xref_accession: - --xref_accession '$xref_accession' -#end if + +chakin phylogeny load_tree $match_on_name @@ -29,20 +22,51 @@ --prefix '$prefix' #end if +#if $xref_db: + --xref_db '$xref_db' +#end if + +#if $input.input_type == "archive": + #if $name: + --name '$name' + #end if + + #if $xref_accession: + --xref_accession '$xref_accession' + #end if + + '$newick' +#else + 'newick_arch/' +#end if + +'$analysis_id' + | 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" /> + <conditional name="input"> + <param name="input_type" type="select" label="Input type"> + <option value="file" selected="true">Newick file</option> + <option value="archive">Tar.gz archive of Newick files</option> + </param> + <when value="file"> + <param name="newick" label="Newick" argument="newick" type="data" format="newick" help="Newick file to load" /> + <param name="name" label="Name" argument="--name" type="text" help="The name given to the phylotree entry in the database" /> + <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)" /> + </when> + <when value="archive"> + <param name="newick_arch" label="Newicks archive" type="data" format="tar" help="Archive of Newick files to load (must be at the root of the archive)" /> + </when> + </conditional> + <!-- 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"/>