# HG changeset patch # User nml # Date 1561662193 14400 # Node ID 41ada87567a21adcb1e67e5469af7d74b5835828 # Parent 267858c28a34647564806bcb05a19267a0841db1 planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 8ad15943a8d365b3924ff7a5e53308cc56d7a6af diff -r 267858c28a34 -r 41ada87567a2 test-data/replacedresults --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/replacedresults Thu Jun 27 15:03:13 2019 -0400 @@ -0,0 +1,1 @@ +(newreference outbreak1 year1 location1:0.29121884); \ No newline at end of file diff -r 267858c28a34 -r 41ada87567a2 test-data/replacedtabs.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/replacedtabs.txt Thu Jun 27 15:03:13 2019 -0400 @@ -0,0 +1,1 @@ +reference newreference outbreak1 year1 location1 diff -r 267858c28a34 -r 41ada87567a2 tree_relabeler.xml --- a/tree_relabeler.xml Thu Jun 20 12:45:02 2019 -0400 +++ b/tree_relabeler.xml Thu Jun 27 15:03:13 2019 -0400 @@ -1,24 +1,20 @@ -<tool id="tree_relabel" name="Tree Relabeler" version="1.0.1"> +<tool id="tree_relabel" name="Tree Relabeler" version="1.1.0"> <description>Relabels the tips of a newick formatted tree.</description> <requirements> <requirement type="package" version="1.7.2">perl-bioperl</requirement> <requirement type="package" version="2.49">perl-getopt-long</requirement> </requirements> - - <stdio> - <exit_code range="1" level="fatal" description="Error opening a file."/> - <exit_code range="2" level="fatal" description="Error with tree format."/> - </stdio> - - <command interpreter="perl"> - nml_tree_relabeler.pl -i $treefile -t $tabfile -o $output -d $delim - </command> - + <command detect_errors="exit_code"> + <![CDATA[ + $__tool_directory__/nml_tree_relabeler.pl -i '$treefile' -t '$tabfile' -o '$output' -d '$delim' $replace + ]]> + </command> <inputs> <param name="treefile" type="data" format="nhx" label="The newick formated tree file to be relabeled:" optional="false"/> <param name="tabfile" type="data" format="txt" label="The tab separated file containing the current labels and the info to be added to the labels" optional="false"/> <param name="delim" type="text" label="Delimiter for new tip labels (space, _, etc)" optional="true" help="If left blank, labels of updated tips will be separated by spaces."/> + <param name="replace" truevalue='--replace' falsevalue='' type="boolean" label="Find and Replace current tip" help="If false, will append to current tip. If true, will replace current tip"/> </inputs> <outputs> @@ -31,6 +27,12 @@ <param name="tabfile" value="tabs.txt"/> <output name="output" file="results"/> </test> + <test> + <param name="treefile" value="phylogeneticTree.newick.nhx"/> + <param name="tabfile" value="replacedtabs.txt"/> + <param name="replace" value="true"/> + <output name="output" file="replacedresults"/> + </test> </tests> <help> @@ -65,4 +67,6 @@ Desired delimiter for updated tip labels </help> + <citations> + </citations> </tool>