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comparison tree_relabeler.xml @ 2:41ada87567a2 draft default tip

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planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 8ad15943a8d365b3924ff7a5e53308cc56d7a6af
author nml
date Thu, 27 Jun 2019 15:03:13 -0400
parents 267858c28a34
children
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1:267858c28a34 2:41ada87567a2
1 <tool id="tree_relabel" name="Tree Relabeler" version="1.0.1"> 1 <tool id="tree_relabel" name="Tree Relabeler" version="1.1.0">
2 <description>Relabels the tips of a newick formatted tree.</description> 2 <description>Relabels the tips of a newick formatted tree.</description>
3 3
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.7.2">perl-bioperl</requirement> 5 <requirement type="package" version="1.7.2">perl-bioperl</requirement>
6 <requirement type="package" version="2.49">perl-getopt-long</requirement> 6 <requirement type="package" version="2.49">perl-getopt-long</requirement>
7 </requirements> 7 </requirements>
8 8 <command detect_errors="exit_code">
9 <stdio> 9 <![CDATA[
10 <exit_code range="1" level="fatal" description="Error opening a file."/> 10 $__tool_directory__/nml_tree_relabeler.pl -i '$treefile' -t '$tabfile' -o '$output' -d '$delim' $replace
11 <exit_code range="2" level="fatal" description="Error with tree format."/> 11 ]]>
12 </stdio> 12 </command>
13
14 <command interpreter="perl">
15 nml_tree_relabeler.pl -i $treefile -t $tabfile -o $output -d $delim
16 </command>
17
18 <inputs> 13 <inputs>
19 <param name="treefile" type="data" format="nhx" label="The newick formated tree file to be relabeled:" optional="false"/> 14 <param name="treefile" type="data" format="nhx" label="The newick formated tree file to be relabeled:" optional="false"/>
20 <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"/> 15 <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"/>
21 <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."/> 16 <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."/>
17 <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"/>
22 </inputs> 18 </inputs>
23 19
24 <outputs> 20 <outputs>
25 <data format="txt" name="output"/> 21 <data format="txt" name="output"/>
26 </outputs> 22 </outputs>
28 <tests> 24 <tests>
29 <test> 25 <test>
30 <param name="treefile" value="phylogeneticTree.newick.nhx"/> 26 <param name="treefile" value="phylogeneticTree.newick.nhx"/>
31 <param name="tabfile" value="tabs.txt"/> 27 <param name="tabfile" value="tabs.txt"/>
32 <output name="output" file="results"/> 28 <output name="output" file="results"/>
29 </test>
30 <test>
31 <param name="treefile" value="phylogeneticTree.newick.nhx"/>
32 <param name="tabfile" value="replacedtabs.txt"/>
33 <param name="replace" value="true"/>
34 <output name="output" file="replacedresults"/>
33 </test> 35 </test>
34 </tests> 36 </tests>
35 <help> 37 <help>
36 38
37 What it does 39 What it does
63 Tab delimted file 65 Tab delimted file
64 66
65 Desired delimiter for updated tip labels 67 Desired delimiter for updated tip labels
66 68
67 </help> 69 </help>
70 <citations>
71 </citations>
68 </tool> 72 </tool>