Mercurial > repos > iuc > hyphy_annotate

comparison hyphy_annotate.xml @ 4:55883bbd620e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2063bc1f8f9cb97de147b86dbe9189fc496b206a"
author iuc
date Wed, 09 Jun 2021 17:04:50 +0000
parents 2219b0ceb19e
children a016c2cb962d
comparison
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3:6f14c426f068 4:55883bbd620e
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hyphy_annotate" name="Annotate" version="@VERSION@"> 2 <tool id="hyphy_annotate" name="Annotate" version="@VERSION@+galaxy0">
3 <description>a newick tree with HyPhy</description> 3 <description>a newick tree with HyPhy</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 cp '$input_tree' input.nhx && 9 cp '$input_tree' input.nhx &&
10 cp '$compressed_msa' input.$compressed_msa.extension && 10 cp '$compressed_msa' input.$compressed_msa.extension &&
11 cp '$__tool_directory__/scripts/annotator.bf' annotator.bf && 11 cp '$__tool_directory__/scripts/annotator.bf' annotator.bf &&
12 hyphy annotator.bf 12 hyphy annotator.bf
13 input.nhx '$root' input.$compressed_msa.extension '$label' labeled_tree. 13 input.nhx '$root' input.$compressed_msa.extension '$label' labeled_tree_
14 @ERRORS@ 14 @ERRORS@
15 ]]></command> 15 ]]></command>
16 <inputs> 16 <inputs>
17 <param name="input_tree" type="data" format="nhx" label="Input tree" /> 17 <param name="input_tree" type="data" format="nhx" label="Input tree" />
18 <param name="compressed_msa" type="data" format="fasta,fasta.gz" label="Multiple alignments" /> 18 <param name="compressed_msa" type="data" format="fasta,fasta.gz" label="Multiple alignments" />
19 <param name="root" type="text" optional="false" value="REFERENCE" label="Root node" /> 19 <param name="root" type="text" optional="false" value="REFERENCE" label="Root node" />
20 <param name="label" type="text" optional="false" value="Tree" label="Label for tree" /> 20 <param name="label" type="text" optional="false" value="Tree" label="Label for tree" />
21 </inputs> 21 </inputs>
22 <outputs> 22 <outputs>
23 <data name="labeled_tree_int" format="nhx" from_work_dir="labeled_tree.int.nwk" label="Labeled tree (int)" /> 23 <data name="labeled_tree_int" format="nhx" from_work_dir="labeled_tree_int.nwk" label="${tool.name} on ${on_string} Labeled tree (int)" />
24 <data name="labeled_tree_clade" format="nhx" from_work_dir="labeled_tree.clade.nwk" label="Labeled tree (clade)" /> 24 <data name="labeled_tree_clade" format="nhx" from_work_dir="labeled_tree_clade.nwk" label="${tool.name} on ${on_string} Labeled tree (clade)" />
25 <data name="labeled_tree_full" format="nhx" from_work_dir="labeled_tree.full.nwk" label="Labeled tree (full)" /> 25 <data name="labeled_tree_full" format="nhx" from_work_dir="labeled_tree_full.nwk" label="${tool.name} on ${on_string} Labeled tree (full)" />
26 <data name="labeled_tree_json" format="hyphy_results.json" from_work_dir="labeled_tree_labels.json" label="${tool.name} on ${on_string} Labels" />
26 </outputs> 27 </outputs>
27 <tests> 28 <tests>
28 <test> 29 <test>
29 <param name="compressed_msa" ftype="fasta.gz" value="annotate-in1.fa.gz"/> 30 <param name="compressed_msa" ftype="fasta.gz" value="annotate-in1.fa.gz"/>
30 <param name="input_tree" ftype="nhx" value="annotate-in1.nhx"/> 31 <param name="input_tree" ftype="nhx" value="annotate-in1.nhx"/>
32 <param name="root" value="REFERENCE" /> 33 <param name="root" value="REFERENCE" />
33 <param name="label" value="Annotated" /> 34 <param name="label" value="Annotated" />
34 <output name="labeled_tree_int" file="annotate-out1-int.nhx" /> 35 <output name="labeled_tree_int" file="annotate-out1-int.nhx" />
35 <output name="labeled_tree_full" file="annotate-out1-full.nhx" /> 36 <output name="labeled_tree_full" file="annotate-out1-full.nhx" />
36 <output name="labeled_tree_clade" file="annotate-out1-clade.nhx" /> 37 <output name="labeled_tree_clade" file="annotate-out1-clade.nhx" />
38 <output name="labeled_tree_json" file="annotate-out1.json" />
37 </test> 39 </test>
38 </tests> 40 </tests>
39 <help><![CDATA[ 41 <help><![CDATA[
40 HyPhy Annotate 42 HyPhy Annotate
41 ============== 43 ==============