Mercurial > repos > iuc > cooc_pubmut

comparison macros.xml @ 1:f193fef5b19d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6
author iuc
date Mon, 31 Jul 2023 15:23:17 +0000
parents d04ea6b052c5
children 0349d8981030
comparison
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0:d04ea6b052c5 1:f193fef5b19d
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@TOOL_VERSION@">0.2</token> 3 <token name="@TOOL_VERSION@">0.9</token>
4 <token name="@VERSION_SUFFIX@">0</token> 4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@PROFILE@">21.01</token> 5 <token name="@PROFILE@">21.01</token>
6 <xml name="biotools"> 6 <xml name="biotools">
7 <xrefs> 7 <xrefs>
8 <xref type="bio.tools">cojac</xref> 8 <xref type="bio.tools">cojac</xref>
16 </xml> 16 </xml>
17 <xml name="version"> 17 <xml name="version">
18 <version_command>echo @TOOL_VERSION@</version_command> 18 <version_command>echo @TOOL_VERSION@</version_command>
19 </xml> 19 </xml>
20 <xml name="vocdir_input"> 20 <xml name="vocdir_input">
21 <conditional name="vocdir_option"> 21 <conditional name="voc_source">
22 <param name="choice" type="select" 22 <param name="choice" type="select"
23 label="Source of YAML files with definition of the variant of concerns" 23 label="Source of lineage definitions"
24 help="Cojac ships with a directory with variant definitions yaml files (https://github.com/cbg-ethz/cojac/tree/master/voc), which the tool can access internally. You can also download the latest version of the yaml files from https://github.com/phe-genomics/variant_definitions and use it as a custom yamls defining the variant of concerns."> 24 help="Cojac detects lineage evidence based on lineage mutation patterns deined in tool-specific yaml format. You can choose between the (possibly outdated) definitions shipped with the tool or definitions provided as a collection of yaml datasets in your history. See the tool help below for more details.">
25 <option value="cache">Definitions shipped with the tool (can be outdated)</option> 25 <option value="builtin">Lineage definitions shipped with the tool</option>
26 <option value="custom">From history</option> 26 <option value="custom">YAML dataset collection in history</option>
27 </param> 27 </param>
28 <when value="cache"/> 28 <when value="builtin"/>
29 <when value="custom"> 29 <when value="custom">
30 <param name="voc_file" type="data" format="yaml" multiple="true" 30 <param name="collection" type="data_collection" collection_type="list" format="yaml" label="Collection of lineage definitions" />
31 label="YAML defining the variant of concern"/>
32 </when> 31 </when>
33 </conditional> 32 </conditional>
34 </xml> 33 </xml>
35 <token name="@VOCDIR_COMMAND@"><![CDATA[ 34 <token name="@VOCDIR_COMMAND@"><![CDATA[
36 #if $vocdir_option.choice == 'custom' 35 #if $voc_config.choice == 'custom'
37 #set vocdir = 'voc/'
38 #set file_paths1 = []
39 mkdir -p voc && 36 mkdir -p voc &&
40 #for $input_file in $voc_file 37 #for $input_file in $voc_config.collection
41 #set $file_path = $vocdir + $input_file.element_identifier 38 ln -s '$input_file' 'voc/$input_file.element_identifier' &&
42 ln -s '$input_file' '$file_path' &&
43 $file_paths1.append($file_path)
44 #end for 39 #end for
45 #else 40 #else
46 DB_PATH="\$(dirname "\$(dirname "\$(which cooc-mutbamscan)")")/share/cojac" && 41 DB_PATH="\$(dirname "\$(dirname "\$(which cojac)")")/share/cojac/voc" &&
47 ln -s "\$DB_PATH" db && 42 ln -s "\$DB_PATH" voc &&
48 #set $vocdir = 'db/voc'
49 #end if 43 #end if
50 ]]></token> 44 ]]></token>
51 <token name="@HELP_HEADER@"><![CDATA[ 45 <token name="@HELP_HEADER@"><![CDATA[
52 What it does 46 What it does
53 ============ 47 ============