Mercurial > repos > iuc > cooc_mutbamscan

annotate macros.xml @ 0:373c1735d31f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
author iuc
date Thu, 11 Aug 2022 13:50:37 +0000
parents
children 9f1660129403
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
2 <macros>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
3 <token name="@TOOL_VERSION@">0.2</token>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
4 <token name="@VERSION_SUFFIX@">0</token>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
5 <token name="@PROFILE@">21.01</token>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
6 <xml name="biotools">
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
7 <xrefs>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
8 <xref type="bio.tools">cojac</xref>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
9 </xrefs>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
10 </xml>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
11 <xml name="requirements">
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
12 <requirements>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
13 <requirement type="package" version="@TOOL_VERSION@">cojac</requirement>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
14 <yield/>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
15 </requirements>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
16 </xml>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
17 <xml name="version">
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
18 <version_command>echo @TOOL_VERSION@</version_command>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
19 </xml>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
20 <xml name="vocdir_input">
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
21 <conditional name="vocdir_option">
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
22 <param name="choice" type="select"
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
23 label="Source of YAML files with definition of the variant of concerns"
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
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.">
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
25 <option value="cache">Definitions shipped with the tool (can be outdated)</option>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
26 <option value="custom">From history</option>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
27 </param>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
28 <when value="cache"/>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
29 <when value="custom">
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
30 <param name="voc_file" type="data" format="yaml" multiple="true"
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
31 label="YAML defining the variant of concern"/>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
32 </when>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
33 </conditional>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
34 </xml>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
35 <token name="@VOCDIR_COMMAND@"><![CDATA[
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
36 #if $vocdir_option.choice == 'custom'
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
37 #set vocdir = 'voc/'
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
38 #set file_paths1 = []
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
39 mkdir -p voc &&
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
40 #for $input_file in $voc_file
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
41 #set $file_path = $vocdir + $input_file.element_identifier
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
42 ln -s '$input_file' '$file_path' &&
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
43 $file_paths1.append($file_path)
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
44 #end for
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
45 #else
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
46 DB_PATH="\$(dirname "\$(dirname "\$(which cooc-mutbamscan)")")/share/cojac" &&
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
47 ln -s "\$DB_PATH" db &&
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
48 #set $vocdir = 'db/voc'
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
49 #end if
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
50 ]]></token>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
51 <token name="@HELP_HEADER@"><![CDATA[
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
52 What it does
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
53 ============
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
54
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
55 The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples.
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
56 ]]></token>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
57 <xml name="citations">
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
58 <citations>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
59 <citation type="doi">10.1101/2021.01.08.21249379</citation>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
60 </citations>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
61 </xml>
373c1735d31f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
parents:
diff changeset
62 </macros>