annotate macros.xml @ 2:74d1e42a87e0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
author iuc
date Wed, 01 Sep 2021 17:56:58 +0000
parents d1dd7d1b07f6
children d82fc956ab4d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
1 <macros>
2
74d1e42a87e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents: 0
diff changeset
2 <!-- same version number is used for nextclade and nextalign releases, even though they are distinct tools -->
74d1e42a87e0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents: 0
diff changeset
3 <token name="@TOOL_VERSION@">1.3.0</token>
0
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
4 <xml name="citations">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
5 <citations>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
6 <citation type="bibtex">@online{nextclade,
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
7 title={nextclade},
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
8 year = 2021,
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
9 url = {https://github.com/nextstrain/nextclade},
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
10 urldate = {2021-03-26}
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
11 }
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
12 </citation>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
13 <yield />
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
14 </citations>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
15 </xml>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
16
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
17 <!--
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
18 command
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
19 -->
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
20 <token name="@REF_FASTA@"><![CDATA[
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
21 #if $reference_source.reference_source_selector == 'history':
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
22 ln -f -s '$reference_source.ref_file' reference.fa &&
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
23 #else:
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
24 ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
25 #end if
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
26 ]]></token>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
27
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
28 <!--
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
29 inputs
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
30 -->
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
31
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
32 <xml name="reference">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
33 <conditional name="reference_source">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
34 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
35 <option value="cached">Use a built-in genome</option>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
36 <option value="history">Use a genome from history</option>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
37 </param>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
38 <when value="cached">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
39 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
40 <options from_data_table="all_fasta">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
41 <filter type="sort_by" column="2"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
42 </options>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
43 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
44 </param>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
45 </when>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
46 <when value="history">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
47 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
48 </when>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
49 </conditional>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
50 </xml>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
51
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
52 <!--
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
53 help
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
54 -->
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
55 <token name="@NEXTCLADE@"><![CDATA[
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
56 Nextclade is a tool that identifies differences between your sequences and a reference sequence, uses these differences to assign your sequences to clades, and reports potential sequence quality issues in your data.
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
57 You can use the tool to analyze sequences before you upload them to a database, or if you want to assign Nextstrain clades to a set of sequences.
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
58 ]]></token>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
59
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
iuc
parents:
diff changeset
60 </macros>