annotate macros.xml @ 0:30fc9f2bcbe4 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
author iuc
date Tue, 19 Jan 2021 20:30:21 +0000
parents
children 1d4f065fa0ef
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
2 <macros>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
3 <token name="@TOOL_VERSION@">1.0.4</token>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
4 <token name="@PROFILE@">18.01</token>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
5 <xml name="requirements">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
6 <requirements>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
7 <requirement type="package" version="1.9">samtools</requirement>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
8 <requirement type="package" version="@TOOL_VERSION@">irissv</requirement>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
9 </requirements>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
10 </xml>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
11 <xml name="version_command">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
12 <version_command>iris</version_command>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
13 </xml>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
14 <xml name="citations">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
15 <citations>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
16 <citation type="bibtex">@online{iris,
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
17 author = {Melanie Kirsche},
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
18 title = {iris},
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
19 year = 2021,
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
20 url = {https://github.com/mkirsche/Iris},
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
21 urldate = {2021-01-13}
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
22 }</citation>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
23 </citations>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
24 </xml>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
25
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
26 <!--
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
27 command
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
28 -->
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
29
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
30 <token name="@REF_FASTA@"><![CDATA[
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
31 #if $reference_source.reference_source_selector == 'history':
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
32 ln -f -s '$reference_source.ref_file' reference.fa &&
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
33 #else:
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
34 ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
35 #end if
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
36 ]]></token>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
37
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
38 <xml name="reference">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
39 <conditional name="reference_source">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
40 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
41 <option value="cached">Use a built-in genome</option>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
42 <option value="history">Use a genome from history</option>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
43 </param>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
44 <when value="cached">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
45 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
46 <options from_data_table="all_fasta">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
47 <filter type="sort_by" column="2"/>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
48 <validator type="no_options" message="No reference genomes are available"/>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
49 </options>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
50 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
51 </param>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
52 </when>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
53 <when value="history">
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
54 <param name="ref_file" type="data" format="fasta,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference"/>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
55 </when>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
56 </conditional>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
57 </xml>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
58 <!--
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
59 Help
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
60 -->
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
61
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
62 <token name="@WID@"><![CDATA[
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
63 *irissv*, or Implement for Refining Insertion Sequences is a tool which corrects the sequences of structural variant calls (currently only insertions). It uses FalconSense to obtain consensus sequences of the reads surrounding each variant and aligns these sequences back to the reference at the insertion site, resulting in an insertion which takes into account the aggregate information of all supporting reads.
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
64 ]]></token>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
65 <token name="@REFERENCES@"><![CDATA[
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
66 More information is available in the `github <https://github.com/mkirsche/Iris>`_.
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
67 ]]></token>
30fc9f2bcbe4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 80a64f32dbd465d72a10e69a749def733dea8ffc"
iuc
parents:
diff changeset
68 </macros>