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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit 00d6705a08a9d9cc9093846b730c4dec247cf5e7
author iuc
date Sat, 18 May 2024 20:34:13 +0000
parents 1d4f065fa0ef
children
comparison
equal deleted inserted replaced
2:b4b6b660293a 3:3242dbeea69c
1 <?xml version="1.0"?>
2 <macros> 1 <macros>
3 <token name="@TOOL_VERSION@">1.0.4</token> 2 <token name="@TOOL_VERSION@">1.0.5</token>
4 <token name="@PROFILE@">20.01</token> 3 <token name="@PROFILE@">20.01</token>
5 <xml name="requirements"> 4 <xml name="requirements">
6 <requirements> 5 <requirements>
7 <requirement type="package" version="1.9">samtools</requirement> 6 <requirement type="package" version="1.19.2">samtools</requirement>
8 <requirement type="package" version="@TOOL_VERSION@">irissv</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">irissv</requirement>
9 </requirements> 8 </requirements>
10 </xml> 9 </xml>
11 <xml name="version_command"> 10 <xml name="version_command">
12 <version_command>iris</version_command> 11 <version_command>iris</version_command>
20 url = {https://github.com/mkirsche/Iris}, 19 url = {https://github.com/mkirsche/Iris},
21 urldate = {2021-01-13} 20 urldate = {2021-01-13}
22 }</citation> 21 }</citation>
23 </citations> 22 </citations>
24 </xml> 23 </xml>
25
26 <!-- 24 <!--
27 command 25 command
28 --> 26 -->
29
30 <token name="@REF_FASTA@"><![CDATA[ 27 <token name="@REF_FASTA@"><![CDATA[
31 #if $reference_source.reference_source_selector == 'history': 28 #if $reference_source.reference_source_selector == 'history':
32 #set reference = $reference_source.ref_file 29 #set reference = $reference_source.ref_file
33 #set ext = $reference.ext 30 #set ext = $reference.ext
34 #else: 31 #else:
39 gunzip -c '$reference' > reference && 36 gunzip -c '$reference' > reference &&
40 #else: 37 #else:
41 ln -sf '$reference' reference && 38 ln -sf '$reference' reference &&
42 #end if 39 #end if
43 ]]></token> 40 ]]></token>
44
45 <xml name="reference"> 41 <xml name="reference">
46 <conditional name="reference_source"> 42 <conditional name="reference_source">
47 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> 43 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
48 <option value="cached">Use a built-in genome</option> 44 <option value="cached">Use a built-in genome</option>
49 <option value="history">Use a genome from history</option> 45 <option value="history">Use a genome from history</option>
63 </conditional> 59 </conditional>
64 </xml> 60 </xml>
65 <!-- 61 <!--
66 Help 62 Help
67 --> 63 -->
68
69 <token name="@WID@"><![CDATA[ 64 <token name="@WID@"><![CDATA[
70 *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. 65 *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.
71 ]]></token> 66 ]]></token>
72 <token name="@REFERENCES@"><![CDATA[ 67 <token name="@REFERENCES@"><![CDATA[
73 More information is available in the `github <https://github.com/mkirsche/Iris>`_. 68 More information is available in the `github <https://github.com/mkirsche/Iris>`_.