Mercurial > repos > iuc > lofreq_alnqual

comparison macros.xml @ 0:606542a18f82 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
author iuc
date Tue, 17 Dec 2019 17:26:09 -0500
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children e61c9ac190ad
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-1:000000000000 0:606542a18f82
1 <macros>
2 <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy</token>
3 <token name="@TOOL_VERSION@">2.1.3.1</token>
4 <xml name="requirements">
5 <requirements>
6 <requirement type="package" version="@TOOL_VERSION@">lofreq</requirement>
7 <yield/>
8 </requirements>
9 </xml>
10 <xml name="citations">
11 <citations>
12 <citation type="doi">10.1093/nar/gks918</citation>
13 <yield />
14 </citations>
15 </xml>
16 <token name="@PREPARE_REF@"><![CDATA[
17 #if str($reference_source.ref_selector) == 'history':
18 #set $reference_fasta_fn = 'reference.fa'
19 ln -s '$reference_source.ref' $reference_fasta_fn &&
20 lofreq faidx $reference_fasta_fn 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&
21 #else
22 #set $reference_fasta_fn = str($reference_source.ref.fields.path)
23 #end if
24 ]]></token>
25 <xml name="reference_interface">
26 <conditional name="reference_source">
27 <param name="ref_selector" type="select"
28 label="Choose the source for the reference genome">
29 <option value="cached">Locally cached</option>
30 <option value="history">History</option>
31 </param>
32 <when value="cached">
33 <param argument="--ref" type="select"
34 label="Reference genome">
35 <options from_data_table="fasta_indexes">
36 <filter type="data_meta" column="dbkey" key="dbkey" ref="reads" />
37 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
38 </options>
39 </param>
40 </when>
41 <when value="history">
42 <param argument="--ref" type="data" format="fasta" label="Reference" help="Reference sequence" />
43 </when>
44 </conditional>
45 </xml>
46 <xml name="handle_existing_alnqual">
47 <conditional name="alnqual_choice">
48 <param name="alnquals_to_use" type="select"
49 label="Use the following alignment quality scores">
50 <option value="">Base and indel alignment qualities (BAQ and IDAQ)</option>
51 <option value="-A">Only base alignment qualities (BAQ)</option>
52 <option value="-B">Only indel alignment qualities (IDAQ)</option>
53 </param>
54 <when value="-B">
55 <param name="extended_baq" type="hidden" value="" />
56 </when>
57 <when value="">
58 <param argument="-e" name="extended_baq" type="boolean" checked="true" truevalue="" falsevalue="-e"
59 label="If BAQ needs to be computed, calculate extended BAQ?" />
60 </when>
61 <when value="-A">
62 <param argument="-e" name="extended_baq" type="boolean" checked="true" truevalue="" falsevalue="-e"
63 label="If BAQ needs to be computed, calculate extended BAQ?" />
64 </when>
65 </conditional>
66 </xml>
67 <xml name="handle_alnqual" token_mode="Use">
68 <conditional name="alnqual_choice">
69 <param name="alnquals_to_use" type="select"
70 label="@MODE@ the following alignment quality scores">
71 <option value="">Base and indel alignment qualities (BAQ and IDAQ)</option>
72 <option value="-A">Only base alignment qualities (BAQ)</option>
73 <option value="-B">Only indel alignment qualities (IDAQ)</option>
74 </param>
75 <when value="-B">
76 <param name="extended_baq" type="hidden" value="" />
77 </when>
78 <when value="">
79 <param argument="-e" name="extended_baq" type="boolean" checked="true" truevalue="" falsevalue="-e"
80 label="Use extended BAQ?" />
81 </when>
82 <when value="-A">
83 <param argument="-e" name="extended_baq" type="boolean" checked="true" truevalue="" falsevalue="-e"
84 label="Use extended BAQ?" />
85 </when>
86 </conditional>
87 </xml>
88 </macros>