Mercurial > repos > iuc > fgbio_findswitchbackreads

comparison macros.xml @ 0:fe8744fd4198 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fgbio commit 88711b338e90adc003a90930a43df3315b2ece70
author iuc
date Tue, 04 Nov 2025 12:26:38 +0000
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-1:000000000000 0:fe8744fd4198
1 <macros>
2 <xml name="requirements">
3 <requirements>
4 <requirement type="package" version="@TOOL_VERSION@">fgbio</requirement>
5 <requirement type="package" version="1.22">samtools</requirement>
6 <yield/>
7 </requirements>
8 </xml>
9 <token name="@TOOL_VERSION@">2.1.0</token>
10 <token name="@VERSION_SUFFIX@">0</token>
11 <token name="@PROFILE@">22.05</token>
12
13 <xml name="optional_reference" token_help="" token_argument="">
14 <conditional name="addref_cond">
15 <param name="addref_select" type="select" label="Use a reference sequence">
16 <help>@HELP@</help>
17 <option value="no">No</option>
18 <option value="history">Use a genome/index from the history</option>
19 <option value="cached">Use a built-in genome</option>
20 </param>
21 <when value="no"/>
22 <when value="history">
23 <param argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/>
24 </when>
25 <when value="cached">
26 <param argument="@ARGUMENT@" type="select" label="Reference">
27 <options from_data_table="fasta_indexes">
28 <filter type="data_meta" ref="input" key="dbkey"/>
29 </options>
30 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset"/>
31 </param>
32 </when>
33 </conditional>
34 </xml>
35
36 <xml name="mandatory_reference" token_help="" token_argument="">
37 <conditional name="addref_cond">
38 <param name="addref_select" type="select" label="Use a reference sequence">
39 <help>@HELP@</help>
40 <option value="history">Use a genome/index from the history</option>
41 <option value="cached">Use a built-in genome</option>
42 </param>
43 <when value="history">
44 <param argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/>
45 </when>
46 <when value="cached">
47 <param argument="@ARGUMENT@" type="select" label="Reference">
48 <options from_data_table="fasta_indexes">
49 <filter type="data_meta" ref="input" key="dbkey"/>
50 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
51 </options>
52 </param>
53 </when>
54 </conditional>
55 </xml>
56
57 <token name="@PREPARE_FASTA_IDX@"><![CDATA[
58 #set use_ref=True
59 #if $addref_cond.addref_select == "history":
60 #if $addref_cond.ref.is_of_type('fasta'):
61 reffa="reference.fa" &&
62 ln -s '${addref_cond.ref}' \$reffa &&
63 samtools faidx \$reffa &&
64 #else:
65 reffa="reference.fa.gz" &&
66 ln -s '${addref_cond.ref}' \$reffa &&
67 {
68 samtools faidx \$reffa ||
69 {
70 echo "Failed to index compressed reference. Trying decompressed ..." 1>&2 &&
71 gzip -dc \$reffa > reference.fa &&
72 reffa="reference.fa" &&
73 samtools faidx \$reffa;
74 }
75 } &&
76 #end if
77 reffai=\$reffa.fai &&
78 #elif $addref_cond.addref_select == "cached":
79 reffa='${addref_cond.ref.fields.path}' &&
80 reffai=\$reffa.fai &&
81 #else
82 #set use_ref=False
83 #end if
84 ]]></token>
85
86 <xml name="citations">
87 <citations>
88 <citation type="doi">10.5281/zenodo.16878970</citation>
89 </citations>
90 </xml>
91
92 <xml name="version_command">
93 <version_command><![CDATA[fgbio --version 2>&1 | grep Version]]></version_command>
94 </xml>
95
96 <xml name="stdio">
97 <stdio>
98 <exit_code range="1:" level="fatal" description="Error" />
99 </stdio>
100 </xml>
101 </macros>