Mercurial > repos > bgruening > nanopolish_variants

comparison macros.xml @ 8:bec636361cfd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
author bgruening
date Thu, 30 Nov 2023 17:57:59 +0000
parents 63af3144371a
children
comparison
equal deleted inserted replaced
7:a3afc5f0a96c 8:bec636361cfd
1 <macros> 1 <macros>
2 <token name="@VERSION@">0.13.2</token> 2 <token name="@VERSION@">0.14.0</token>
3 <token name="@VERSION_SUFFIX@">0</token>
4 <token name="@PROFILE@">22.01</token>
5
3 <xml name="requirements"> 6 <xml name="requirements">
4 <requirements> 7 <requirements>
5 <requirement type="package" version="@VERSION@">nanopolish</requirement> 8 <requirement type="package" version="@VERSION@">nanopolish</requirement>
6 <yield/> 9 <yield/>
7 </requirements> 10 </requirements>
17 <output name="output_index_fai" file="reads.fasta.index.fai" /> 20 <output name="output_index_fai" file="reads.fasta.index.fai" />
18 <output name="output_index_gzi" file="reads.fasta.index.gzi" /> 21 <output name="output_index_gzi" file="reads.fasta.index.gzi" />
19 <output name="output_index_readdb" file="reads.fasta.index.readdb" /> 22 <output name="output_index_readdb" file="reads.fasta.index.readdb" />
20 --> 23 -->
21 24
25
26 <token name="@PREPROCESS_INPUTS@"><![CDATA[
27 ln -s '$input_merged' reads.fasta &&
28
29 mkdir fast5_files &&
30 #if $input_reads_raw.extension == 'fast5':
31 ln -s '$input_reads_raw' fast5_files/read1.fast5 &&
32
33 #else if $input_reads_raw.extension == 'fast5.tar':
34 ln -s '$input_reads_raw' fast5_files.tar &&
35 tar -xf fast5_files.tar -C fast5_files &&
36
37 #else if $input_reads_raw.extension == 'fast5.tar.bz2':
38 ln -s '$input_reads_raw' fast5_files.tar.bz2 &&
39 tar -xjf fast5_files.tar.bz2 -C fast5_files &&
40
41 #else if $input_reads_raw.extension == 'fast5.tar.xz':
42 ln -s '$input_reads_raw' fast5_files.tar.xz &&
43 tar -xf fast5_files.tar.xz -C fast5_files &&
44
45 #else if $input_reads_raw.extension == 'fast5.tar.gz':
46 ln -s '$input_reads_raw' fast5_files.tar.gz &&
47 tar -xzf fast5_files.tar.gz -C fast5_files &&
48
49 #else:
50 echo 'Unsupported fast5 input type' &&
51 exit 1 &&
52
53 #end if
54
55 nanopolish index
56 -d fast5_files/
57 #if $adv.input_seq_summary:
58 -s '$adv.input_seq_summary'
59 #end if
60 reads.fasta &&
61
62 ln -s '$b' reads.bam &&
63 ln -s '${b.metadata.bam_index}' reads.bam.bai &&
64 #if $reference_source.reference_source_selector == 'history':
65 ln -f -s '$reference_source.ref_file' genome.fa &&
66 #else:
67 ln -f -s '$reference_source.ref_file.fields.path' genome.fa &&
68 #end if
69 ]]></token>
70
22 <xml name="citations"> 71 <xml name="citations">
23 <citations> 72 <citations>
24 <citation type="doi">10.1038/nmeth.3444</citation> 73 <citation type="doi">10.1038/nmeth.3444</citation>
25 <citation type="doi">10.1038/nmeth.4184</citation> 74 <citation type="doi">10.1038/nmeth.4184</citation>
26 <yield /> 75 <yield />