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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 59e86ba957774b2fb86b3f5dbd7be24f99dd60f7
author artbio
date Sun, 15 May 2022 15:11:49 +0000
parents ff53cf0d0bbd
children
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1:ff53cf0d0bbd 2:a5758bb680c8
1 <tool id="xpore_dataprep" name="xpore-dataprep" version="0.5.6+galaxy2"> 1 <tool id="xpore_dataprep" name="xpore-dataprep" version="2.1+galaxy0">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.5.6">xpore</requirement> 4 <requirement type="package" version="2.1">xpore</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:" level="fatal" description="Tool exception" /> 7 <exit_code range="1:" level="fatal" description="Tool exception" />
8 </stdio> 8 </stdio>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 xpore-dataprep 10 xpore dataprep
11 --eventalign '$eventalign_reads' 11 --eventalign '$eventalign_reads'
12 --summary '$eventalign_summary'
13 --out_dir out 12 --out_dir out
14 --n_processes \${GALAXY_SLOTS:-4} && 13 --n_processes \${GALAXY_SLOTS:-4} &&
15 mv ./out/data.index $data_index && 14 mv ./out/data.index $data_index &&
16 mv ./out/eventalign.hdf5 $eventalign_hdf5 &&
17 mv ./out/data.log $data_log && 15 mv ./out/data.log $data_log &&
18 mv ./out/eventalign.log $eventalign_log && 16 mv ./out/eventalign.index $eventalign_index &&
19 mv ./out/data.readcount $data_readcount && 17 mv ./out/data.readcount $data_readcount &&
20 mv ./out/data.json $data_json 18 mv ./out/data.json $data_json
21 19
22 20
23 ]]></command> 21 ]]></command>
24 <inputs> 22 <inputs>
25 <param name="eventalign_reads" type="data" format="txt,tabular" label="aligned nanopore events" 23 <param name="eventalign_reads" type="data" format="txt,tabular" label="aligned nanopore events"
26 help="a nanopolish eventalign output that aligns the nanopore events to a reference" /> 24 help="a nanopolish eventalign output that aligns the nanopore events to a reference" />
27 <param name="eventalign_summary" type="data" format="txt,tabular" label="nanopore eventalign summary"
28 help="a summary of nanopolish eventalign by read_name,read_index" />
29 </inputs> 25 </inputs>
30 26
31 <outputs> 27 <outputs>
32 <data format="txt" name="data_index" label="data.index" /> 28 <data format="txt" name="data_index" label="data.index" />
33 <data format="h5" name="eventalign_hdf5" label="eventalign.hdf5" />
34 <data format="txt" name="data_log" label="data.log" /> 29 <data format="txt" name="data_log" label="data.log" />
35 <data format="txt" name="eventalign_log" label="eventalign.log" />
36 <data format="txt" name="data_readcount" label="data.readcount" /> 30 <data format="txt" name="data_readcount" label="data.readcount" />
31 <data format="txt" name="eventalign_index" label="eventalign.index" />
37 <data format="json" name="data_json" label="data.json" /> 32 <data format="json" name="data_json" label="data.json" />
38 </outputs> 33 </outputs>
39 34
40 <tests> 35 <tests>
41 <test> 36 <test>
42 <param name="eventalign_reads" value="dataprep_eventaligh_reads.tsv" ftype="tabular" /> 37 <param name="eventalign_reads" value="dataprep_eventaligh_reads.tsv" ftype="tabular" />
43 <param name="eventalign_summary" value="dataprep_eventaligh_summary.tsv" ftype="tabular" />
44 <output file="data.index" name="data_index" /> 38 <output file="data.index" name="data_index" />
39 <output file="eventalign.index" name="eventalign_index" />
45 <output file="data.log" name="data_log" /> 40 <output file="data.log" name="data_log" />
46 <output file="eventalign.log" name="eventalign_log" />
47 <output file="data.readcount" name="data_readcount" /> 41 <output file="data.readcount" name="data_readcount" />
48 <output file="data.json" name="data_json" /> 42 <output file="data.json" name="data_json" />
49 <output file="eventalign.hdf5" name="eventalign_hdf5" compare="sim_size" delta="3000" />
50 </test> 43 </test>
51 </tests> 44 </tests>
52 <help> 45 <help>
53 46
54 **What it does** 47 **What it does**
61 In its current version, only preparation of data for analysis by xpore-diffmod based on a 54 In its current version, only preparation of data for analysis by xpore-diffmod based on a
62 **transcripts** collection reference is implemented. 55 **transcripts** collection reference is implemented.
63 56
64 **Inputs** 57 **Inputs**
65 58
66 This tools requires the following inputs:: 59 This tools requires the following input::
67 60
68 - the "aligned nanopore events" file returned from nanopolish eventalign (also named squiggles) 61 - the "aligned nanopore events" file returned from nanopolish eventalign (also named squiggles)
69 - the "nanopolish summary" file also returned by nanopolish eventalign
70 62
71 **Outputs** 63 **Outputs**
72 64
73 3 datasets that will be required by xpore-diffmod:: 65 3 datasets that will be required by xpore-diffmod::
74 66
75 - data.index 67 - data.index
76 - data.json 68 - data.json
77 - data.readcount 69 - data.readcount
78 70
79 plus 3 datasets not required by xpore-diffmod:: 71 plus 2 datasets not required by xpore-diffmod::
80 72
81 - data.log 73 - data.log
82 - eventalign.hdf5 74 - eventalign.index
83 - eventalign.log
84 75
85 for details on xpore-data prep, see https://xpore.readthedocs.io/en/latest/index.html 76 for details on xpore-data prep, see https://xpore.readthedocs.io/en/latest/index.html
86 and https://github.com/GoekeLab/xpore 77 and https://github.com/GoekeLab/xpore
87 78
88 </help> 79 </help>