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comparison xpore_dataprep.xml @ 0:b64b9a2bf4f0 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
author artbio
date Wed, 26 May 2021 23:14:24 +0000
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1 <tool id="xpore_dataprep" name="xpore-dataprep" version="0.5.6+galaxy1">
2 <description></description>
3 <requirements>
4 <requirement type="package" version="0.5.6">xpore</requirement>
5 <requirement type="package" version="1.9.0">pyensembl</requirement>
6 </requirements>
7 <stdio>
8 <exit_code range="1:" level="fatal" description="Tool exception" />
9 </stdio>
10 <command detect_errors="exit_code"><![CDATA[
11 xpore-dataprep
12 --eventalign '$eventalign_reads'
13 --summary '$eventalign_summary'
14 --out_dir out
15 --n_processes \${GALAXY_SLOTS:-4} &&
16 ls -la out
17 ]]></command>
18 <inputs>
19 <param name="eventalign_reads" type="data" format="txt,tabular" label="aligned nanopore events"
20 help="a nanopolish eventalign output that aligns the nanopore events to a reference" />
21 <param name="eventalign_summary" type="data" format="txt,tabular" label="nanopore eventalign summary"
22 help="a summary of nanopolish eventalign by read_name,read_index" />
23 </inputs>
24
25 <outputs>
26 <data format="txt" name="data_index" label="data.index" from_work_dir="./out/data.index" />
27 <data format="h5" name="eventalign_hdf5" label="eventalign.hdf5" from_work_dir="./out/eventalign.hdf5" />
28 <data format="txt" name="data_log" label="data.log" from_work_dir="./out/data.log" />
29 <data format="txt" name="eventalign_log" label="eventalign.log" from_work_dir="./out/eventalign.log" />
30 <data format="txt" name="data_readcount" label="data.readcount" from_work_dir="./out/data.readcount" />
31 <data format="json" name="data_json" label="data.json" from_work_dir="./out/data.json"/>
32 </outputs>
33
34 <tests>
35 <test>
36 <param name="eventalign_reads" value="dataprep_eventaligh_reads.tsv" ftype="tabular" />
37 <param name="eventalign_summary" value="dataprep_eventaligh_summary.tsv" ftype="tabular" />
38 <output file="data.index" name="data_index" />
39 <output file="data.log" name="data_log" />
40 <output file="eventalign.log" name="eventalign_log" />
41 <output file="data.readcount" name="data_readcount" />
42 <output file="data.json" name="data_json" />
43 <output file="eventalign.hdf5" name="eventalign_hdf5" compare="sim_size" delta="3000" />
44 </test>
45 </tests>
46 <help>
47
48 **What it does**
49
50 Prepare data for differential analysis by xpore-diffmod analysis of differential RNA
51 modification across all tested positions.
52
53 .. class:: warningmark
54
55 In its current version, only preparation of data for analysis by xpore-diffmod based on a
56 **transcripts** collection reference is implemented.
57
58 **Inputs**
59
60 This tools requires the following inputs::
61
62 - the "aligned nanopore events" file returned from nanopolish eventalign (also named squiggles)
63 - the "nanopolish summary" file also returned by nanopolish eventalign
64
65 **Outputs**
66
67 3 datasets that will be required by xpore-diffmod::
68
69 - data.index
70 - data.json
71 - data.readcount
72
73 plus 3 datasets not required by xpore-diffmod::
74
75 - data.log
76 - eventalign.hdf5
77 - eventalign.log
78
79 for details on xpore-data prep, see https://xpore.readthedocs.io/en/latest/index.html
80 and https://github.com/GoekeLab/xpore
81
82 </help>
83
84 <citations>
85 <citation type="doi">10.1101/2020.06.18.160010</citation>
86 </citations>
87 </tool>