Mercurial > repos > iuc > ont_fast5_api_fast5_subset

comparison fast5_subset.xml @ 0:eb1f4aa80c72 draft

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"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit 84504d6786e9edf00367739210d6bae78cb42cc8"
author iuc
date Mon, 08 Jun 2020 15:57:10 -0400
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-1:000000000000 0:eb1f4aa80c72
1 <?xml version="1.0"?>
2 <tool id="ont_fast5_api_fast5_subset" name="Fast5 subset" version="@TOOL_VERSION@+galaxy0" profile="18.01">
3 <description>of multi read file</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <version_command></version_command>
9 <command detect_errors="exit_code"><![CDATA[
10 ## initialize
11 mkdir data &&
12 #for $num, $current in enumerate($input):
13 ln -s '$current' './data/batch${num}.fast5' &&
14 #end for
15
16 ## run
17 fast5_subset
18 ## required
19 --input ./data
20 -s ./results
21 --read_id_list '$read_id_list'
22 ## optional
23 --batch_size $batch_size
24 -t \${GALAXY_SLOTS:-4}
25 ]]></command>
26 <inputs>
27 <param argument="--input" type="data" format="fast5" multiple="true"
28 label="Select multi read input file(s)"/>
29 <param argument="--read_id_list" type="data" format="tabular"
30 label="Select file with read_ids" help="Either containing 1 read_id per line or a tabular file with a column named read_id."/>
31 <param argument="--batch_size" type="integer" value="4000" min="1"
32 label="Set batch size" help="Number of single reads to include in each multi read file"/>
33 </inputs>
34 <outputs>
35 <data name="out_results" format="fast5">
36 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fast5" format="fast5" directory="results" assign_primary_output="true" visible="true"/>
37 </data>
38 </outputs>
39 <tests>
40 <test expect_num_outputs="1">
41 <param name="input" value="batch.fast5"/>
42 <param name="read_id_list" value="list.txt"/>
43 <param name="batch_size" value="2"/>
44 <output name="out_results">
45 <assert_contents>
46 <has_size value="23304"/>
47 </assert_contents>
48 <!-- batch0 is represented by out_results -->
49 <discovered_dataset designation="batch1" ftype="fast5">
50 <assert_contents>
51 <has_size value="17328"/>
52 </assert_contents>
53 </discovered_dataset>
54 </output>
55 </test>
56 </tests>
57 <help><![CDATA[
58 .. class:: infomark
59
60 **What it does**
61
62 @WID@
63
64 fast5_subset extracts reads from multi_read_fast5_file(s) based on a list of read IDs.
65
66 **Input**
67
68 A multi read file in FAST5 format and a list of read IDs that should be extracted.
69
70 **Output**
71
72 A multi read file in FAST5 format containing a subset of the input file.
73
74 .. class:: infomark
75
76 **References**
77
78 @REFERENCES@
79 ]]></help>
80 <expand macro="citations"/>
81 </tool>