Mercurial > repos > jdv > albacore

comparison albacore_denoise.xml @ 1:0a4f83207e53 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
author jdv
date Wed, 06 Sep 2017 12:12:52 -0400
parents
children b658298e65d8
comparison
equal deleted inserted replaced
0:f8e25d69167d 1:0a4f83207e53
1 <tool id="albacore_denoise" name="Albacore de-noise" version="0.001">
2
3 <description>Filter noise from barcode bins</description>
4
5 <!-- ***************************************************************** -->
6
7 <!--
8 <requirements>
9 <requirement type="package" version="1.2.6">albacore</requirement>
10 </requirements>
11 -->
12
13 <!-- ***************************************************************** -->
14
15 <version_command>echo "0.001"</version_command>
16
17 <!-- ***************************************************************** -->
18
19 <command detect_errors="aggressive">
20 <![CDATA[
21
22 perl $__tool_directory__/denoise.pl
23
24 --table $table
25
26 #if $filter.type == 'topN'
27 --n_keep ${filter.n_keep}
28 #else
29 --min_score ${filter.min_score}
30 --min_frac ${filter.min_frac}
31 #end if
32
33 $remove_unclassified
34
35 #for $input in $inputs
36 --input ${input}
37 --name ${input.name}
38 #end for
39
40 --summary $summary
41
42 ]]>
43 </command>
44
45 <!-- ***************************************************************** -->
46
47 <inputs>
48
49 <param name="inputs" type="data_collection" collection_type="list" format="fast5_archive" label="Input reads" multiple="true" />
50 <param name="table" type="data" format="tabular" label="Read table" />
51 <conditional name="filter">
52 <param name="type" type="select" label="Filtering type">
53 <option value="cutoffs" selected="true">By cutoff</option>
54 <option value="topN">Top N bins</option>
55 </param>
56 <when value="cutoffs">
57 <param name="min_score" value="70" type="float" min="0" max="100" label="Minimum average score (0-100)" />
58 <param name="min_frac" value="0.05" type="float" min="0" label="Minimum fraction of average count" />
59 </when>
60 <when value="topN">
61 <param name="n_keep" value="1" type="integer" min="1" label="Number of top bins to keep" />
62 </when>
63 </conditional>
64 <param name="remove_unclassified" type="boolean" checked="true" truevalue="--remove_unclassified" falsevalue="" label="Remove unclassified reads" />
65
66 </inputs>
67
68 <!-- ***************************************************************** -->
69
70 <outputs>
71
72 <collection type="list" name="outputs" label="${tool.name} on ${on_string} (reads)">
73 <discover_datasets pattern="(?P&lt;name&gt;.*)\.fast5\.tar\.gz$" directory="outputs" format="fast5_archive" />
74 </collection>
75
76 <data name="summary" format="tabular" label="${tool.name} on ${on_string} (summary)" />
77
78 </outputs>
79
80 <!-- ***************************************************************** -->
81
82 <!--
83 <tests>
84 <test>
85 <param name="input" value="test_data.fast5.tar.gz" ftype="fast5_archive" />
86 <output name="output" file="test_data.fastq" compare="diff" />
87 </test>
88 </tests>
89 -->
90
91 <!-- ***************************************************************** -->
92
93 <help>
94 <![CDATA[
95
96 **Description**
97
98 This script will filter "noise" bins from the barcoded output of Albacore
99 based on read counts and mean quality scores for each barcode bin. It can
100 either filter the top N bins (if you know the number of barcodes in your
101 sample) or filter based on minimum read count (as ratio to average value over
102 all bin) and minimum average score.
103
104 ]]>
105 </help>
106
107 <!-- ***************************************************************** -->
108
109 <citations>
110 </citations>
111
112 </tool>