Mercurial > repos > iuc > ivar_trim

annotate ivar_trim.xml @ 2:9ebf6615d8f7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
author iuc
date Wed, 22 Apr 2020 10:01:06 +0000
parents d2f4ea1496a3
children f78f33bdfce1
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
1 <tool id="ivar_trim" name="ivar trim" version="@VERSION@+galaxy0">
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
2 <description>Trim reads in aligned BAM</description>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
3 <macros>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
5 </macros>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
6 <expand macro="requirements" />
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
7 <expand macro="version_command" />
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
2
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
9 #if $primer.source == "history"
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
10 ln -s '$primer.input_bed' bed.bed &&
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
11 #else
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
12 ln -s '$primer.cached_bed.fields.path' bed.bed &&
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
13 #end if
0
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
14 ln -s '$input_bam' sorted.bam &&
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
15 ivar trim
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
16 -i sorted.bam
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
17 -b bed.bed
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
18 -m $min_len
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
19 -q $min_qual
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
20 -s $window_width
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
21 $inc_primers
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
22 -p trimmed &&
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
23 samtools sort -@ \${GALAXY_SLOTS:-1} -o trimmed.sorted.bam trimmed.bam &&
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
24 samtools index -@ \${GALAXY_SLOTS:-1} trimmed.sorted.bam
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
25 ]]> </command>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
26 <inputs>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
27 <param name="input_bam" argument="-i" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/>
2
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
28 <conditional name="primer">
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
29 <param label="Source of primer information" name="source" type="select">
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
30 <option value="history" selected="true">History</option>
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
31 <option value="cached">Built-in</option>
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
32 </param>
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
33 <when value="history">
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
34 <param name="input_bed" argument="-b" type="data" format="bed" label="BED file with primer sequences and positions"/>
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
35 </when>
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
36 <when value="cached">
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
37 <param name="cached_bed" type="select" label="Primer scheme name" help="Select primer scheme bed file from a list">
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
38 <options from_data_table="primer_scheme_bedfiles">
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
39 <filter type="sort_by" column="1" />
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
40 <validator type="no_options" message="No primer schemes are available" />
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
41 </options>
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
42 </param>
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
43 </when>
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
44 </conditional>
0
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
45 <param name="min_len" argument="-m" type="integer" min="0" value="30" label="Minimum length of read to retain after trimming"/>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
46 <param name="min_qual" argument="-q" type="integer" min="0" value="20" label="Minimum quality threshold for sliding window to pass"/>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
47 <param name="window_width" argument="-s" type="integer" min="0" value="4" label="Width of sliding window"/>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
48 <param name="inc_primers" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Include reads with no primers"/>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
49 </inputs>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
50 <outputs>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
51 <data name="output_bam" format="bam" label="${tool.name} on ${on_string} Trimmed bam" from_work_dir="trimmed.sorted.bam"/>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
52 </outputs>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
53 <tests>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
54 <!-- #1: SARS-Cov data-->
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
55 <test>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
56 <param name="input_bam" value="covid19/PC00101P_sub.sorted.bam" />
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
57 <param name="input_bed" value="covid19/ARTIC-V1.bed" />
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
58 <param name="inc_primers" value="true" />
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
59 <output name="output_bam" file="covid19/PC00101P_sub.sorted.bam" compare="sim_size" delta="300000"/>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
60 </test>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
61 <!-- #1: Zika data-->
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
62 <test>
2
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
63 <conditional name="primer">
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
64 <param name="source" value="history" />
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
65 <param name="input_bed" value="zika/db/zika_primers.bed" />
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
66 </conditional>
0
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
67 <param name="input_bam" value="zika/Z52_a.sorted.bam" />
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
68 <output name="output_bam" file="zika/Z52_a.trimmed.sorted.bam" compare="sim_size" delta="100000"/>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
69 </test>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
70 <test>
2
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
71 <conditional name="primer">
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
72 <param name="source" value="history" />
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
73 <param name="input_bed" value="zika/db/zika_primers.bed" />
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
74 </conditional>
0
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
75 <param name="input_bam" value="zika/Z52_b.sorted.bam" />
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
76 <output name="output_bam" file="zika/Z52_b.trimmed.sorted.bam" compare="sim_size" delta="100000"/>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
77 </test>
2
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
78 <test>
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
79 <conditional name="primer">
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
80 <param name="source" value="cached" />
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
81 <param name="cached_bed" value="SARS-CoV-2-ARTICv1" />
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
82 </conditional>
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
83 <param name="input_bam" value="sars-cov-2/sars_cov2_untrimmed.bam" ftype="bam" />
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
84 <output name="output_bam" file="sars-cov-2/sars_cov2_trimmed.bam" />
9ebf6615d8f7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
iuc
parents: 0
diff changeset
85 </test>
0
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
86 </tests>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
87 <help><![CDATA[
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
88 iVar uses primer positions supplied in a BED file to soft clip primer
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
89 sequences from an aligned and sorted BAM file. Following this, the reads are
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
90 trimmed based on a quality threshold(Default: 20). To do the quality
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
91 trimming, iVar uses a sliding window approach(Default: 4). The windows
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
92 slides from the 5' end to the 3' end and if at any point the average base
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
93 quality in the window falls below the threshold, the remaining read is soft
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
94 clipped. If after trimming, the length of the read is greater than the
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
95 minimum length specified(Default: 30), the read is written to the new
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
96 trimmed BAM file
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
97
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
98 Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_.
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
99 ]]> </help>
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
100 <expand macro="citations" />
d2f4ea1496a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
parents:
diff changeset
101 </tool>