Mercurial > repos > iuc > sequali

annotate sequali.xml @ 2:52c07e141113 draft default tip

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/sequali commit da3ee7408074f14eb25d956ccb7418084be772dd
author iuc
date Mon, 15 Sep 2025 08:22:10 +0000
parents abea23542a6b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
1 <tool id="sequali" name="sequali" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
2 <description>Fast sequencing data quality metrics for short and long reads</description>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
3 <macros>
2
52c07e141113 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit da3ee7408074f14eb25d956ccb7418084be772dd
iuc
parents: 1
diff changeset
4 <token name="@TOOL_VERSION@">1.0.2</token>
0
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
5 <token name="@VERSION_SUFFIX@">0</token>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
6 </macros>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
7 <xrefs>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
8 <xref type="bio.tools">sequali</xref>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
9 </xrefs>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
10 <requirements>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
11 <requirement type="package" version="@TOOL_VERSION@">sequali</requirement>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
12 </requirements>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
13 <version_command><![CDATA[
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
14 sequali --version
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
15 ]]>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
16 </version_command>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
17 <command detect_errors="exit_code"><![CDATA[
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
18 #import re
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
19 #if $input_reads.is_collection:
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
20 #set $input_1 = re.sub('[^\w\-_\.]', '_', $input_reads[0].element_identifier)
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
21 #set $input_2 = re.sub('[^\w\-_\.]', '_', $input_reads[1].element_identifier)
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
22 ln -s '${input_reads[0]}' ${input_1} &&
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
23 ln -s '${input_reads[1]}' ${input_2} &&
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
24 #else if $input_type_selector == 'single':
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
25 #set $input_1 = re.sub('[^\w\-_\.]', '_', str($input_reads.element_identifier))
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
26 ln -s '${input_reads}' ${input_1} &&
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
27 #set $input_2 = ''
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
28 #else if $input_type_selector == 'paired':
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
29 #set $input_1 = re.sub('[^\w\-_\.]', '_', str($input_reads.element_identifier))
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
30 ln -s '${input_reads}' '$input_1' &&
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
31 #set $input_2 = re.sub('[^\w\-_\.]', '_', str($input_reads_rev.element_identifier))
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
32 ln -s '${input_reads_rev}' '$input_2' &&
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
33 #end if
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
34
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
35 mkdir -p '${html_report.files_path}' &&
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
36 sequali
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
37 #if $adapter:
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
38 --adapter-file '${adapter}'
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
39 #end if
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
40 #if str($overrepresentation_threshold) != '':
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
41 --overrepresentation-threshold-fraction '${overrepresentation_threshold}'
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
42 #end if
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
43 #if str($overrep_min_threshold) != '':
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
44 --overrepresentation-min-threshold '${overrep_min_threshold}'
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
45 #end if
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
46 #if str($overrep_max_threshold) != '':
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
47 --overrepresentation-max-threshold '${overrep_max_threshold}'
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
48 #end if
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
49 #if str($overrep_max_unique_fragments) != '':
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
50 --overrepresentation-max-unique-fragments '${overrep_max_unique_fragments}'
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
51 #end if
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
52 #if str($overrep_fragment_length) != '':
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
53 --overrepresentation-fragment-length '${overrep_fragment_length}'
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
54 #end if
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
55 #if str($overrep_sample_every) != '':
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
56 --overrepresentation-sample-every '${overrep_sample_every}'
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
57 #end if
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
58 #if str($dup_max_stored_fingerprints) != '':
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
59 --duplication-max-stored-fingerprints '${dup_max_stored_fingerprints}'
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
60 #end if
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
61 #if str($fp_front_length) != '':
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
62 --fingerprint-front-length '${fp_front_length}'
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
63 #end if
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
64 #if str($fp_back_length) != '':
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
65 --fingerprint-back-length '${fp_back_length}'
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
66 #end if
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
67 #if str($fp_front_offset) != '':
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
68 --fingerprint-front-offset '${fp_front_offset}'
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
69 #end if
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
70 #if str($fp_back_offset) != '':
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
71 --fingerprint-back-offset '${fp_back_offset}'
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
72 #end if
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
73 --html '$html_report'
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
74 --json '$json_report'
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
75 --threads \${GALAXY_SLOTS:-2}
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
76 '${input_1}'
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
77 #if $input_2:
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
78 '${input_2}'
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
79 #end if
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
80
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
81 ]]></command>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
82 <inputs>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
83 <conditional name="input_type">
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
84 <param name="input_type_selector" type="select" label="Single file or paired-end reads" help="Select between paired-end reads and single file (fastq, ubam) to process">
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
85 <option value="single">Single file</option>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
86 <option value="paired">Paired-end</option>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
87 <option value="paired_collection">Paired Collection</option>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
88 </param>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
89 <when value="single">
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
90 <param name="input_reads" type="data" format="fastq,fastq.gz,unsorted.bam" label="Select fastq dataset" help="Specify dataset with single reads (fastq or unaligned bam)."/>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
91 </when>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
92 <when value="paired">
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
93 <param name="input_reads" type="data" format="fastq,fastq.gz" label="Forward reads" help="Specify FASTQ(.gz) dataset with forward reads."/>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
94 <param name="input_reads_rev" type="data" format="fastq,fastq.gz" label="Reverse reads" help="Specify FASTQ(.gz) dataset with reverse reads."/>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
95 </when>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
96 <when value="paired_collection">
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
97 <param name="input_reads" type="data_collection" format="fastq,fastq.gz" label="Collection with paired-end reads" help="Specify collection with paired-end reads."/>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
98 </when>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
99 </conditional>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
100 <param argument="--adapter-file" name="adapter" format="tabular" type="data" optional= "true" label="Adapters to search for"
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
101 help="TSV file with header: Name, Sequencing Technology, Probe sequence, sequence position. Default: https://github.com/rhpvorderman/sequali/tree/develop/src/sequali/adapters/adapter_list.tsv"/>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
102 <section name="overrepresentation-param" title="Overrepresentation parameters" expanded="False">
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
103 <param argument="--overrepresentation-threshold-fraction" name="overrepresentation_threshold" type="float" optional="true" min="0" max="1"
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
104 label="Fraction to be determined as overrepresented" help="The threshold is calculated as fraction times the number of sampled sequences. Default: 0.001 (1 in 1,000)."/>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
105 <param argument="--overrepresentation-min-threshold" name="overrep_min_threshold" type="integer" optional="true" min="0"
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
106 label="Minimum occurrences to be considered overrepresented"
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
107 help="The minimum amount of occurrences for a sequence to be considered overrepresented, regardless of the bound set by the threshold fraction. Useful for smaller files. Default: 100."/>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
108 <param argument="--overrepresentation-max-threshold" name="overrep_max_threshold" type="integer" optional="true" min="0"
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
109 label="Amount of occurrences to be considered overrepresented"
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
110 help="The amount of occurrences for a sequence to be considered overrepresented, regardless of the bound set by the threshold fraction. Useful for very large files. Default: unlimited."/>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
111 <param argument="--overrepresentation-max-unique-fragments" name="overrep_max_unique_fragments" type="integer" optional="true" min="0"
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
112 label="Maximum amount of unique fragments to store"
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
113 help="Larger amounts increase the sensitivity of finding overrepresented sequences at the cost of increasing memory usage. Default: 5,000,000."/>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
114 <param argument="--overrepresentation-fragment-length" name="overrep_fragment_length" type="integer" optional="true" min="3" max="31"
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
115 label="Length of fragments to sample"
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
116 help="The maximum is 31. Default: 21."/>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
117 <param argument="--overrepresentation-sample-every" name="overrep_sample_every" type="integer" optional="true"
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
118 label="Sample one every N sequences"
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
119 help="More sequences sampled leads to better precision, lower speed, and also more bias towards the beginning of the file as the fragment store gets filled up with more sequences from the beginning. Default is N=8, so one in 8 sequences is analysed."/>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
120 </section>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
121 <section name="duplication-param" title="Duplication parameters" expanded="False">
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
122 <param argument="--duplication-max-stored-fingerprints" name="dup_max_stored_fingerprints" type="integer" optional="true" min="0"
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
123 label="Maximum number of fingerprints stored"
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
124 help="Determines how many fingerprints are maximally stored to estimate the duplication rate. More fingerprints leads to a more accurate estimate, but also more memory usage. Default: 1,000,000."/>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
125 <param argument="--fingerprint-front-length" name="fp_front_length" type="integer" optional="true" min="0"
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
126 label="Number of bases from the front of the sequence"
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
127 help="Number of bases to be taken for the deduplication fingerprint from the front of the sequence. Default: 8."/>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
128 <param argument="--fingerprint-back-length" name="fp_back_length" type="integer" optional="true" min="0"
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
129 label="Number of bases from the back of the sequence"
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
130 help="Number of bases to be taken for the deduplication fingerprint from the back of the sequence. Default: 8."/>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
131 <param argument="--fingerprint-front-offset" name="fp_front_offset" type="integer" optional="true" min="0"
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
132 label="Front offset of the deduplication fingerprint"
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
133 help="Useful for avoiding adapter sequences. Default: 64 for single end, 0 for paired sequences."/>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
134 <param argument="--fingerprint-back-offset" name="fp_back_offset" type="integer" optional="true" min="0"
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
135 label="Back offset of the deduplication fingerprint"
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
136 help="Useful for avoiding adapter sequences. Default: 64 for single end, 0 for paired sequences."/>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
137 </section>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
138 </inputs>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
139 <outputs>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
140 <data format="html" name="html_report" label="${tool.name} on ${on_string}: HTML report" />
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
141 <data format="json" name="json_report" label="${tool.name} on ${on_string}: JSON report" />
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
142 </outputs>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
143 <tests>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
144 <test expect_num_outputs="2">
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
145 <conditional name="input_type">
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
146 <param name="input_type_selector" value="single" />
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
147 <param name="input_reads" value="input_fwd.fastq" />
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
148 </conditional>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
149 <output name="html_report" ftype="html">
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
150 <assert_contents>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
151 <has_text text="Sequali report"/>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
152 </assert_contents>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
153 </output>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
154 <output name="json_report" ftype="json">
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
155 <assert_contents>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
156 <has_text text="sequali_version"/>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
157 </assert_contents>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
158 </output>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
159 </test>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
160 <test expect_num_outputs="2">
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
161 <conditional name="input_type">
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
162 <param name="input_type_selector" value="paired" />
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
163 <param name="input_reads" value="input_fwd.fastq" />
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
164 <param name="input_reads_rev" value="input_rev.fastq" />
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
165 </conditional>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
166 <output name="html_report" ftype="html">
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
167 <assert_contents>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
168 <has_text text="Sequali report"/>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
169 <has_text text="Filename read 2"/>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
170 </assert_contents>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
171 </output>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
172 <output name="json_report" ftype="json">
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
173 <assert_contents>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
174 <has_text text="sequali_version"/>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
175 <has_text text="filename_read2"/>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
176 </assert_contents>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
177 </output>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
178 </test>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
179 <test expect_num_outputs="2">
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
180 <conditional name="input_type">
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
181 <param name="input_type_selector" value="single" />
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
182 <param name="input_reads" value="input_nanopore.fastq" />
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
183 </conditional>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
184 <output name="html_report" ftype="html">
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
185 <assert_contents>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
186 <has_text text="Sequali report"/>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
187 </assert_contents>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
188 </output>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
189 <output name="json_report" ftype="json">
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
190 <assert_contents>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
191 <has_text text="sequali_version"/>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
192 </assert_contents>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
193 </output>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
194 </test>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
195 <test expect_failure="true">
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
196 <conditional name="input_type">
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
197 <param name="input_type_selector" value="single" />
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
198 <param name="input_reads" value="input_fail.fastq" />
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
199 </conditional>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
200 </test>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
201 </tests>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
202 <help><![CDATA[
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
203 .. class:: infomark
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
204
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
205 **Purpose**
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
206
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
207 Sequali_ is a tool for fast sequencing data quality metrics for short and long reads.
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
208
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
209 Features:
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
210
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
211 - Informative graphs that allow for judging the quality of a sequence at a quick glance.
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
212 - Overrepresentation analysis using 21 bp sequence fragments. Overrepresented sequences are checked against the NCBI univec database.
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
213 - Estimate duplication rate using a fingerprint subsampling technique which is also used in filesystem duplication estimation.
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
214 - Checks for 6 illumina adapter sequences and 17 nanopore adapter sequences for single read data.
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
215 - Determines adapters by overlap analysis for paired read data.
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
216 - Insert size metrics for paired read data.
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
217 - Per tile quality plots for illumina reads.
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
218 - Channel and other plots for nanopore reads.
1
abea23542a6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 483a13382456fea4f1934e35804e0dc6c86703c5
iuc
parents: 0
diff changeset
219 - Reproducible reports without timestamps.
0
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
220
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
221 -----
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
222
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
223 **Supported formats**
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
224
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
225 - FASTQ. Only the Sanger variation with a phred offset of 33 and the error rate calculation of 10 ^ (-phred/10) is supported. All sequencers use this format today.
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
226 - Paired end sequencing data is supported.
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
227 - For sequences called by illumina base callers an additional plot with the per tile quality will be provided.
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
228 - For sequences called by guppy additional plots for nanopore specific data will be provided.
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
229 - (unaligned) BAM with single reads. Read-pair information is currently ignored.
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
230 - For BAM data as delivered by dorado additional nanopore plots will be provided.
1
abea23542a6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 483a13382456fea4f1934e35804e0dc6c86703c5
iuc
parents: 0
diff changeset
231 - For aligned BAM files, secondary and supplementary reads are ignored similar to how samtools fastq handles the data.
0
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
232
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
233 -----
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
234
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
235 **Outputs**
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
236
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
237 Sequali produces informative HTML report with dynamic plots for each quality metric.
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
238
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
239 .. _Sequali: https://sequali.readthedocs.io/en/latest/
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
240 ]]></help>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
241 <citations>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
242 <citation type="doi">10.1093/bioadv/vbaf010</citation>
8e2c32a7c0a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
243 </citations>
1
abea23542a6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 483a13382456fea4f1934e35804e0dc6c86703c5
iuc
parents: 0
diff changeset
244 </tool>