Mercurial > repos > iuc > sequali

annotate sequali.xml @ 1:845bd6c1c0c1 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/sequali commit 483a13382456fea4f1934e35804e0dc6c86703c5
author iuc
date Tue, 27 May 2025 11:03:28 +0000
parents 51c7fadc13e4
children 03bb009d5042
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
51c7fadc13e4 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">
51c7fadc13e4 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>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
3 <macros>
1
845bd6c1c0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 483a13382456fea4f1934e35804e0dc6c86703c5
iuc
parents: 0
diff changeset
4 <token name="@TOOL_VERSION@">1.0.1</token>
0
51c7fadc13e4 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>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
6 </macros>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
7 <xrefs>
51c7fadc13e4 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>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
9 </xrefs>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
10 <requirements>
51c7fadc13e4 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>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
12 </requirements>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
13 <version_command><![CDATA[
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
14 sequali --version
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
15 ]]>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
16 </version_command>
51c7fadc13e4 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[
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
18 #import re
51c7fadc13e4 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:
51c7fadc13e4 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)
51c7fadc13e4 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\-_\.]', '_', $input_reads[1].element_identifier)
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
22 ln -s '${input_reads[0]}' ${input_1} &&
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
23 ln -s '${input_reads[1]}' ${input_2} &&
51c7fadc13e4 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':
51c7fadc13e4 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))
51c7fadc13e4 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} &&
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
27 #set $input_2 = ''
51c7fadc13e4 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':
51c7fadc13e4 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))
51c7fadc13e4 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' &&
51c7fadc13e4 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))
51c7fadc13e4 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' &&
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
33 #end if
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
34
51c7fadc13e4 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}' &&
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
36 sequali
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
37 #if $adapter:
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
38 --adapter-file '${adapter}'
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
39 #end if
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
40 #if str($overrepresentation_threshold) != '':
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
41 --overrepresentation-threshold-fraction '${overrepresentation_threshold}'
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
42 #end if
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
43 #if str($overrep_min_threshold) != '':
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
44 --overrepresentation-min-threshold '${overrep_min_threshold}'
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
45 #end if
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
46 #if str($overrep_max_threshold) != '':
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
47 --overrepresentation-max-threshold '${overrep_max_threshold}'
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
48 #end if
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
49 #if str($overrep_max_unique_fragments) != '':
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
50 --overrepresentation-max-unique-fragments '${overrep_max_unique_fragments}'
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
51 #end if
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
52 #if str($overrep_fragment_length) != '':
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
53 --overrepresentation-fragment-length '${overrep_fragment_length}'
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
54 #end if
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
55 #if str($overrep_sample_every) != '':
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
56 --overrepresentation-sample-every '${overrep_sample_every}'
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
57 #end if
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
58 #if str($dup_max_stored_fingerprints) != '':
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
59 --duplication-max-stored-fingerprints '${dup_max_stored_fingerprints}'
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
60 #end if
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
61 #if str($fp_front_length) != '':
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
62 --fingerprint-front-length '${fp_front_length}'
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
63 #end if
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
64 #if str($fp_back_length) != '':
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
65 --fingerprint-back-length '${fp_back_length}'
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
66 #end if
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
67 #if str($fp_front_offset) != '':
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
68 --fingerprint-front-offset '${fp_front_offset}'
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
69 #end if
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
70 #if str($fp_back_offset) != '':
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
71 --fingerprint-back-offset '${fp_back_offset}'
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
72 #end if
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
73 --html '$html_report'
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
74 --json '$json_report'
51c7fadc13e4 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}
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
76 '${input_1}'
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
77 #if $input_2:
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
78 '${input_2}'
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
79 #end if
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
80
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
81 ]]></command>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
82 <inputs>
51c7fadc13e4 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">
51c7fadc13e4 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">
51c7fadc13e4 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>
51c7fadc13e4 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>
51c7fadc13e4 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>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
88 </param>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
89 <when value="single">
51c7fadc13e4 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)."/>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
91 </when>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
92 <when value="paired">
51c7fadc13e4 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."/>
51c7fadc13e4 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."/>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
95 </when>
51c7fadc13e4 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">
51c7fadc13e4 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."/>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
98 </when>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
99 </conditional>
51c7fadc13e4 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"
51c7fadc13e4 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"/>
51c7fadc13e4 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">
51c7fadc13e4 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"
51c7fadc13e4 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)."/>
51c7fadc13e4 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"
51c7fadc13e4 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"
51c7fadc13e4 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."/>
51c7fadc13e4 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"
51c7fadc13e4 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"
51c7fadc13e4 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."/>
51c7fadc13e4 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"
51c7fadc13e4 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"
51c7fadc13e4 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."/>
51c7fadc13e4 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"
51c7fadc13e4 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"
51c7fadc13e4 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."/>
51c7fadc13e4 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"
51c7fadc13e4 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"
51c7fadc13e4 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."/>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
120 </section>
51c7fadc13e4 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">
51c7fadc13e4 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"
51c7fadc13e4 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"
51c7fadc13e4 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."/>
51c7fadc13e4 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"
51c7fadc13e4 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"
51c7fadc13e4 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."/>
51c7fadc13e4 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"
51c7fadc13e4 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"
51c7fadc13e4 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."/>
51c7fadc13e4 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"
51c7fadc13e4 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"
51c7fadc13e4 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."/>
51c7fadc13e4 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"
51c7fadc13e4 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"
51c7fadc13e4 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."/>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
137 </section>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
138 </inputs>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
139 <outputs>
51c7fadc13e4 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 ${on_string}: HTML report" />
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
141 <data format="json" name="json_report" label="${tool.name} on ${on_string}: JSON report" />
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
142 </outputs>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
143 <tests>
51c7fadc13e4 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">
51c7fadc13e4 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">
51c7fadc13e4 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" />
51c7fadc13e4 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" />
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
148 </conditional>
51c7fadc13e4 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">
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
150 <assert_contents>
51c7fadc13e4 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"/>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
152 </assert_contents>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
153 </output>
51c7fadc13e4 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">
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
155 <assert_contents>
51c7fadc13e4 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"/>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
157 </assert_contents>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
158 </output>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
159 </test>
51c7fadc13e4 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">
51c7fadc13e4 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">
51c7fadc13e4 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" />
51c7fadc13e4 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" />
51c7fadc13e4 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" />
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
165 </conditional>
51c7fadc13e4 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">
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
167 <assert_contents>
51c7fadc13e4 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"/>
51c7fadc13e4 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"/>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
170 </assert_contents>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
171 </output>
51c7fadc13e4 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">
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
173 <assert_contents>
51c7fadc13e4 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"/>
51c7fadc13e4 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"/>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
176 </assert_contents>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
177 </output>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
178 </test>
51c7fadc13e4 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">
51c7fadc13e4 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">
51c7fadc13e4 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" />
51c7fadc13e4 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" />
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
183 </conditional>
51c7fadc13e4 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">
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
185 <assert_contents>
51c7fadc13e4 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"/>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
187 </assert_contents>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
188 </output>
51c7fadc13e4 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">
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
190 <assert_contents>
51c7fadc13e4 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"/>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
192 </assert_contents>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
193 </output>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
194 </test>
51c7fadc13e4 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">
51c7fadc13e4 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">
51c7fadc13e4 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" />
51c7fadc13e4 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" />
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
199 </conditional>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
200 </test>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
201 </tests>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
202 <help><![CDATA[
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
203 .. class:: infomark
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
204
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
205 **Purpose**
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
206
51c7fadc13e4 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.
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
208
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
209 Features:
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
210
51c7fadc13e4 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.
51c7fadc13e4 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.
51c7fadc13e4 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.
51c7fadc13e4 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.
51c7fadc13e4 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.
51c7fadc13e4 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.
51c7fadc13e4 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.
51c7fadc13e4 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
845bd6c1c0c1 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
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
220
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
221 -----
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
222
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
223 **Supported formats**
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
224
51c7fadc13e4 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.
51c7fadc13e4 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.
51c7fadc13e4 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.
51c7fadc13e4 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.
51c7fadc13e4 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.
51c7fadc13e4 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
845bd6c1c0c1 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
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
232
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
233 -----
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
234
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
235 **Outputs**
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
236
51c7fadc13e4 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.
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
238
51c7fadc13e4 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/
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
240 ]]></help>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
241 <citations>
51c7fadc13e4 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>
51c7fadc13e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 035d59f19f3a55032be215a3a226c83ad167059c
iuc
parents:
diff changeset
243 </citations>
1
845bd6c1c0c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sequali commit 483a13382456fea4f1934e35804e0dc6c86703c5
iuc
parents: 0
diff changeset
244 </tool>