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lint fixes for various tools #107

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lint fixes for various tools #107

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f725af8
add linter exceptions for all linters that are currently failing
bernt-matthias Jul 27, 2024
86a7364
undo changes to tool
bernt-matthias Jul 29, 2024
0035534
fix linting errors in abricate
bgruening Aug 25, 2024
406d8c2
fix amplican
bgruening Aug 25, 2024
c8fee7e
fix lint in bamutils
bgruening Aug 25, 2024
7965ac3
fix barrnap linting
bgruening Aug 25, 2024
692e187
fix bioperl linting
bgruening Aug 25, 2024
f87aaad
fix cdhit
bgruening Aug 25, 2024
714fb96
fix circexplorer2 linting
bgruening Aug 25, 2024
42c65c4
fix crossmap linting
bgruening Aug 25, 2024
83d1ec6
fix delly linting
bgruening Aug 25, 2024
ff16af6
fix dropletutils
bgruening Aug 25, 2024
546a0eb
reset autoformat
bgruening Aug 25, 2024
7950412
reset autoformat
bgruening Aug 25, 2024
acf451e
Merge branch 'topic/skip_lint' into lf_01
bernt-matthias Sep 2, 2024
8a76dd7
Update tools/abricate/abricate_list.xml
bgruening Sep 3, 2024
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34 changes: 10 additions & 24 deletions tools/abricate/abricate.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,11 +5,10 @@
<macros>
<import>macros.xml</import>
</macros>
<expand macro='xrefs'/>
<expand macro='edam_ontology'/>
<expand macro="requirements" />
<expand macro="version_command" />

<expand macro="edam_ontology"/>
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If we fix a linter error we should remove it from the tool's .lint_skip file.

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abcriacte didn't had a lint_skip file imho

<expand macro="xrefs"/>
<expand macro="requirements"/>
<expand macro="version_command"/>
<command detect_errors="exit_code"><![CDATA[
#import re
#set $sample_name = re.sub('[^\w\-_\.]', '_', $file_input.element_identifier)
Expand All @@ -27,9 +26,8 @@
--db=$adv.db
> '$report'
]]></command>

<inputs>
<param name="file_input" type="data" format="fasta,genbank,embl" label="Input file (Fasta, Genbank or EMBL file)" help="To screen for antibiotic resistant genes, can be a fasta file, a genbank file or an EMBL file." />
<param name="file_input" type="data" format="fasta,genbank,embl" label="Input file (Fasta, Genbank or EMBL file)" help="To screen for antibiotic resistant genes, can be a fasta file, a genbank file or an EMBL file."/>
<section name="adv" title="Advanced options" expanded="False">
<param argument="--db" type="select" label="Database to use - default is 'resfinder'" help="Option to switch to other AMR/other database">
<option value="argannot">ARG-ANNOT</option>
Expand All @@ -42,72 +40,61 @@
<option value="megares">megares</option>
<option value="ecoli_vf">Ecoli_VF</option>
</param>
<param name="no_header" argument="--noheader" type="boolean" truevalue="--noheader" falsevalue="" label="Suppress header" help="Suppress output file's column headings" />
<param name="min_dna_id" argument="--minid" type="float" value="80" min="0" max="100" optional="true" label="Minimum DNA %identity" />
<param name="min_cov" argument="--mincov" type="float" value="80" min="0" max="100" optional="true" label="Minimum DNA %coverage" />
<param name="no_header" argument="--noheader" type="boolean" truevalue="--noheader" falsevalue="" label="Suppress header" help="Suppress output file's column headings"/>
<param name="min_dna_id" argument="--minid" type="float" min="0" max="100" value="80" optional="true" label="Minimum DNA %identity"/>
<param name="min_cov" argument="--mincov" type="float" min="0" max="100" value="80" optional="true" label="Minimum DNA %coverage"/>
</section>
</inputs>

<outputs>
<data name="report" format="tabular" label="${tool.name} on ${on_string} report file" />
<data name="report" format="tabular" label="${tool.name} on ${on_string} report file"/>
</outputs>

<tests>
<!-- Basic test 0 - will produce no results. -->
<test>
<param name="file_input" value="Acetobacter.fna"/>
<output name="report" ftype="tabular" file="output_noresults.txt" />
<output name="report" ftype="tabular" file="output_noresults.txt"/>
</test>

<!-- Basic test 1 - will produce results. -->
<test>
<param name="file_input" value="MRSA0252.fna"/>
<output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/>
</test>

<!-- Advanced test 2 - No header. -->
<test>
<param name="file_input" value="MRSA0252.fna"/>
<param name="no_header" value="True"/>
<output name="report" ftype="tabular" file="output_noheader.txt" compare="contains"/>
</test>

<!-- Advanced test 3 - Changed DB to card -->
<test>
<param name="file_input" value="MRSA0252.fna"/>
<param name="db" value="card"/>
<output name="report" ftype="tabular" file="output_db-card.txt" compare="contains"/>
</test>

<!-- Advanced test 4 - Changed DB to megares -->
<test>
<param name="file_input" value="MRSA0252.fna"/>
<param name="db" value="megares"/>
<output name="report" ftype="tabular" file="output_db-megares.txt" compare="contains"/>
</test>

<!-- Advanced test 5 - Min DNA ID 100 -->
<test>
<param name="file_input" value="MRSA0252.fna"/>
<param name="min_dna_id" value="100"/>
<output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/>
</test>

<!-- Advanced test 6 - Min Coverage 100 -->
<test>
<param name="file_input" value="MRSA0252.fna"/>
<param name="min_cov" value="100"/>
<output name="report" ftype="tabular" file="output_mincov100.txt" compare="contains"/>
</test>

<!-- Filetype test 7 - input a gbk -->
<test>
<param name="file_input" value="test.gbk"/>
<output name="report" ftype="tabular" file="output_gbk.txt" compare="contains"/>
</test>

</tests>

<help><![CDATA[
**What it does**

Expand Down Expand Up @@ -156,6 +143,5 @@ ABRicate will produce a tab-seperated output file with the following outputs:
6159.fna NC_017338.1 727191 728356 norA_1 1-1166/1167 =============== 0/0 99.91 92.367 resfinder M97169
6159.fna NC_017339.1 10150 10995 blaZ_32 1-846/846 =============== 0/0 100.00 100.000 resfinder AP004832
]]></help>

<expand macro="citations"/>
</tool>
17 changes: 6 additions & 11 deletions tools/abricate/abricate_list.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,33 +5,28 @@
<macros>
<import>macros.xml</import>
</macros>
<expand macro='xrefs'/>
<expand macro='edam_ontology'/>
<expand macro="requirements" />
<expand macro="version_command" />

<expand macro="edam_ontology"/>
<expand macro="xrefs"/>
<expand macro="requirements"/>
<expand macro="version_command"/>
<command detect_errors="exit_code"><![CDATA[
abricate --list > '$report'
]]></command>

<inputs>
<param name="hidden_input" type="hidden" label="This is to please our linter in this expeptional case"/>
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</inputs>

<outputs>
<data name="report" format="txt" label="${tool.name} - list of databases"/>
</outputs>

<tests>
<test>
<output name="report" ftype="txt" file="output_list.txt" compare="contains" />
<output name="report" ftype="txt" file="output_list.txt" compare="contains"/>
</test>
</tests>

<help><![CDATA[
**What it does**

ABRicate List will list all the antibiotic databases used by ABRicate. The database of these genes is built from ResFinder.
]]></help>

<expand macro="citations"/>
</tool>
18 changes: 6 additions & 12 deletions tools/abricate/abricate_summary.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,11 +5,10 @@
<macros>
<import>macros.xml</import>
</macros>
<expand macro='xrefs'/>
<expand macro='edam_ontology'/>
<expand macro="requirements" />
<expand macro="version_command" />

<expand macro="edam_ontology"/>
<expand macro="xrefs"/>
<expand macro="requirements"/>
<expand macro="version_command"/>
<command detect_errors="exit_code"><![CDATA[
mkdir reports &&
#import re
Expand All @@ -21,22 +20,18 @@
abricate --summary *
> '$summary'
]]></command>

<inputs>
<param name="abricate_reports" type="data" multiple="true" format="tabular" label="Abricate output reports to summarize"/>
<param name="abricate_reports" type="data" multiple="true" format="tabular" label="Abricate output reports to summarize"/>
</inputs>

<outputs>
<data name="summary" format="tabular"/>
</outputs>

<tests>
<test>
<param name="abricate_reports" value="output_db-card.txt,output_db-megares.txt"/>
<output name="summary" ftype="tabular" file="output_summary.txt" />
<output name="summary" ftype="tabular" file="output_summary.txt"/>
</test>
</tests>

<help><![CDATA[
**What it does**

Expand All @@ -51,6 +46,5 @@ ABRicate can combine results into a simple matrix of gene presence/absence. An a
sample2 24 100.00 . 100.00;100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00;100.00 . 100.00 100.00 100.00;100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 . 100.00 . . . 100.00 . . . . . . . . .

]]></help>

<expand macro="citations"/>
</tool>
19 changes: 7 additions & 12 deletions tools/abricate/macros.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,17 +2,14 @@
<xml name="requirements">
<requirements>
<requirement type="package" version="@VERSION@">abricate</requirement>
<yield />
<yield/>
</requirements>
</xml>

<xml name="version_command">
<version_command><![CDATA[abricate --version]]></version_command>
</xml>

<token name="@VERSION@">1.0.1</token>
<token name="@PROFILE@">20.01</token>

<xml name="edam_ontology">
<edam_topics>
<edam_topic>topic_0622</edam_topic>
Expand All @@ -22,23 +19,21 @@
<edam_operation>operation_3482</edam_operation>
</edam_operations>
</xml>

<xml name="xrefs">
<xrefs>
<xref type='bio.tools'>ABRicate</xref>
</xrefs>
<xrefs>
<xref type="bio.tools">ABRicate</xref>
</xrefs>
</xml>

<xml name="citations">
<citations>
<citation type="bibtex">
<citations>
<citation type="bibtex">
@UNPUBLISHED{Seemann2016,
author = {Seemann, Torsten},
title = {ABRicate: mass screening of contigs for antiobiotic resistance genes},
year = {2016},
url = {https://github.com/tseemann/abricate},
}
</citation>
</citations>
</citations>
</xml>
</macros>
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