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cutadapt: replace adapter sanitizer by validator (galaxyproject#6161)
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@bernt-matthias
bernt-matthias authored Jul 18, 2024
1 parent b37248e commit fff23da
Showing 1 changed file with 3 additions and 29 deletions.
32 changes: 3 additions & 29 deletions tools/cutadapt/macros.xml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
<macros>
<token name="@TOOL_VERSION@">4.9</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@FASTQ_TYPES@">fastq.bz2,fastq.gz,fastq,fasta.bz2,fasta.gz,fasta</token>
<xml name="edam_ontology">
<edam_topics>
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#end if
</token>
<xml name="adapter_sanitizer">
<sanitizer>
<valid initial="string.digits">
<add value="A"/><!--standard nucleotides-->
<add value="T"/>
<add value="C"/>
<add value="G"/>
<add value="U"/><!--ambiguous nucleotides-->
<add value="R"/>
<add value="Y"/>
<add value="S"/>
<add value="W"/>
<add value="K"/>
<add value="M"/>
<add value="B"/>
<add value="D"/>
<add value="H"/>
<add value="V"/>
<add value="N"/>
<add value="X"/><!-- don't match any nucleotide-->
<add value="{"/><!--specify repeats .. needs digits which are added as default-->
<add value="}"/>
<add value="^"/><!--anchoring-->
<add value="$"/>
<add value="."/>
<add value="("/><!--specify what to keep-->
<add value=")"/>
</valid>
</sanitizer>
<sanitizer sanitize="false" />
<validator type="regex" message="Invalid adapter sequence. Allowed are strings consisting of digits IUPAC nucleotides (including wildcards) and any of the following '{}^$.()'. See https://cutadapt.readthedocs.io/en/stable/guide.html#specifying-adapter-sequences"><![CDATA[[0-9ATCGURYSWKMBDHVNX{}^$.()]+$]]></validator>
</xml>
<xml name="adapter_conditional" tokens="adapter_type,argument">
<conditional name="adapter_source">
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