# HG changeset patch # User iuc # Date 1752088991 0 # Node ID 8511b6d85fc78d62baf6b17a77a1a18f72ed65f1 # Parent a019807f4e67e1c5e36557365b6f6a9552a467cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit c819f01ae147fb23a1e5e91cee3626b6a19b9e03 diff -r a019807f4e67 -r 8511b6d85fc7 macros.xml --- a/macros.xml Wed Oct 16 09:08:52 2024 +0000 +++ b/macros.xml Wed Jul 09 19:23:11 2025 +0000 @@ -3,18 +3,19 @@ <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">seqtk</requirement> - <requirement type="package" version="2.3.4">pigz</requirement> - <yield/> + <requirement type="package" version="2.8">pigz</requirement> </requirements> </xml> + <xml name="awk_requirement"> + <requirement type="package" version="5.3.1">gawk</requirement> + </xml> <xml name="bio_tools"> <xrefs> <xref type="bio.tools">seqtk</xref> </xrefs> </xml> - <token name="@TOOL_VERSION@">1.4</token> + <token name="@TOOL_VERSION@">1.5</token> <token name="@VERSION_SUFFIX@">0</token> - <token name="@AWK_VERSION@">4.2.1</token> <xml name="stdio"> <stdio> <!-- Anything other than zero is an error --> diff -r a019807f4e67 -r 8511b6d85fc7 seqtk_comp.xml --- a/seqtk_comp.xml Wed Oct 16 09:08:52 2024 +0000 +++ b/seqtk_comp.xml Wed Jul 09 19:23:11 2025 +0000 @@ -6,7 +6,7 @@ </macros> <expand macro="bio_tools"/> <expand macro="requirements"> - <requirement type="package" version="@AWK_VERSION@">gawk</requirement> + <expand macro="awk_requirement"/> </expand> <expand macro="stdio"/> <command><![CDATA[ diff -r a019807f4e67 -r 8511b6d85fc7 seqtk_fqchk.xml --- a/seqtk_fqchk.xml Wed Oct 16 09:08:52 2024 +0000 +++ b/seqtk_fqchk.xml Wed Jul 09 19:23:11 2025 +0000 @@ -6,7 +6,7 @@ </macros> <expand macro="bio_tools"/> <expand macro="requirements"> - <requirement type="package" version="@AWK_VERSION@">gawk</requirement> + <expand macro="awk_requirement"/> </expand> <expand macro="stdio"/> <command><![CDATA[ diff -r a019807f4e67 -r 8511b6d85fc7 seqtk_hety.xml --- a/seqtk_hety.xml Wed Oct 16 09:08:52 2024 +0000 +++ b/seqtk_hety.xml Wed Jul 09 19:23:11 2025 +0000 @@ -6,7 +6,7 @@ </macros> <expand macro="bio_tools"/> <expand macro="requirements"> - <requirement type="package" version="@AWK_VERSION@">gawk</requirement> + <expand macro="awk_requirement"/> </expand> <expand macro="stdio"/> <command><![CDATA[ diff -r a019807f4e67 -r 8511b6d85fc7 seqtk_listhet.xml --- a/seqtk_listhet.xml Wed Oct 16 09:08:52 2024 +0000 +++ b/seqtk_listhet.xml Wed Jul 09 19:23:11 2025 +0000 @@ -6,7 +6,7 @@ </macros> <expand macro="bio_tools"/> <expand macro="requirements"> - <requirement type="package" version="@AWK_VERSION@">gawk</requirement> + <expand macro="awk_requirement"/> </expand> <expand macro="stdio"/> <command><![CDATA[ diff -r a019807f4e67 -r 8511b6d85fc7 seqtk_seq.xml --- a/seqtk_seq.xml Wed Oct 16 09:08:52 2024 +0000 +++ b/seqtk_seq.xml Wed Jul 09 19:23:11 2025 +0000 @@ -22,7 +22,9 @@ #end if -L $L $c -$r +#if $direction != 'forward' + $direction +#end if $A $C $N @@ -58,7 +60,11 @@ <param argument="-M" type="data" format="bed,txt" optional="true" label="Mask regions in BED or name list file" /> <param argument="-L" type="integer" value="0" label="Drop sequences with length shorter than INT" /> <param argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Mask complement region" help="Effective with -M" /> - <param argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false" label="Reverse complement" /> + <param name="direction" type="select" optional="false" label="Output complement"> + <option value="forward" selected="true">Forward only (Default)</option> + <option value="-r">Reverse only (-r)</option> + <option value="-R">Forward and Reverse (-R)</option> + </param> <param argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false" label="Force FASTA output (discard quality)" /> <param argument="-C" type="boolean" truevalue="-C" falsevalue="" checked="false" label="Drop comments at the header lines" /> <param argument="-N" type="boolean" truevalue="-N" falsevalue="" checked="false" label="Drop sequences containing ambiguous bases" /> @@ -76,17 +82,23 @@ principle. --> <test expect_num_outputs="1"> <param name="in_file" value="seqtk_seq.fa"/> - <param name="r" value="True"/> + <param name="direction" value="-r"/> <param name="n" value=""/> <output name="default" file="seqtk_seq_revcom.fa" ftype="fasta"/> </test> <test expect_num_outputs="1"> <param name="in_file" value="seqtk_seq.fa.gz" ftype="fasta.gz"/> - <param name="r" value="True"/> + <param name="direction" value="-r"/> <param name="n" value=""/> <output name="default" file="seqtk_seq_revcom.fa.gz" ftype="fasta.gz"/> </test> <test expect_num_outputs="1"> + <param name="in_file" value="seqtk_seq.fa"/> + <param name="direction" value="-R"/> + <param name="n" value=""/> + <output name="default" file="seqtk_seq_revcom_forw.fa" ftype="fasta"/> + </test> + <test expect_num_outputs="1"> <param name="in_file" value="seqtk_trimfq.fq" ftype="fastq"/> <param name="A" value="True" /> <output name="default" file="seqtk_seq_A.fasta" ftype="fasta"/> diff -r a019807f4e67 -r 8511b6d85fc7 seqtk_subseq.xml --- a/seqtk_subseq.xml Wed Oct 16 09:08:52 2024 +0000 +++ b/seqtk_subseq.xml Wed Jul 09 19:23:11 2025 +0000 @@ -3,10 +3,11 @@ <description>extract subsequences from FASTA/Q files</description> <macros> <import>macros.xml</import> - <requirement type="package" version="@AWK_VERSION@">gawk</requirement> </macros> <expand macro="bio_tools"/> - <expand macro="requirements"/> + <expand macro="requirements"> + <expand macro="awk_requirement"/> + </expand> <expand macro="stdio"/> <command><![CDATA[ seqtk subseq diff -r a019807f4e67 -r 8511b6d85fc7 test-data/seqtk_seq_revcom_forw.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seqtk_seq_revcom_forw.fa Wed Jul 09 19:23:11 2025 +0000 @@ -0,0 +1,4 @@ +>test+ +AACTGATCGATCGATCGNNNNNNNNNNNACATG +>test- +CATGTNNNNNNNNNNNCGATCGATCGATCAGTT