# 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