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changeset 11:8511b6d85fc7 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit c819f01ae147fb23a1e5e91cee3626b6a19b9e03
author iuc
date Wed, 09 Jul 2025 19:23:11 +0000
parents a019807f4e67
children
files macros.xml seqtk_comp.xml seqtk_fqchk.xml seqtk_hety.xml seqtk_listhet.xml seqtk_seq.xml seqtk_subseq.xml test-data/seqtk_seq_revcom_forw.fa
diffstat 8 files changed, 32 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- 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 -->
--- 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[
--- 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[
--- 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[
--- 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[
--- 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"/>
--- 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
--- /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