Mercurial > repos > iuc > seqtk

diff seqtk_seq.xml @ 11:8511b6d85fc7 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
line wrap: on
line diff
--- 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"/>