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changeset 8:3da72230c066 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 690c73637e3b8be3a52fe3afc8ba6436c4bab46f"
author iuc
date Thu, 14 Oct 2021 09:22:39 +0000
parents 58c8ece95b53
children 4b494533146a
files macros.xml seqtk_comp.xml seqtk_cutN.xml seqtk_dropse.xml seqtk_fqchk.xml seqtk_hety.xml seqtk_listhet.xml seqtk_mergefa.xml seqtk_mergepe.xml seqtk_mutfa.xml seqtk_randbase.xml seqtk_sample.xml seqtk_seq.xml seqtk_subseq.xml seqtk_trimfq.xml test-data/seqtk_mutfa.snp
diffstat 16 files changed, 21 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Tue Sep 10 13:58:48 2019 -0400
+++ b/macros.xml	Thu Oct 14 09:22:39 2021 +0000
@@ -7,6 +7,11 @@
             <yield/>
         </requirements>
     </xml>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">seqtk</xref>
+        </xrefs>
+    </xml>
     <token name="@TOOL_VERSION@">1.3</token>
     <token name="@AWK_VERSION@">4.2.1</token>
     <xml name="stdio">
--- a/seqtk_comp.xml	Tue Sep 10 13:58:48 2019 -0400
+++ b/seqtk_comp.xml	Thu Oct 14 09:22:39 2021 +0000
@@ -1,6 +1,7 @@
 <?xml version="1.0"?>
 <tool id="seqtk_comp" name="seqtk_comp" version="@TOOL_VERSION@.1">
     <description>get the nucleotide composition of FASTA/Q</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/seqtk_cutN.xml	Tue Sep 10 13:58:48 2019 -0400
+++ b/seqtk_cutN.xml	Thu Oct 14 09:22:39 2021 +0000
@@ -1,6 +1,7 @@
 <?xml version="1.0"?>
 <tool id="seqtk_cutN" name="seqtk_cutN" version="@TOOL_VERSION@.1">
     <description>cut sequence at long N</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/seqtk_dropse.xml	Tue Sep 10 13:58:48 2019 -0400
+++ b/seqtk_dropse.xml	Thu Oct 14 09:22:39 2021 +0000
@@ -1,6 +1,7 @@
 <?xml version="1.0"?>
 <tool id="seqtk_dropse" name="seqtk_dropse" version="@TOOL_VERSION@.1">
     <description>drop unpaired from interleaved Paired End FASTA/Q</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/seqtk_fqchk.xml	Tue Sep 10 13:58:48 2019 -0400
+++ b/seqtk_fqchk.xml	Thu Oct 14 09:22:39 2021 +0000
@@ -1,6 +1,7 @@
 <?xml version="1.0"?>
 <tool id="seqtk_fqchk" name="seqtk_fqchk" version="@TOOL_VERSION@.1">
     <description>fastq QC (base/quality summary)</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/seqtk_hety.xml	Tue Sep 10 13:58:48 2019 -0400
+++ b/seqtk_hety.xml	Thu Oct 14 09:22:39 2021 +0000
@@ -1,6 +1,7 @@
 <?xml version="1.0"?>
 <tool id="seqtk_hety" name="seqtk_hety" version="@TOOL_VERSION@.1">
     <description>regional heterozygosity</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/seqtk_listhet.xml	Tue Sep 10 13:58:48 2019 -0400
+++ b/seqtk_listhet.xml	Thu Oct 14 09:22:39 2021 +0000
@@ -1,6 +1,7 @@
 <?xml version="1.0"?>
 <tool id="seqtk_listhet" name="seqtk_listhet" version="@TOOL_VERSION@.1">
     <description>extract the position of each het</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/seqtk_mergefa.xml	Tue Sep 10 13:58:48 2019 -0400
+++ b/seqtk_mergefa.xml	Thu Oct 14 09:22:39 2021 +0000
@@ -1,6 +1,7 @@
 <?xml version="1.0"?>
 <tool id="seqtk_mergefa" name="seqtk_mergefa" version="@TOOL_VERSION@.1">
     <description>merge two FASTA/Q files</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/seqtk_mergepe.xml	Tue Sep 10 13:58:48 2019 -0400
+++ b/seqtk_mergepe.xml	Thu Oct 14 09:22:39 2021 +0000
@@ -1,6 +1,7 @@
 <?xml version="1.0"?>
 <tool id="seqtk_mergepe" name="seqtk_mergepe" version="@TOOL_VERSION@.1">
     <description>interleave two unpaired FASTA/Q files for a paired-end file</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/seqtk_mutfa.xml	Tue Sep 10 13:58:48 2019 -0400
+++ b/seqtk_mutfa.xml	Thu Oct 14 09:22:39 2021 +0000
@@ -1,6 +1,7 @@
 <?xml version="1.0"?>
 <tool id="seqtk_mutfa" name="seqtk_mutfa" version="@TOOL_VERSION@.1">
     <description>point mutate FASTA at specified positions</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/seqtk_randbase.xml	Tue Sep 10 13:58:48 2019 -0400
+++ b/seqtk_randbase.xml	Thu Oct 14 09:22:39 2021 +0000
@@ -1,6 +1,7 @@
 <?xml version="1.0"?>
 <tool id="seqtk_randbase" name="seqtk_randbase" version="@TOOL_VERSION@.1">
     <description>choose a random base from hets</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/seqtk_sample.xml	Tue Sep 10 13:58:48 2019 -0400
+++ b/seqtk_sample.xml	Thu Oct 14 09:22:39 2021 +0000
@@ -1,6 +1,7 @@
 <?xml version="1.0"?>
 <tool id="seqtk_sample" name="seqtk_sample" version="@TOOL_VERSION@.2">
     <description>random subsample of fasta or fastq sequences</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/seqtk_seq.xml	Tue Sep 10 13:58:48 2019 -0400
+++ b/seqtk_seq.xml	Thu Oct 14 09:22:39 2021 +0000
@@ -1,6 +1,7 @@
 <?xml version="1.0"?>
 <tool id="seqtk_seq" name="seqtk_seq" version="@TOOL_VERSION@.3">
     <description>common transformation of FASTA/Q</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/seqtk_subseq.xml	Tue Sep 10 13:58:48 2019 -0400
+++ b/seqtk_subseq.xml	Thu Oct 14 09:22:39 2021 +0000
@@ -1,6 +1,7 @@
 <?xml version="1.0"?>
 <tool id="seqtk_subseq" name="seqtk_subseq" version="@TOOL_VERSION@.1">
     <description>extract subsequences from FASTA/Q files</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
         <requirement type="package" version="@AWK_VERSION@">gawk</requirement>
--- a/seqtk_trimfq.xml	Tue Sep 10 13:58:48 2019 -0400
+++ b/seqtk_trimfq.xml	Thu Oct 14 09:22:39 2021 +0000
@@ -1,6 +1,7 @@
 <?xml version="1.0"?>
 <tool id="seqtk_trimfq" name="seqtk_trimfq" version="@TOOL_VERSION@.1">
     <description>trim FASTQ using the Phred algorithm</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
--- a/test-data/seqtk_mutfa.snp	Tue Sep 10 13:58:48 2019 -0400
+++ b/test-data/seqtk_mutfa.snp	Thu Oct 14 09:22:39 2021 +0000
@@ -1,2 +1,2 @@
-test0 1 . G
-test0 4 . A
+test0	1	.	G
+test0	4	.	A