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changeset 5:a09586d5149a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 83ecfe7d9bbf03c91f27ba18776352a1ebf8cf6f
author iuc
date Fri, 11 Jan 2019 05:15:20 -0500
parents ecf1c30da3a2
children 288f7f69fe25
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_randbase.out.gz
diffstat 16 files changed, 34 insertions(+), 23 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Wed Oct 17 05:59:21 2018 -0400
+++ b/macros.xml	Fri Jan 11 05:15:20 2019 -0500
@@ -2,11 +2,13 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="1.3">seqtk</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">seqtk</requirement>
+            <requirement type="package" version="2.3.4">pigz</requirement>
             <yield/>
         </requirements>
     </xml>
-    <token name="@WRAPPER_VERSION@">1.3</token>
+    <token name="@TOOL_VERSION@">1.3</token>
+    <token name="@AWK_VERSION@">4.2.1</token>
     <xml name="stdio">
         <stdio>
             <!-- Anything other than zero is an error -->
@@ -24,7 +26,7 @@
         <param name="in_file" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file"/>
     </xml>
     <token name="@CONDITIONAL_GZIP_OUT@"><![CDATA[
-    #echo "| gzip --no-name" if $in_file.is_of_type('fasta.gz', 'fastq.gz') else "" # > '$default'
+    #echo "| pigz --no-name --no-time" if $in_file.is_of_type('fasta.gz', 'fastq.gz') else "" # > '$default'
     ]]></token>
     <token name="@ATTRIBUTION@"><![CDATA[
 **Attribution**
--- a/seqtk_comp.xml	Wed Oct 17 05:59:21 2018 -0400
+++ b/seqtk_comp.xml	Fri Jan 11 05:15:20 2019 -0500
@@ -1,10 +1,12 @@
 <?xml version="1.0"?>
-<tool id="seqtk_comp" name="seqtk_comp" version="@WRAPPER_VERSION@.0">
+<tool id="seqtk_comp" name="seqtk_comp" version="@TOOL_VERSION@.1">
     <description>get the nucleotide composition of FASTA/Q</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
+    <expand macro="requirements">
+        <requirement type="package" version="@AWK_VERSION@">gawk</requirement>
+    </expand>
     <expand macro="stdio"/>
     <command><![CDATA[
 seqtk comp
--- a/seqtk_cutN.xml	Wed Oct 17 05:59:21 2018 -0400
+++ b/seqtk_cutN.xml	Fri Jan 11 05:15:20 2019 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="seqtk_cutN" name="seqtk_cutN" version="@WRAPPER_VERSION@.0">
+<tool id="seqtk_cutN" name="seqtk_cutN" version="@TOOL_VERSION@.1">
     <description>cut sequence at long N</description>
     <macros>
         <import>macros.xml</import>
--- a/seqtk_dropse.xml	Wed Oct 17 05:59:21 2018 -0400
+++ b/seqtk_dropse.xml	Fri Jan 11 05:15:20 2019 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="seqtk_dropse" name="seqtk_dropse" version="@WRAPPER_VERSION@.0">
+<tool id="seqtk_dropse" name="seqtk_dropse" version="@TOOL_VERSION@.1">
     <description>drop unpaired from interleaved Paired End FASTA/Q</description>
     <macros>
         <import>macros.xml</import>
--- a/seqtk_fqchk.xml	Wed Oct 17 05:59:21 2018 -0400
+++ b/seqtk_fqchk.xml	Fri Jan 11 05:15:20 2019 -0500
@@ -1,10 +1,12 @@
 <?xml version="1.0"?>
-<tool id="seqtk_fqchk" name="seqtk_fqchk" version="@WRAPPER_VERSION@.0">
+<tool id="seqtk_fqchk" name="seqtk_fqchk" version="@TOOL_VERSION@.1">
     <description>fastq QC (base/quality summary)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
+    <expand macro="requirements">
+        <requirement type="package" version="@AWK_VERSION@">gawk</requirement>
+    </expand>
     <expand macro="stdio"/>
     <command><![CDATA[
 seqtk fqchk
--- a/seqtk_hety.xml	Wed Oct 17 05:59:21 2018 -0400
+++ b/seqtk_hety.xml	Fri Jan 11 05:15:20 2019 -0500
@@ -1,10 +1,12 @@
 <?xml version="1.0"?>
-<tool id="seqtk_hety" name="seqtk_hety" version="@WRAPPER_VERSION@.0">
+<tool id="seqtk_hety" name="seqtk_hety" version="@TOOL_VERSION@.1">
     <description>regional heterozygosity</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
+    <expand macro="requirements">
+        <requirement type="package" version="@AWK_VERSION@">gawk</requirement>
+    </expand>
     <expand macro="stdio"/>
     <command><![CDATA[
 seqtk hety
--- a/seqtk_listhet.xml	Wed Oct 17 05:59:21 2018 -0400
+++ b/seqtk_listhet.xml	Fri Jan 11 05:15:20 2019 -0500
@@ -1,10 +1,12 @@
 <?xml version="1.0"?>
-<tool id="seqtk_listhet" name="seqtk_listhet" version="@WRAPPER_VERSION@.0">
+<tool id="seqtk_listhet" name="seqtk_listhet" version="@TOOL_VERSION@.1">
     <description>extract the position of each het</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
+    <expand macro="requirements">
+        <requirement type="package" version="@AWK_VERSION@">gawk</requirement>
+    </expand>
     <expand macro="stdio"/>
     <command><![CDATA[
 seqtk listhet
--- a/seqtk_mergefa.xml	Wed Oct 17 05:59:21 2018 -0400
+++ b/seqtk_mergefa.xml	Fri Jan 11 05:15:20 2019 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="seqtk_mergefa" name="seqtk_mergefa" version="@WRAPPER_VERSION@.0">
+<tool id="seqtk_mergefa" name="seqtk_mergefa" version="@TOOL_VERSION@.1">
     <description>merge two FASTA/Q files</description>
     <macros>
         <import>macros.xml</import>
@@ -15,7 +15,7 @@
 $h
 '$in_fa1'
 '$in_fa2'
-#echo "| gzip --no-name" if $in_fa1.is_of_type('fasta.gz', 'fastq.gz') else "" # > '$default'
+#echo "| pigz --no-name --no-time" if $in_fa1.is_of_type('fasta.gz', 'fastq.gz') else "" # > '$default'
     ]]></command>
     <inputs>
         <param name="in_fa1" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #1"/>
--- a/seqtk_mergepe.xml	Wed Oct 17 05:59:21 2018 -0400
+++ b/seqtk_mergepe.xml	Fri Jan 11 05:15:20 2019 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="seqtk_mergepe" name="seqtk_mergepe" version="@WRAPPER_VERSION@.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>
     <macros>
         <import>macros.xml</import>
@@ -10,7 +10,7 @@
 seqtk mergepe
 '$in_fq1'
 '$in_fq2'
- #echo "| gzip --no-name" if $in_fq1.is_of_type('fasta.gz', 'fastq.gz') else "" # > '$default'
+ #echo "| pigz --no-name --no-time" if $in_fq1.is_of_type('fasta.gz', 'fastq.gz') else "" # > '$default'
     ]]></command>
     <inputs>
         <param name="in_fq1" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #1"/>
--- a/seqtk_mutfa.xml	Wed Oct 17 05:59:21 2018 -0400
+++ b/seqtk_mutfa.xml	Fri Jan 11 05:15:20 2019 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="seqtk_mutfa" name="seqtk_mutfa" version="@WRAPPER_VERSION@.0">
+<tool id="seqtk_mutfa" name="seqtk_mutfa" version="@TOOL_VERSION@.1">
     <description>point mutate FASTA at specified positions</description>
     <macros>
         <import>macros.xml</import>
--- a/seqtk_randbase.xml	Wed Oct 17 05:59:21 2018 -0400
+++ b/seqtk_randbase.xml	Fri Jan 11 05:15:20 2019 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="seqtk_randbase" name="seqtk_randbase" version="@WRAPPER_VERSION@.0">
+<tool id="seqtk_randbase" name="seqtk_randbase" version="@TOOL_VERSION@.1">
     <description>choose a random base from hets</description>
     <macros>
         <import>macros.xml</import>
--- a/seqtk_sample.xml	Wed Oct 17 05:59:21 2018 -0400
+++ b/seqtk_sample.xml	Fri Jan 11 05:15:20 2019 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="seqtk_sample" name="seqtk_sample" version="@WRAPPER_VERSION@.0">
+<tool id="seqtk_sample" name="seqtk_sample" version="@TOOL_VERSION@.1">
     <description>random subsample of fasta or fastq sequences</description>
     <macros>
         <import>macros.xml</import>
--- a/seqtk_seq.xml	Wed Oct 17 05:59:21 2018 -0400
+++ b/seqtk_seq.xml	Fri Jan 11 05:15:20 2019 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="seqtk_seq" name="seqtk_seq" version="@WRAPPER_VERSION@.2">
+<tool id="seqtk_seq" name="seqtk_seq" version="@TOOL_VERSION@.3">
     <description>common transformation of FASTA/Q</description>
     <macros>
         <import>macros.xml</import>
--- a/seqtk_subseq.xml	Wed Oct 17 05:59:21 2018 -0400
+++ b/seqtk_subseq.xml	Fri Jan 11 05:15:20 2019 -0500
@@ -1,8 +1,9 @@
 <?xml version="1.0"?>
-<tool id="seqtk_subseq" name="seqtk_subseq" version="@WRAPPER_VERSION@.0">
+<tool id="seqtk_subseq" name="seqtk_subseq" version="@TOOL_VERSION@.1">
     <description>extract subsequences from FASTA/Q files</description>
     <macros>
         <import>macros.xml</import>
+        <requirement type="package" version="@AWK_VERSION@">gawk</requirement>
     </macros>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
--- a/seqtk_trimfq.xml	Wed Oct 17 05:59:21 2018 -0400
+++ b/seqtk_trimfq.xml	Fri Jan 11 05:15:20 2019 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="seqtk_trimfq" name="seqtk_trimfq" version="@WRAPPER_VERSION@.0">
+<tool id="seqtk_trimfq" name="seqtk_trimfq" version="@TOOL_VERSION@.1">
     <description>trim FASTQ using the Phred algorithm</description>
     <macros>
         <import>macros.xml</import>
Binary file test-data/seqtk_randbase.out.gz has changed