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changeset 4:ecf1c30da3a2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
author iuc
date Wed, 17 Oct 2018 05:59:21 -0400
parents bc7d99f46a5d
children a09586d5149a
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/paired_dat.fq.gz test-data/paired_dat1.fq.gz test-data/paired_dat2.fq.gz test-data/seqtk_comp.fa.gz test-data/seqtk_cutn.fa.gz test-data/seqtk_cutn.out.gz test-data/seqtk_dropse.fq.gz test-data/seqtk_dropse.out.gz test-data/seqtk_fqchk.fq.gz test-data/seqtk_hety.fa.gz test-data/seqtk_listhet.fa.gz test-data/seqtk_mergefa1.fa.gz test-data/seqtk_mergefa2.fa.gz test-data/seqtk_mergefa2.out.gz test-data/seqtk_mutfa.fa.gz test-data/seqtk_mutfa.out.gz test-data/seqtk_randbase.fa.gz test-data/seqtk_randbase.out.gz test-data/seqtk_sample.fa.gz test-data/seqtk_sample.out.gz test-data/seqtk_seq.fa.gz test-data/seqtk_seq_revcom.fa.gz test-data/seqtk_subseq.fa.gz test-data/seqtk_subseq.out.gz test-data/seqtk_trimfq.fq.gz test-data/seqtk_trimfq_be.fq.gz
diffstat 41 files changed, 104 insertions(+), 29 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Mon Jun 05 13:27:11 2017 -0400
+++ b/macros.xml	Wed Oct 17 05:59:21 2018 -0400
@@ -2,11 +2,11 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="1.2">seqtk</requirement>
+            <requirement type="package" version="1.3">seqtk</requirement>
             <yield/>
         </requirements>
     </xml>
-    <token name="@WRAPPER_VERSION@">1.2</token>
+    <token name="@WRAPPER_VERSION@">1.3</token>
     <xml name="stdio">
         <stdio>
             <!-- Anything other than zero is an error -->
@@ -18,11 +18,14 @@
         </stdio>
     </xml>
     <xml name="in_fq">
-        <param name="in_file" type="data" format="fastq" label="Input FASTQ file"/>
+        <param name="in_file" type="data" format="fastq,fastq.gz" label="Input FASTQ file"/>
     </xml>
     <xml name="in_faq">
-        <param name="in_file" type="data" format="fasta,fastq" label="Input FASTA/Q file"/>
+        <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'
+    ]]></token>
     <token name="@ATTRIBUTION@"><![CDATA[
 **Attribution**
 
--- a/seqtk_comp.xml	Mon Jun 05 13:27:11 2017 -0400
+++ b/seqtk_comp.xml	Wed Oct 17 05:59:21 2018 -0400
@@ -26,6 +26,10 @@
             <param name="in_file" value="seqtk_comp.fa" ftype="fasta"/>
             <output name="default" file="seqtk_comp.out" ftype="tabular"/>
         </test>
+        <test>
+            <param name="in_file" value="seqtk_comp.fa.gz" ftype="fasta.gz"/>
+            <output name="default" file="seqtk_comp.out" ftype="tabular"/>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**
--- a/seqtk_cutN.xml	Mon Jun 05 13:27:11 2017 -0400
+++ b/seqtk_cutN.xml	Wed Oct 17 05:59:21 2018 -0400
@@ -12,7 +12,7 @@
 -p $p
 $g
 '$in_file'
-> '$default'
+@CONDITIONAL_GZIP_OUT@
     ]]></command>
     <inputs>
         <expand macro="in_faq"/>
@@ -29,6 +29,11 @@
             <param name="n" value="1"/>
             <output name="default" file="seqtk_cutn.out" ftype="fasta"/>
         </test>
+        <test>
+            <param name="in_file" value="seqtk_cutn.fa.gz" ftype="fasta.gz"/>
+            <param name="n" value="1"/>
+            <output name="default" file="seqtk_cutn.out.gz" ftype="fasta.gz"/>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**
--- a/seqtk_dropse.xml	Mon Jun 05 13:27:11 2017 -0400
+++ b/seqtk_dropse.xml	Wed Oct 17 05:59:21 2018 -0400
@@ -9,7 +9,7 @@
     <command><![CDATA[
 seqtk dropse
 '$in_file'
-> '$default'
+@CONDITIONAL_GZIP_OUT@
     ]]></command>
     <inputs>
         <expand macro="in_faq"/>
@@ -19,8 +19,12 @@
     </outputs>
     <tests>
         <test>
-            <param name="in_file" value="seqtk_dropse.fq"/>
-            <output name="default" file="seqtk_dropse.out" ftype="fastq"/>
+            <param name="in_file" value="seqtk_dropse.fq" ftype="fastqsanger"/>
+            <output name="default" file="seqtk_dropse.out" ftype="fastqsanger"/>
+        </test>
+        <test>
+            <param name="in_file" value="seqtk_dropse.fq.gz" ftype="fastqsanger.gz"/>
+            <output name="default" file="seqtk_dropse.out.gz" ftype="fastqsanger.gz"/>
         </test>
     </tests>
     <help><![CDATA[
--- a/seqtk_fqchk.xml	Mon Jun 05 13:27:11 2017 -0400
+++ b/seqtk_fqchk.xml	Wed Oct 17 05:59:21 2018 -0400
@@ -21,7 +21,11 @@
     </outputs>
     <tests>
         <test>
-            <param name="in_file" value="seqtk_fqchk.fq"/>
+            <param name="in_file" value="seqtk_fqchk.fq" ftype="fastq"/>
+            <output name="default" file="seqtk_fqchk.out" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="in_file" value="seqtk_fqchk.fq.gz" ftype="fastq.gz"/>
             <output name="default" file="seqtk_fqchk.out" ftype="tabular"/>
         </test>
     </tests>
--- a/seqtk_hety.xml	Mon Jun 05 13:27:11 2017 -0400
+++ b/seqtk_hety.xml	Wed Oct 17 05:59:21 2018 -0400
@@ -29,6 +29,11 @@
             <param name="w" value="8"/>
             <output name="default" file="seqtk_hety.out" ftype="tabular"/>
         </test>
+        <test>
+            <param name="in_file" value="seqtk_hety.fa.gz" ftype="fasta.gz"/>
+            <param name="w" value="8"/>
+            <output name="default" file="seqtk_hety.out" ftype="tabular"/>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**
--- a/seqtk_listhet.xml	Mon Jun 05 13:27:11 2017 -0400
+++ b/seqtk_listhet.xml	Wed Oct 17 05:59:21 2018 -0400
@@ -22,6 +22,10 @@
             <param name="in_file" value="seqtk_listhet.fa"/>
             <output name="default" file="seqtk_listhet.out" ftype="tabular"/>
         </test>
+        <test>
+            <param name="in_file" value="seqtk_listhet.fa.gz" ftype="fasta.gz"/>
+            <output name="default" file="seqtk_listhet.out" ftype="tabular"/>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**
--- a/seqtk_mergefa.xml	Mon Jun 05 13:27:11 2017 -0400
+++ b/seqtk_mergefa.xml	Wed Oct 17 05:59:21 2018 -0400
@@ -15,11 +15,11 @@
 $h
 '$in_fa1'
 '$in_fa2'
-> '$default'
+#echo "| gzip --no-name" if $in_fa1.is_of_type('fasta.gz', 'fastq.gz') else "" # > '$default'
     ]]></command>
     <inputs>
-        <param name="in_fa1" type="data" format="fasta,fastq" label="Input FASTA/Q file #1"/>
-        <param name="in_fa2" type="data" format="fasta,fastq" label="Input FASTA/Q file #2"/>
+        <param name="in_fa1" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #1"/>
+        <param name="in_fa2" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #2"/>
         <param argument="-q" type="integer" value="0" label="Quality threshold"/>
         <param argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Take intersection" />
         <param argument="-m" type="boolean" truevalue="-m" falsevalue="" checked="false" label="Convert to lowercase when one of the input base is N" />
@@ -41,6 +41,12 @@
             <param name="m" value="True" />
             <output name="default" file="seqtk_mergefa2.out" ftype="fasta"/>
         </test>
+        <test>
+            <param name="in_fa1" value="seqtk_mergefa1.fa.gz" ftype="fasta.gz"/>
+            <param name="in_fa2" value="seqtk_mergefa2.fa.gz" ftype="fasta.gz"/>
+            <param name="m" value="True" />
+            <output name="default" file="seqtk_mergefa2.out.gz" ftype="fasta.gz"/>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**
--- a/seqtk_mergepe.xml	Mon Jun 05 13:27:11 2017 -0400
+++ b/seqtk_mergepe.xml	Wed Oct 17 05:59:21 2018 -0400
@@ -10,20 +10,25 @@
 seqtk mergepe
 '$in_fq1'
 '$in_fq2'
-> '$default'
+ #echo "| gzip --no-name" if $in_fq1.is_of_type('fasta.gz', 'fastq.gz') else "" # > '$default'
     ]]></command>
     <inputs>
-        <param name="in_fq1" type="data" format="fasta,fastq" label="Input FASTA/Q file #1"/>
-        <param name="in_fq2" type="data" format="fasta,fastq" label="Input FASTA/Q file #2"/>
+        <param name="in_fq1" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #1"/>
+        <param name="in_fq2" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #2"/>
     </inputs>
     <outputs>
         <data name="default" format_source="in_fq1" label="$in_fq1.name and $in_fq2.name as interleaved paired-end"/>
     </outputs>
     <tests>
         <test>
-            <param name="in_fq1" value="paired_dat1.fq"/>
-            <param name="in_fq2" value="paired_dat2.fq"/>
-            <output name="default" file="paired_dat.fq" ftype="fastq"/>
+            <param name="in_fq1" value="paired_dat1.fq" ftype="fastqsanger"/>
+            <param name="in_fq2" value="paired_dat2.fq" ftype="fastqsanger"/>
+            <output name="default" file="paired_dat.fq" ftype="fastqsanger"/>
+        </test>
+        <test>
+            <param name="in_fq1" value="paired_dat1.fq.gz" ftype="fastqsanger.gz"/>
+            <param name="in_fq2" value="paired_dat2.fq.gz" ftype="fastqsanger.gz"/>
+            <output name="default" file="paired_dat.fq.gz" ftype="fastqsanger.gz"/>
         </test>
     </tests>
     <help><![CDATA[
--- a/seqtk_mutfa.xml	Mon Jun 05 13:27:11 2017 -0400
+++ b/seqtk_mutfa.xml	Wed Oct 17 05:59:21 2018 -0400
@@ -10,7 +10,7 @@
 seqtk mutfa
 '$in_file'
 '$in_snp'
-> '$default'
+@CONDITIONAL_GZIP_OUT@
     ]]></command>
     <inputs>
         <expand macro="in_faq"/>
@@ -25,6 +25,11 @@
             <param name="in_snp" value="seqtk_mutfa.snp"/>
             <output name="default" file="seqtk_mutfa.out" ftype="fasta"/>
         </test>
+        <test>
+            <param name="in_file" value="seqtk_mutfa.fa.gz" ftype="fasta.gz"/>
+            <param name="in_snp" value="seqtk_mutfa.snp"/>
+            <output name="default" file="seqtk_mutfa.out.gz" ftype="fasta.gz"/>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**
--- a/seqtk_randbase.xml	Mon Jun 05 13:27:11 2017 -0400
+++ b/seqtk_randbase.xml	Wed Oct 17 05:59:21 2018 -0400
@@ -9,7 +9,7 @@
     <command><![CDATA[
 seqtk randbase
 '$in_file'
-> '$default'
+@CONDITIONAL_GZIP_OUT@
     ]]></command>
     <inputs>
         <expand macro="in_faq"/>
@@ -20,7 +20,11 @@
     <tests>
         <test>
             <param name="in_file" value="seqtk_randbase.fa"/>
-            <output name="default" file="seqtk_randbase.out" ftype="fasta"/>
+            <output name="default" file="seqtk_randbase.out" ftype="fasta" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="in_file" value="seqtk_randbase.fa.gz" ftype="fasta.gz"/>
+            <output name="default" file="seqtk_randbase.out.gz" ftype="fasta.gz" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[
--- a/seqtk_sample.xml	Mon Jun 05 13:27:11 2017 -0400
+++ b/seqtk_sample.xml	Wed Oct 17 05:59:21 2018 -0400
@@ -11,7 +11,7 @@
 -s $s
 '$in_file'
 $subsample_size
-> '$default'
+@CONDITIONAL_GZIP_OUT@
     ]]></command>
     <inputs>
         <expand macro="in_faq" />
@@ -28,6 +28,12 @@
             <param name="s" value="4"/>
             <output name="default" file="seqtk_sample.out" ftype="fasta"/>
         </test>
+        <test>
+            <param name="in_file" value="seqtk_sample.fa.gz" ftype="fasta.gz"/>
+            <param name="subsample_size" value="4"/>
+            <param name="s" value="4"/>
+            <output name="default" file="seqtk_sample.out.gz" ftype="fasta.gz"/>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**
--- a/seqtk_seq.xml	Mon Jun 05 13:27:11 2017 -0400
+++ b/seqtk_seq.xml	Wed Oct 17 05:59:21 2018 -0400
@@ -31,7 +31,7 @@
     -V
 #end if
 '$in_file'
-> '$default'
+@CONDITIONAL_GZIP_OUT@
     ]]></command>
     <inputs>
         <expand macro="in_faq"/>
@@ -66,6 +66,12 @@
             <param name="n" value=""/>
             <output name="default" file="seqtk_seq_revcom.fa" ftype="fasta"/>
         </test>
+        <test>
+            <param name="in_file" value="seqtk_seq.fa.gz" ftype="fasta.gz"/>
+            <param name="r" value="True"/>
+            <param name="n" value=""/>
+            <output name="default" file="seqtk_seq_revcom.fa.gz" ftype="fasta.gz"/>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**
--- a/seqtk_subseq.xml	Mon Jun 05 13:27:11 2017 -0400
+++ b/seqtk_subseq.xml	Wed Oct 17 05:59:21 2018 -0400
@@ -19,7 +19,7 @@
 #if $t == '-t':
     | awk 'BEGIN{print "chr\tunknown\tseq"}1'
 #end if
-> '$default'
+@CONDITIONAL_GZIP_OUT@
     ]]></command>
     <inputs>
         <expand macro="in_faq"/>
@@ -53,6 +53,13 @@
             <param name="name_list" value="seqtk_subseq_list.txt"/>
             <output name="default" file="seqtk_subseq.out" ftype="fasta"/>
         </test>
+        <test>
+            <param name="in_file" value="seqtk_subseq.fa.gz" ftype="fasta.gz"/>
+            <param name="type" value="name"/>
+            <param name="t" value="False" />
+            <param name="name_list" value="seqtk_subseq_list.txt"/>
+            <output name="default" file="seqtk_subseq.out.gz" ftype="fasta.gz"/>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**
--- a/seqtk_trimfq.xml	Mon Jun 05 13:27:11 2017 -0400
+++ b/seqtk_trimfq.xml	Wed Oct 17 05:59:21 2018 -0400
@@ -16,7 +16,7 @@
     -e $mode.e
 #end if
 '$in_file'
-> '$default'
+@CONDITIONAL_GZIP_OUT@
     ]]></command>
     <inputs>
         <expand macro="in_faq"/>
@@ -40,18 +40,25 @@
     </outputs>
     <tests>
         <test>
-            <param name="in_file" value="seqtk_trimfq.fq"/>
+            <param name="in_file" value="seqtk_trimfq.fq" ftype="fastqsanger"/>
             <param name="mode_select" value="quality"/>
             <param name="q" value="0.05"/>
             <param name="l" value="30"/>
-            <output name="default" file="seqtk_trimfq_default.fq" ftype="fastq"/>
+            <output name="default" file="seqtk_trimfq_default.fq" ftype="fastqsanger"/>
         </test>
         <test>
-            <param name="in_file" value="seqtk_trimfq.fq"/>
+            <param name="in_file" value="seqtk_trimfq.fq" ftype="fastqsanger"/>
             <param name="mode_select" value="position"/>
             <param name="b" value="5"/>
             <param name="e" value="5"/>
-            <output name="default" file="seqtk_trimfq_be.fq" ftype="fastq"/>
+            <output name="default" file="seqtk_trimfq_be.fq" ftype="fastqsanger"/>
+        </test>
+        <test>
+            <param name="in_file" value="seqtk_trimfq.fq.gz" ftype="fastqsanger.gz"/>
+            <param name="mode_select" value="position"/>
+            <param name="b" value="5"/>
+            <param name="e" value="5"/>
+            <output name="default" file="seqtk_trimfq_be.fq.gz" ftype="fastqsanger.gz"/>
         </test>
     </tests>
     <help><![CDATA[
Binary file test-data/paired_dat.fq.gz has changed
Binary file test-data/paired_dat1.fq.gz has changed
Binary file test-data/paired_dat2.fq.gz has changed
Binary file test-data/seqtk_comp.fa.gz has changed
Binary file test-data/seqtk_cutn.fa.gz has changed
Binary file test-data/seqtk_cutn.out.gz has changed
Binary file test-data/seqtk_dropse.fq.gz has changed
Binary file test-data/seqtk_dropse.out.gz has changed
Binary file test-data/seqtk_fqchk.fq.gz has changed
Binary file test-data/seqtk_hety.fa.gz has changed
Binary file test-data/seqtk_listhet.fa.gz has changed
Binary file test-data/seqtk_mergefa1.fa.gz has changed
Binary file test-data/seqtk_mergefa2.fa.gz has changed
Binary file test-data/seqtk_mergefa2.out.gz has changed
Binary file test-data/seqtk_mutfa.fa.gz has changed
Binary file test-data/seqtk_mutfa.out.gz has changed
Binary file test-data/seqtk_randbase.fa.gz has changed
Binary file test-data/seqtk_randbase.out.gz has changed
Binary file test-data/seqtk_sample.fa.gz has changed
Binary file test-data/seqtk_sample.out.gz has changed
Binary file test-data/seqtk_seq.fa.gz has changed
Binary file test-data/seqtk_seq_revcom.fa.gz has changed
Binary file test-data/seqtk_subseq.fa.gz has changed
Binary file test-data/seqtk_subseq.out.gz has changed
Binary file test-data/seqtk_trimfq.fq.gz has changed
Binary file test-data/seqtk_trimfq_be.fq.gz has changed