| Previous changeset 4:ecf1c30da3a2 (2018-10-17) Next changeset 6:288f7f69fe25 (2019-09-06) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 83ecfe7d9bbf03c91f27ba18776352a1ebf8cf6f |
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modified:
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 |
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| diff -r ecf1c30da3a2 -r a09586d5149a macros.xml --- a/macros.xml Wed Oct 17 05:59:21 2018 -0400 +++ b/macros.xml Fri Jan 11 05:15:20 2019 -0500 |
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| @@ -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** |
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| diff -r ecf1c30da3a2 -r a09586d5149a seqtk_comp.xml --- a/seqtk_comp.xml Wed Oct 17 05:59:21 2018 -0400 +++ b/seqtk_comp.xml Fri Jan 11 05:15:20 2019 -0500 |
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| @@ -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 |
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| diff -r ecf1c30da3a2 -r a09586d5149a seqtk_cutN.xml --- a/seqtk_cutN.xml Wed Oct 17 05:59:21 2018 -0400 +++ b/seqtk_cutN.xml Fri Jan 11 05:15:20 2019 -0500 |
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| @@ -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> |
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| diff -r ecf1c30da3a2 -r a09586d5149a seqtk_dropse.xml --- a/seqtk_dropse.xml Wed Oct 17 05:59:21 2018 -0400 +++ b/seqtk_dropse.xml Fri Jan 11 05:15:20 2019 -0500 |
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| @@ -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> |
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| diff -r ecf1c30da3a2 -r a09586d5149a seqtk_fqchk.xml --- a/seqtk_fqchk.xml Wed Oct 17 05:59:21 2018 -0400 +++ b/seqtk_fqchk.xml Fri Jan 11 05:15:20 2019 -0500 |
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| @@ -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 |
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| diff -r ecf1c30da3a2 -r a09586d5149a seqtk_hety.xml --- a/seqtk_hety.xml Wed Oct 17 05:59:21 2018 -0400 +++ b/seqtk_hety.xml Fri Jan 11 05:15:20 2019 -0500 |
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| @@ -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 |
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| diff -r ecf1c30da3a2 -r a09586d5149a seqtk_listhet.xml --- a/seqtk_listhet.xml Wed Oct 17 05:59:21 2018 -0400 +++ b/seqtk_listhet.xml Fri Jan 11 05:15:20 2019 -0500 |
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| @@ -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 |
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| diff -r ecf1c30da3a2 -r a09586d5149a seqtk_mergefa.xml --- a/seqtk_mergefa.xml Wed Oct 17 05:59:21 2018 -0400 +++ b/seqtk_mergefa.xml Fri Jan 11 05:15:20 2019 -0500 |
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| @@ -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"/> |
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| diff -r ecf1c30da3a2 -r a09586d5149a seqtk_mergepe.xml --- a/seqtk_mergepe.xml Wed Oct 17 05:59:21 2018 -0400 +++ b/seqtk_mergepe.xml Fri Jan 11 05:15:20 2019 -0500 |
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| @@ -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"/> |
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| diff -r ecf1c30da3a2 -r a09586d5149a seqtk_mutfa.xml --- a/seqtk_mutfa.xml Wed Oct 17 05:59:21 2018 -0400 +++ b/seqtk_mutfa.xml Fri Jan 11 05:15:20 2019 -0500 |
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| @@ -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> |
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| diff -r ecf1c30da3a2 -r a09586d5149a seqtk_randbase.xml --- a/seqtk_randbase.xml Wed Oct 17 05:59:21 2018 -0400 +++ b/seqtk_randbase.xml Fri Jan 11 05:15:20 2019 -0500 |
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| @@ -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> |
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| diff -r ecf1c30da3a2 -r a09586d5149a seqtk_sample.xml --- a/seqtk_sample.xml Wed Oct 17 05:59:21 2018 -0400 +++ b/seqtk_sample.xml Fri Jan 11 05:15:20 2019 -0500 |
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| @@ -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> |
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| diff -r ecf1c30da3a2 -r a09586d5149a seqtk_seq.xml --- a/seqtk_seq.xml Wed Oct 17 05:59:21 2018 -0400 +++ b/seqtk_seq.xml Fri Jan 11 05:15:20 2019 -0500 |
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| @@ -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> |
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| diff -r ecf1c30da3a2 -r a09586d5149a seqtk_subseq.xml --- a/seqtk_subseq.xml Wed Oct 17 05:59:21 2018 -0400 +++ b/seqtk_subseq.xml Fri Jan 11 05:15:20 2019 -0500 |
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| @@ -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"/> |
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| diff -r ecf1c30da3a2 -r a09586d5149a seqtk_trimfq.xml --- a/seqtk_trimfq.xml Wed Oct 17 05:59:21 2018 -0400 +++ b/seqtk_trimfq.xml Fri Jan 11 05:15:20 2019 -0500 |
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| @@ -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> |
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| diff -r ecf1c30da3a2 -r a09586d5149a test-data/seqtk_randbase.out.gz |
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| Binary file test-data/seqtk_randbase.out.gz has changed |