| Previous changeset 18:5c7e7d905b33 (2018-12-13) Next changeset 20:e4691e1589d3 (2019-04-08) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 6318c53e772ed592862729f3048ed9bd3a711969 |
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modified:
cutadapt.xml macros.xml |
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added:
test-data/barcodes.fasta |
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| diff -r 5c7e7d905b33 -r 49370cb85f0f cutadapt.xml --- a/cutadapt.xml Thu Dec 13 20:54:04 2018 -0500 +++ b/cutadapt.xml Tue Dec 18 14:09:53 2018 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="cutadapt" name="Cutadapt" version="1.16.4" profile="17.09"> +<tool id="cutadapt" name="Cutadapt" version="1.16.5" profile="17.09"> <description>Remove adapter sequences from Fastq/Fasta</description> <macros> <import>macros.xml</import> @@ -444,16 +444,8 @@ <section name="r1" > <repeat name="front_adapters"> <conditional name="front_adapter_source"> - <param name="front_adapter_source_list" value="user"/> - <param name="front_adapter_name" value="A1" /> - <param name="front_adapter" value="^GTCGGTAA" /> - </conditional> - </repeat> - <repeat name="front_adapters"> - <conditional name="front_adapter_source"> - <param name="front_adapter_source_list" value="user"/> - <param name="front_adapter_name" value="A2" /> - <param name="front_adapter" value="^AGGTCACT" /> + <param name="front_adapter_source_list" value="file"/> + <param name="front_adapter_file" ftype="fasta" value="barcodes.fasta" /> </conditional> </repeat> </section> @@ -499,7 +491,7 @@ - FASTQ.GZ, FASTQ.BZ2, FASTQ or FASTA -To trim an adapter, input the ADAPTER sequence e.g. AACCGGTT (with the characters: **$**, **^**, **...**, if anchored or linked). +To trim an adapter, input the ADAPTER sequence in plain text or in a FASTA file e.g. AACCGGTT (with the characters: **$**, **^**, **...**, if anchored or linked). ============================================= =================== **Option** **Sequence** |
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| diff -r 5c7e7d905b33 -r 49370cb85f0f macros.xml --- a/macros.xml Thu Dec 13 20:54:04 2018 -0500 +++ b/macros.xml Tue Dec 18 14:09:53 2018 -0500 |
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| b'@@ -7,6 +7,8 @@\n #for $a in $library.r1.adapters\n #if $a.adapter_source.adapter_source_list == \'builtin\':\n -a "${a.adapter_source.adapter.fields.name}"=\'${a.adapter_source.adapter}\'\n+ #else if $a.adapter_source.adapter_source_list == \'file\':\n+ -a file:\'${a.adapter_source.adapter_file}\'\n #else if str($a.adapter_source.adapter_name) != "":\n -a \'${a.adapter_source.adapter_name}\'=\'${a.adapter_source.adapter}\'\n #else\n@@ -16,6 +18,8 @@\n #for $aa in $library.r1.anywhere_adapters\n #if $aa.anywhere_adapter_source.anywhere_adapter_source_list == \'builtin\':\n -b ${aa.anywhere_adapter_source.anywhere_adapter.fields.name}"=\'${aa.anywhere_adapter_source.anywhere_adapter}\'\n+ #else if $aa.anywhere_adapter_source.anywhere_adapter_source_list == \'file\':\n+ -b file:\'${aa.anywhere_adapter_source.anywhere_adapter_file}\'\n #else if str($aa.anywhere_adapter_source.anywhere_adapter_name) != "":\n -b \'${aa.anywhere_adapter_source.anywhere_adapter_name}\'=\'${aa.anywhere_adapter_source.anywhere_adapter}\'\n #else\n@@ -25,6 +29,8 @@\n #for $fa in $library.r1.front_adapters\n #if $fa.front_adapter_source.front_adapter_source_list == \'builtin\':\n -g "${fa.front_adapter_source.front_adapter.fields.name}"=\'${fa.front_adapter_source.front_adapter}\'\n+ #else if $fa.front_adapter_source.front_adapter_source_list == \'file\':\n+ -g file:\'${fa.front_adapter_source.front_adapter_file}\'\n #else if str($fa.front_adapter_source.front_adapter_name) != "":\n -g \'${fa.front_adapter_source.front_adapter_name}\'=\'${fa.front_adapter_source.front_adapter}\'\n #else\n@@ -66,6 +72,8 @@\n #for $a in $library.r2.adapters2\n #if $a.adapter_source2.adapter_source_list2 == \'builtin\':\n -A "${a.adapter_source2.adapter2.fields.name}"=\'${a.adapter_source2.adapter2}\'\n+ #else if $a.adapter_source2.adapter_source_list2 == \'file\':\n+ -A file:\'${a.adapter_source2.adapter_file2}\'\n #else if str($a.adapter_source2.adapter_name2) != "":\n -A \'${a.adapter_source2.adapter_name2}\'=\'${a.adapter_source2.adapter2}\'\n #else\n@@ -75,6 +83,8 @@\n #for $aa in $library.r2.anywhere_adapters2\n #if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == \'builtin\':\n -B "${aa.anywhere_adapter_source2.anywhere_adapter2.fields.name}"=\'${aa.anywhere_adapter_source2.anywhere_adapter2}\'\n+ #else if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == \'file\':\n+ -B file:\'${aa.anywhere_adapter_source2.anywhere_adapter_file2}\'\n #else if str($aa.anywhere_adapter_source2.anywhere_adapter_name2) != "":\n -B \'${aa.anywhere_adapter_source2.anywhere_adapter_name2}\'=\'${aa.anywhere_adapter_source2.anywhere_adapter2}\'\n #else\n@@ -84,6 +94,8 @@\n #for $fa in $library.r2.front_adapters2\n #if $fa.front_adapter_source2.front_adapter_source_list2 == \'builtin\':\n -G "${fa.front_adapter_source2.front_adapter2.fields.name}"=\'${fa.front_adapter_source2.front_adapter2}\'\n+ #else if $fa.front_adapter_source2.front_adapter_source_list2 == \'file\':\n+ -G file:\'${fa.front_adapter_source2.front_adapter_file2}\'\n #else if str($fa.front_adapter_source2.front_adapter_name2) != "":\n -G \'${fa.front_adapter_source2.front_adapter_name2}\'=\'${fa.front_adapter_source2.front_adapter2}\'\n #else\n@@ -118,6 +130,7 @@\n <param name="adapter_source_list" type="select" label="Source" >\n <option value="builtin" selected="True">Standard (select from the list below)</option>\n <option value="user">Enter cu'..b' type="data" help="Should be of datatype "FASTA"" label="Choose file containing 5\' adapters" />\n+ </when>\n </conditional>\n </repeat>\n \n@@ -161,6 +182,7 @@\n <param name="anywhere_adapter_source_list" type="select" label="Source">\n <option value="builtin" selected="True">Standard (select from the list below)</option>\n <option value="user">Enter custom sequence</option>\n+ <option value="file">File From History</option>\n </param>\n \n <when value="user">\n@@ -174,6 +196,9 @@\n </options>\n </param>\n </when>\n+ <when value="file">\n+ <param name="anywhere_adapter_file" argument="-b" format="fasta" type="data" help="Should be of datatype "FASTA"" label="Choose file containing 3\' or 5\' adapters" />\n+ </when>\n </conditional>\n </repeat>\n \n@@ -196,6 +221,7 @@\n <param name="adapter_source_list2" type="select" label="Source" >\n <option value="builtin" selected="True">Standard (select from the list below)</option>\n <option value="user">Enter custom sequence</option>\n+ <option value="file">File From History</option>\n </param>\n \n <when value="user">\n@@ -210,6 +236,9 @@\n </options>\n </param>\n </when>\n+ <when value="file">\n+ <param name="adapter_file2" argument="-a" format="fasta" type="data" help="Should be of datatype "FASTA"" label="Choose file containing 3\' adapters" />\n+ </when>\n </conditional>\n </repeat>\n \n@@ -218,6 +247,7 @@\n <param name="front_adapter_source_list2" type="select" label="Source">\n <option value="builtin" selected="True">Standard (select from the list below)</option>\n <option value="user">Enter custom sequence</option>\n+ <option value="file">File From History</option>\n </param>\n \n <when value="user">\n@@ -231,6 +261,9 @@\n </options>\n </param>\n </when>\n+ <when value="file">\n+ <param name="front_adapter_file2" argument="-g" format="fasta" type="data" help="Should be of datatype "FASTA"" label="Choose file containing 5\' adapters" />\n+ </when>\n </conditional>\n </repeat>\n \n@@ -239,6 +272,7 @@\n <param name="anywhere_adapter_source_list2" type="select" label="Source">\n <option value="builtin" selected="True">Standard (select from the list below)</option>\n <option value="user">Enter custom sequence</option>\n+ <option value="file">File From History</option>\n </param>\n \n <when value="user">\n@@ -252,6 +286,9 @@\n </options>\n </param>\n </when>\n+ <when value="file">\n+ <param name="anywhere_adapter_file2" argument="-b" format="fasta" type="data" help="Should be of datatype "FASTA"" label="Choose file containing 3\' or 5\' adapters" />\n+ </when>\n </conditional>\n </repeat>\n \n' |
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| diff -r 5c7e7d905b33 -r 49370cb85f0f test-data/barcodes.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/barcodes.fasta Tue Dec 18 14:09:53 2018 -0500 |
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| @@ -0,0 +1,4 @@ +>A2 +^AGGTCACT +>A1 +^GTCGGTAA |