Mercurial > repos > lparsons > cutadapt
changeset 19:49370cb85f0f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 6318c53e772ed592862729f3048ed9bd3a711969
| author | iuc |
|---|---|
| date | Tue, 18 Dec 2018 14:09:53 -0500 |
| parents | 5c7e7d905b33 |
| children | e4691e1589d3 |
| files | cutadapt.xml macros.xml test-data/barcodes.fasta |
| diffstat | 3 files changed, 45 insertions(+), 12 deletions(-) [+] |
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--- a/cutadapt.xml Thu Dec 13 20:54:04 2018 -0500 +++ b/cutadapt.xml Tue Dec 18 14:09:53 2018 -0500 @@ -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**
--- a/macros.xml Thu Dec 13 20:54:04 2018 -0500 +++ b/macros.xml Tue Dec 18 14:09:53 2018 -0500 @@ -7,6 +7,8 @@ #for $a in $library.r1.adapters #if $a.adapter_source.adapter_source_list == 'builtin': -a "${a.adapter_source.adapter.fields.name}"='${a.adapter_source.adapter}' + #else if $a.adapter_source.adapter_source_list == 'file': + -a file:'${a.adapter_source.adapter_file}' #else if str($a.adapter_source.adapter_name) != "": -a '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}' #else @@ -16,6 +18,8 @@ #for $aa in $library.r1.anywhere_adapters #if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'builtin': -b ${aa.anywhere_adapter_source.anywhere_adapter.fields.name}"='${aa.anywhere_adapter_source.anywhere_adapter}' + #else if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'file': + -b file:'${aa.anywhere_adapter_source.anywhere_adapter_file}' #else if str($aa.anywhere_adapter_source.anywhere_adapter_name) != "": -b '${aa.anywhere_adapter_source.anywhere_adapter_name}'='${aa.anywhere_adapter_source.anywhere_adapter}' #else @@ -25,6 +29,8 @@ #for $fa in $library.r1.front_adapters #if $fa.front_adapter_source.front_adapter_source_list == 'builtin': -g "${fa.front_adapter_source.front_adapter.fields.name}"='${fa.front_adapter_source.front_adapter}' + #else if $fa.front_adapter_source.front_adapter_source_list == 'file': + -g file:'${fa.front_adapter_source.front_adapter_file}' #else if str($fa.front_adapter_source.front_adapter_name) != "": -g '${fa.front_adapter_source.front_adapter_name}'='${fa.front_adapter_source.front_adapter}' #else @@ -66,6 +72,8 @@ #for $a in $library.r2.adapters2 #if $a.adapter_source2.adapter_source_list2 == 'builtin': -A "${a.adapter_source2.adapter2.fields.name}"='${a.adapter_source2.adapter2}' + #else if $a.adapter_source2.adapter_source_list2 == 'file': + -A file:'${a.adapter_source2.adapter_file2}' #else if str($a.adapter_source2.adapter_name2) != "": -A '${a.adapter_source2.adapter_name2}'='${a.adapter_source2.adapter2}' #else @@ -75,6 +83,8 @@ #for $aa in $library.r2.anywhere_adapters2 #if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'builtin': -B "${aa.anywhere_adapter_source2.anywhere_adapter2.fields.name}"='${aa.anywhere_adapter_source2.anywhere_adapter2}' + #else if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'file': + -B file:'${aa.anywhere_adapter_source2.anywhere_adapter_file2}' #else if str($aa.anywhere_adapter_source2.anywhere_adapter_name2) != "": -B '${aa.anywhere_adapter_source2.anywhere_adapter_name2}'='${aa.anywhere_adapter_source2.anywhere_adapter2}' #else @@ -84,6 +94,8 @@ #for $fa in $library.r2.front_adapters2 #if $fa.front_adapter_source2.front_adapter_source_list2 == 'builtin': -G "${fa.front_adapter_source2.front_adapter2.fields.name}"='${fa.front_adapter_source2.front_adapter2}' + #else if $fa.front_adapter_source2.front_adapter_source_list2 == 'file': + -G file:'${fa.front_adapter_source2.front_adapter_file2}' #else if str($fa.front_adapter_source2.front_adapter_name2) != "": -G '${fa.front_adapter_source2.front_adapter_name2}'='${fa.front_adapter_source2.front_adapter2}' #else @@ -118,6 +130,7 @@ <param name="adapter_source_list" type="select" label="Source" > <option value="builtin" selected="True">Standard (select from the list below)</option> <option value="user">Enter custom sequence</option> + <option value="file">File From History</option> </param> <when value="user"> @@ -132,6 +145,10 @@ </options> </param> </when> + + <when value="file"> + <param name="adapter_file" argument="-a" format="fasta" type="data" help="Should be of datatype FASTA" label="Choose file containing 3' adapters" /> + </when> </conditional> </repeat> @@ -140,6 +157,7 @@ <param name="front_adapter_source_list" type="select" label="Source"> <option value="builtin" selected="True">Standard (select from the list below)</option> <option value="user">Enter custom sequence</option> + <option value="file">File From History</option> </param> <when value="user"> @@ -153,6 +171,9 @@ </options> </param> </when> + <when value="file"> + <param name="front_adapter_file" argument="-g" format="fasta" type="data" help="Should be of datatype "FASTA"" label="Choose file containing 5' adapters" /> + </when> </conditional> </repeat> @@ -161,6 +182,7 @@ <param name="anywhere_adapter_source_list" type="select" label="Source"> <option value="builtin" selected="True">Standard (select from the list below)</option> <option value="user">Enter custom sequence</option> + <option value="file">File From History</option> </param> <when value="user"> @@ -174,6 +196,9 @@ </options> </param> </when> + <when value="file"> + <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" /> + </when> </conditional> </repeat> @@ -196,6 +221,7 @@ <param name="adapter_source_list2" type="select" label="Source" > <option value="builtin" selected="True">Standard (select from the list below)</option> <option value="user">Enter custom sequence</option> + <option value="file">File From History</option> </param> <when value="user"> @@ -210,6 +236,9 @@ </options> </param> </when> + <when value="file"> + <param name="adapter_file2" argument="-a" format="fasta" type="data" help="Should be of datatype "FASTA"" label="Choose file containing 3' adapters" /> + </when> </conditional> </repeat> @@ -218,6 +247,7 @@ <param name="front_adapter_source_list2" type="select" label="Source"> <option value="builtin" selected="True">Standard (select from the list below)</option> <option value="user">Enter custom sequence</option> + <option value="file">File From History</option> </param> <when value="user"> @@ -231,6 +261,9 @@ </options> </param> </when> + <when value="file"> + <param name="front_adapter_file2" argument="-g" format="fasta" type="data" help="Should be of datatype "FASTA"" label="Choose file containing 5' adapters" /> + </when> </conditional> </repeat> @@ -239,6 +272,7 @@ <param name="anywhere_adapter_source_list2" type="select" label="Source"> <option value="builtin" selected="True">Standard (select from the list below)</option> <option value="user">Enter custom sequence</option> + <option value="file">File From History</option> </param> <when value="user"> @@ -252,6 +286,9 @@ </options> </param> </when> + <when value="file"> + <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" /> + </when> </conditional> </repeat>