Mercurial > repos > lparsons > cutadapt
changeset 22:093678460093 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
| author | iuc |
|---|---|
| date | Sat, 04 Jul 2020 06:52:59 -0400 |
| parents | 104d86c98776 |
| children | c4b82dce8335 |
| files | cutadapt.xml macros.xml |
| diffstat | 2 files changed, 76 insertions(+), 49 deletions(-) [+] |
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--- a/cutadapt.xml Thu Mar 05 06:45:31 2020 -0500 +++ b/cutadapt.xml Sat Jul 04 06:52:59 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="cutadapt" name="Cutadapt" version="1.16.7" profile="17.09"> +<tool id="cutadapt" name="Cutadapt" version="1.16.8" profile="17.09"> <description>Remove adapter sequences from Fastq/Fasta</description> <macros> <import>macros.xml</import> @@ -113,7 +113,7 @@ #if str($filter_options.max): --maximum-length=$filter_options.max #end if -#if $filter_options.max_n: +#if str($filter_options.max_n): --max-n=$filter_options.max_n #end if #if str( $library.type ) != "single": @@ -131,16 +131,16 @@ #end if $read_mod_options.trim_n #if $read_mod_options.prefix != '': - --prefix="$read_mod_options.prefix" + --prefix='$read_mod_options.prefix' #end if #if $read_mod_options.suffix != '': - --suffix="$read_mod_options.suffix" + --suffix='$read_mod_options.suffix' #end if #if str($read_mod_options.length) != '0': --length=$read_mod_options.length #end if #if $read_mod_options.length_tag != '': - --length-tag="$read_mod_options.length_tag" + --length-tag='$read_mod_options.length_tag' #end if '${read1}' @@ -518,14 +518,14 @@ <param name="discard_untrimmed" value="true"/> <param name="min" value="1"/> <param name="max" value="1000"/> - <param name="max_n" value="1"/> + <param name="max_n" value="0"/> <param name="pair_filter" value="both"/> </section> <assert_command> <has_text text="--discard-untrimmed"/> <has_text text="--minimum-length=1"/> <has_text text="--maximum-length=1000"/> - <has_text text="--max-n=1"/> + <has_text text="--max-n=0"/> <has_text text="--pair-filter=both"/> </assert_command> </test>
--- a/macros.xml Thu Mar 05 06:45:31 2020 -0500 +++ b/macros.xml Sat Jul 04 06:52:59 2020 -0400 @@ -6,7 +6,7 @@ #for $a in $library.r1.adapters #if $a.adapter_source.adapter_source_list == 'builtin': - -a "${a.adapter_source.adapter.fields.name}"='${a.adapter_source.adapter}' + -a '${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) != "": @@ -17,7 +17,7 @@ #end for #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}' + -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) != "": @@ -28,7 +28,7 @@ #end for #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}"='${fa.front_adapter_source.front_adapter}' + -g '${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) != "": @@ -71,7 +71,7 @@ #for $a in $library.r2.adapters2 #if $a.adapter_source2.adapter_source_list2 == 'builtin': - -A "${a.adapter_source2.adapter2.fields.name}"='${a.adapter_source2.adapter2}' + -A '${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) != "": @@ -82,7 +82,7 @@ #end for #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}"='${aa.anywhere_adapter_source2.anywhere_adapter2}' + -B '${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) != "": @@ -93,7 +93,7 @@ #end for #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}"='${fa.front_adapter_source2.front_adapter2}' + -G '${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($fa.front_adapter_source2.front_adapter_name2) != "": @@ -121,6 +121,57 @@ ]]></token> + <xml name="adapter_sanitizer"> + <sanitizer> + <valid initial="string.digits"> + <add value="A"/><!--standard nucleotides--> + <add value="T"/> + <add value="C"/> + <add value="G"/> + + <add value="U"/><!--ambiguous nucleotides--> + <add value="R"/> + <add value="Y"/> + <add value="S"/> + <add value="W"/> + <add value="K"/> + <add value="M"/> + <add value="B"/> + <add value="D"/> + <add value="H"/> + <add value="V"/> + <add value="N"/> + + <add value="X"/><!-- don't match any nucleotide--> + + <add value="{"/><!--specify repeats .. needs digits which are added as default--> + <add value="}"/> + + <add value="^"/><!--anchoring--> + <add value="$"/> + <add value="."/> + <add value="("/><!--specify what to keep--> + <add value=")"/> + + </valid> + </sanitizer> + </xml> + + <xml name="adapter" token_name="" token_argument="" token_value="" token_label=""> + <param name="@NAME@" argument="@ARGUMENT@" type="text" value="@VALUE@" label="@LABEL@"> + <expand macro="adapter_sanitizer"/> + </param> + </xml> + + <xml name="adapter_select" token_name="" token_argument="" token_label=""> + <param name="@NAME@" argument="@ARGUMENT@" type="select" label="@LABEL@"> + <options from_data_table="adapters"> + <filter type="sort_by" column="1" /> + </options> + <expand macro="adapter_sanitizer"/> + </param> + </xml> + <xml name="single_end_options" > <section name="r1" title="Read 1 Options" expanded="True"> @@ -135,15 +186,11 @@ <when value="user"> <param name="adapter_name" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional if Multiple output is 'No')" /> - <param name="adapter" argument="-a" type="text" value="AATTGGCC" label="Enter custom 3' adapter sequence" /> + <expand macro="adapter" name="adapter" argument="-a" type="text" value="AATTGGCC" label="Enter custom 3' adapter sequence" /> </when> <when value="builtin"> - <param name="adapter" argument="-a" type="select" label="Choose 3' adapter"> - <options from_data_table="adapters"> - <filter type="sort_by" column="1" /> - </options> - </param> + <expand macro="adapter_select" name="adapter" argument="-a" label="Choose 3' adapter"/> </when> <when value="file"> @@ -162,14 +209,10 @@ <when value="user"> <param name="front_adapter_name" type="text" value="" optional="True" label="Enter custom 5' adapter name (Optional if Multiple output is 'No')" /> - <param name="front_adapter" argument="-g" type="text" value="AATTGGCC" label="Enter custom 5' adapter sequence" /> + <expand macro="adapter" name="front_adapter" argument="-g" value="AATTGGCC" label="Enter custom 5' adapter sequence" /> </when> <when value="builtin"> - <param name="front_adapter" argument="-g" type="select" label="Choose 5' adapter"> - <options from_data_table="adapters"> - <filter type="sort_by" column="1" /> - </options> - </param> + <expand macro="adapter_select" name="front_adapter" argument="-g" label="Choose 5' adapter"/> </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" /> @@ -187,14 +230,10 @@ <when value="user"> <param name="anywhere_adapter_name" type="text" value="" optional="True" label="Enter custom 5' or 3' adapter name (Optional if Multiple output is 'No')" /> - <param name="anywhere_adapter" argument="-b" type="text" value="AATTGGCC" label="Enter custom 5' or 3' adapter sequence" /> + <expand macro="adapter" name="anywhere_adapter" argument="-b" value="AATTGGCC" label="Enter custom 5' or 3' adapter sequence" /> </when> <when value="builtin"> - <param name="anywhere_adapter" argument="-b" type="select" label="Choose 5' or 3' adapter"> - <options from_data_table="adapters"> - <filter type="sort_by" column="1" /> - </options> - </param> + <expand macro="adapter_select" name="anywhere_adapter" argument="-b" label="Choose 5' or 3' adapter"/> </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" /> @@ -226,15 +265,11 @@ <when value="user"> <param name="adapter_name2" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional)" /> - <param name="adapter2" argument="-A" type="text" label="Enter custom 3' adapter sequence" value="AATTGGCC" /> + <expand macro="adapter" name="adapter2" argument="-A" label="Enter custom 3' adapter sequence" value="AATTGGCC" /> </when> <when value="builtin"> - <param name="adapter2" argument="-A" type="select" label="Choose 3' adapter"> - <options from_data_table="adapters"> - <filter type="sort_by" column="1" /> - </options> - </param> + <expand macro="adapter_select" name="adapter2" argument="-A" label="Choose 3' adapter"/> </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" /> @@ -252,14 +287,10 @@ <when value="user"> <param name="front_adapter_name2" type="text" value="" label="Enter custom 5' adapter name (Optional)" /> - <param name="front_adapter2" argument="-G" type="text" value="AATTGGCC" label="Enter custom 5' adapter sequence" /> + <expand macro="adapter" name="front_adapter2" argument="-G" value="AATTGGCC" label="Enter custom 5' adapter sequence" /> </when> <when value="builtin"> - <param name="front_adapter2" argument="-G" type="select" label="Choose 5' adapter"> - <options from_data_table="adapters"> - <filter type="sort_by" column="1" /> - </options> - </param> + <expand macro="adapter_select" name="front_adapter2" argument="-G" label="Choose 5' adapter"/> </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" /> @@ -277,14 +308,10 @@ <when value="user"> <param name="anywhere_adapter_name2" type="text" value="" optional="True" label="Enter custom 5' or 3' adapter name (Optional)" /> - <param name="anywhere_adapter2" argument="-B" type="text" label="Enter custom 5' or 3' adapter sequence" value="AATTGGCC" /> + <expand macro="adapter" name="anywhere_adapter2" argument="-B" label="Enter custom 5' or 3' adapter sequence" value="AATTGGCC" /> </when> <when value="builtin"> - <param name="anywhere_adapter2" argument="-B" type="select" label="Choose 5' or 3' adapter"> - <options from_data_table="adapters"> - <filter type="sort_by" column="1" /> - </options> - </param> + <expand macro="adapter_select" name="anywhere_adapter2" argument="-B" type="select" label="Choose 5' or 3' adapter"/> </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" />