Mercurial > repos > lparsons > cutadapt
changeset 21:104d86c98776 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
author | iuc |
---|---|
date | Thu, 05 Mar 2020 06:45:31 -0500 (2020-03-05) |
parents | e4691e1589d3 |
children | 093678460093 |
files | cutadapt.xml |
diffstat | 1 files changed, 69 insertions(+), 33 deletions(-) [+] |
line wrap: on
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--- a/cutadapt.xml Mon Apr 08 13:49:22 2019 -0400 +++ b/cutadapt.xml Thu Mar 05 06:45:31 2020 -0500 @@ -1,4 +1,4 @@ -<tool id="cutadapt" name="Cutadapt" version="1.16.6" profile="17.09"> +<tool id="cutadapt" name="Cutadapt" version="1.16.7" profile="17.09"> <description>Remove adapter sequences from Fastq/Fasta</description> <macros> <import>macros.xml</import> @@ -107,10 +107,10 @@ $filter_options.discard $filter_options.discard_untrimmed -#if str($filter_options.min) != '0': +#if str($filter_options.min): --minimum-length=$filter_options.min #end if -#if str($filter_options.max) != '0': +#if str($filter_options.max): --maximum-length=$filter_options.max #end if #if $filter_options.max_n: @@ -197,10 +197,10 @@ <!-- Filter Options --> <section name="filter_options" title="Filter Options"> - <param name="discard" argument="--discard-trimmed" type="boolean" value="False" truevalue="--discard" falsevalue="" label="Discard Trimmed Reads" help="Discard reads that contain the adapter instead of trimming them. Use the 'Minimum overlap length' option in order to avoid throwing away too many randomly matching reads!" /> + <param name="discard" argument="--discard-trimmed" type="boolean" value="False" truevalue="--discard-trimmed" falsevalue="" label="Discard Trimmed Reads" help="Discard reads that contain the adapter instead of trimming them. Use the 'Minimum overlap length' option in order to avoid throwing away too many randomly matching reads!" /> <param name="discard_untrimmed" argument="--discard_untrimmed" type="boolean" value="False" truevalue="--discard-untrimmed" falsevalue="" label="Discard Untrimmed Reads" help="Discard reads that do not contain the adapter." /> - <param name="min" argument="--minimum-length" type="integer" min="0" optional="True" value="0" label="Minimum length" help="Discard trimmed reads that are shorter than LENGTH. Reads that are too short even before adapter removal are also discarded. In colorspace, an initial primer is not counted. Value of 0 means no minimum length." /> - <param name="max" argument="--maximum-length" type="integer" min="0" optional="True" value="0" label="Maximum length" help="Discard trimmed reads that are longer than LENGTH. Reads that are too long even before adapter removal are also discarded. In colorspace, an initial primer is not counted. Value of 0 means no maximum length." /> + <param name="min" argument="--minimum-length" type="integer" min="0" optional="True" value="" label="Minimum length" help="Discard trimmed reads that are shorter than LENGTH. Reads that are too short even before adapter removal are also discarded. In colorspace, an initial primer is not counted." /> + <param name="max" argument="--maximum-length" type="integer" min="0" optional="True" value="" label="Maximum length" help="Discard trimmed reads that are longer than LENGTH. Reads that are too long even before adapter removal are also discarded. In colorspace, an initial primer is not counted." /> <param name="max_n" argument="--max-n" type="float" min="0" optional="True" label="Max N" help="Discard reads with more than this number of 'N' bases. A number between 0 and 1 is interpreted as a fraction of the read length." /> <param name="pair_filter" argument="--pair-filter" type="select" optional="True" label="Pair filter" help="Which of the reads in a paired-end read have to match the filtering criterion in order for the pair to be filtered. Default: any"> <option value="any" selected="True">any</option> @@ -330,6 +330,14 @@ <param name="adapter2" value="AGATCGGAAGAGC"/> <output name="out1" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/> <output name="out2" decompress="True" file="cutadapt_out2.fq.gz" ftype="fastq.gz"/> + <assert_command> + <not_has_text text="--discard-trimmed"/> + <not_has_text text="--discard-untrimmed"/> + <not_has_text text="--minimum-length"/> + <not_has_text text="--maximum-length"/> + <not_has_text text="--max-n"/> + <has_text text="--pair-filter=any"/> + </assert_command> </test> <!-- Ensure paired collection works --> <test> @@ -361,10 +369,15 @@ <param name="adapter_source_list" value="user"/> <param name="adapter" value="TTAGACATATCTCCGTCG"/> <param name="output_filtering" value="filter"/> - <param name="discard" value="True"/> + <section name="filter_options"> + <param name="discard" value="True"/> + </section> <param name="read_modification" value="none"/> <param name="output_type" value="default"/> <output name="out1" file="cutadapt_discard.out" ftype="fastq"/> + <assert_command> + <has_text text="--discard-trimmed"/> + </assert_command> </test> <!-- Ensure rest file output works --> <test> @@ -440,32 +453,31 @@ </output_collection> </test> - - <test> - <conditional name="library"> - <param name="type" value="single" /> - <param name="input_1" ftype="fastq.gz" value="cutadapt_in_split.fastq.gz" /> - <section name="r1" > - <repeat name="front_adapters"> - <conditional name="front_adapter_source"> - <param name="front_adapter_source_list" value="file"/> - <param name="front_adapter_file" ftype="fasta" value="barcodes.fasta" /> - </conditional> - </repeat> - </section> - </conditional> - <param name="report" value="False" /> - <param name="info_file" value="False" /> - <param name="multiple_output" value="True" /> - <output_collection name="split_output" type="list" count="3"> - <element name="A1" decompress="True" file="A1.fastq.gz" ftype="fastq.gz"> - </element> - <element name="A2" decompress="True" file="A2.fastq.gz" ftype="fastq.gz"> - </element> - <element name="unknown" decompress="True" file="unknown.fastq.gz" ftype="fastq.gz"> - </element> - </output_collection> - </test> + <test> + <conditional name="library"> + <param name="type" value="single" /> + <param name="input_1" ftype="fastq.gz" value="cutadapt_in_split.fastq.gz" /> + <section name="r1" > + <repeat name="front_adapters"> + <conditional name="front_adapter_source"> + <param name="front_adapter_source_list" value="file"/> + <param name="front_adapter_file" ftype="fasta" value="barcodes.fasta" /> + </conditional> + </repeat> + </section> + </conditional> + <param name="report" value="False" /> + <param name="info_file" value="False" /> + <param name="multiple_output" value="True" /> + <output_collection name="split_output" type="list" count="3"> + <element name="A1" decompress="True" file="A1.fastq.gz" ftype="fastq.gz"> + </element> + <element name="A2" decompress="True" file="A2.fastq.gz" ftype="fastq.gz"> + </element> + <element name="unknown" decompress="True" file="unknown.fastq.gz" ftype="fastq.gz"> + </element> + </output_collection> + </test> <!-- Ensure untrimmed file output works --> <test> @@ -493,6 +505,30 @@ --> <output name="untrimmed_output" file="cutadapt_untrimmed.out.gz" compare="sim_size" delta="4000" ftype="fastq.gz"/> </test> + <!-- same as 1st test with paired data + filter options (because of discard_untrimmed no comparison is done) --> + <test> + <param name="type" value="paired" /> + <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" /> + <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" /> + <param name="adapter_source_list" value="user"/> + <param name="adapter" value="AGATCGGAAGAGC"/> + <param name="adapter_source_list2" value="user"/> + <param name="adapter2" value="AGATCGGAAGAGC"/> + <section name="filter_options"> + <param name="discard_untrimmed" value="true"/> + <param name="min" value="1"/> + <param name="max" value="1000"/> + <param name="max_n" value="1"/> + <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="--pair-filter=both"/> + </assert_command> + </test> </tests> <help><![CDATA[