Mercurial > repos > lparsons > cutadapt
changeset 40:aa784cb3810d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 8bdd212b8708a9d080e87303dd543fb93bc05c2f
| author | iuc |
|---|---|
| date | Mon, 08 Jul 2024 16:21:21 +0000 |
| parents | fe74900d6dc7 |
| children | 5eb7e84243f2 |
| files | cutadapt.xml macros.xml test-data/cutadapt_action_crop.out |
| diffstat | 3 files changed, 115 insertions(+), 19 deletions(-) [+] |
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--- a/cutadapt.xml Fri May 17 13:32:03 2024 +0000 +++ b/cutadapt.xml Mon Jul 08 16:21:21 2024 +0000 @@ -155,6 +155,13 @@ --length=-$other_trimming_options.shorten_options.length #end if #end if +#if $paired and str($other_trimming_options.shorten_options_r2.shorten_values_r2) == 'True': + #if str($other_trimming_options.shorten_options_r2.shorten_end_r2) == '3prime' + -L $other_trimming_options.shorten_options_r2.length2 + #else + -L -$other_trimming_options.shorten_options_r2.length2 + #end if +#end if $filter_options.discard_trimmed $filter_options.discard_untrimmed @@ -278,6 +285,7 @@ <option value="retain">Retain: the read is trimmed, but the adapter sequence is not removed</option> <option value="mask">Mask: mask adapters with 'N' characters instead of trimming them</option> <option value="lowercase">Lowercase: convert to lowercase</option> + <option value="crop">Crop: trim upstream and downstream sequences, i.e. retain adapter sequences only</option> <option value="none">None: leave unchanged</option> </param> <param argument="--error-rate" type="float" min="0" max="1" value="0.1" label="Maximum error rate" help="Maximum allowed error rate (no. of errors divided by the length of the matching region)." /> @@ -321,6 +329,21 @@ <when value="False"> </when> </conditional> + <conditional name="shorten_options_r2"> + <param name="shorten_values_r2" type="select" label="Separate shortening of R2 reads to a fixed length?" help="For paired-end data, shortening of R2 reads can be handled separately. Ignored for single-end data."> + <option value="True">Separate shortening of R2 reads</option> + <option value="False" selected="true">Treat R2 reads the same as R1 reads</option> + </param> + <when value="True"> + <param argument="-L" name="length2" type="integer" value="0" label="Length" help="Shorten R2 reads to this length. This modification is applied after adapter trimming." /> + <param name="shorten_end_r2" type="select" label="End at which to apply the slice"> + <option value="3prime">3' ends</option> + <option value="5prime">5' ends</option> + </param> + </when> + <when value="False"> + </when> + </conditional> </section> <!-- Filter Options --> <section name="filter_options" title="Read Filtering Options"> @@ -886,6 +909,22 @@ </repeat> </section> <section name="adapter_options"> + <param name="action" value="crop"/> + </section> + <output name="out1" file="cutadapt_action_crop.out" ftype="fastq"/> + </test> + <test expect_num_outputs="1"> + <param name="type" value="single" /> + <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" /> + <section name="r1"> + <repeat name="adapters"> + <conditional name="adapter_source"> + <param name="adapter_source_list" value="user"/> + <param name="adapter" value="CGTCCGAANTAG"/> + </conditional> + </repeat> + </section> + <section name="adapter_options"> <param name="action" value="none"/> </section> <output name="out1" file="cutadapt_action_none.out" ftype="fastq"/> @@ -907,7 +946,7 @@ </section> <output name="out1" file="cutadapt_revcomp.out" ftype="fastq"/> </test> - <!-- Test minimum lenghth paired-reads --> + <!-- Test minimum length paired-reads --> <test expect_num_outputs="2"> <param name="type" value="paired" /> <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" /> @@ -986,14 +1025,6 @@ </conditional> </repeat> </section> - <section name="r2"> - <repeat name="adapters2"> - <conditional name="adapter_source2"> - <param name="adapter_source_list2" value="user"/> - <param name="adapter2" value="AGATCGGAAGAGC"/> - </conditional> - </repeat> - </section> <section name="filter_options"> <param name="pair_filter" value="both"/> <param name="minimum_length" value="10"/> @@ -1020,14 +1051,6 @@ </conditional> </repeat> </section> - <section name="r2"> - <repeat name="adapters2"> - <conditional name="adapter_source2"> - <param name="adapter_source_list2" value="user"/> - <param name="adapter2" value="AGATCGGAAGAGC"/> - </conditional> - </repeat> - </section> <section name="filter_options"> <param name="pair_filter" value="both"/> <param name="minimum_length" value="10"/> @@ -1089,6 +1112,67 @@ </section> <output name="out1" file="cutadapt_shorten_5prime.out" ftype="fastq"/> </test> + <test expect_num_outputs="2"> + <param name="type" value="paired" /> + <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" /> + <section name="r1"> + <repeat name="adapters"> + <conditional name="adapter_source"> + <param name="adapter_source_list" value="user"/> + <param name="adapter" value="AGCCGCTANGACG"/> + </conditional> + </repeat> + </section> + <section name="r2"> + <repeat name="adapters2"> + <conditional name="adapter_source"> + <param name="adapter_source_list" value="user"/> + <param name="adapter" value="AGCCGCTANGACG"/> + </conditional> + </repeat> + </section> + <section name="other_trimming_options"> + <conditional name="shorten_options"> + <param name="shorten_values" value="True"/> + <param name="shorten_end" value="3prime"/> + <param name="length" value="10"/> + </conditional> + <conditional name="shorten_options_r2"> + <param name="shorten_values_r2" value="True"/> + <param name="shorten_end_r2" value="5prime"/> + <param name="length2" value="10"/> + </conditional> + </section> + <section name="filter_options"> + <param name="minimum_length" value="0"/> + </section> + <output name="out1" file="cutadapt_shorten_3prime.out" ftype="fastq"/> + <output name="out2" file="cutadapt_shorten_5prime.out" ftype="fastq"/> + </test> + <test expect_num_outputs="2"> + <param name="type" value="paired" /> + <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" /> + <section name="r2"> + <repeat name="adapters2"> + <conditional name="adapter_source"> + <param name="adapter_source_list" value="user"/> + <param name="adapter" value="AGCCGCTANGACG"/> + </conditional> + </repeat> + </section> + <section name="other_trimming_options"> + <conditional name="shorten_options_r2"> + <param name="shorten_values_r2" value="True"/> + <param name="shorten_end_r2" value="3prime"/> + <param name="length2" value="10"/> + </conditional> + </section> + <section name="filter_options"> + <param name="minimum_length" value="0"/> + </section> + <output name="out1" file="cutadapt_small.fastq" ftype="fastq"/> + <output name="out2" file="cutadapt_shorten_3prime.out" ftype="fastq"/> + </test> <!-- Test max expected errors options --> <test expect_num_outputs="1"> <param name="type" value="single" />
--- a/macros.xml Fri May 17 13:32:03 2024 +0000 +++ b/macros.xml Mon Jul 08 16:21:21 2024 +0000 @@ -1,6 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">4.8</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">4.9</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@FASTQ_TYPES@">fastq.bz2,fastq.gz,fastq,fasta.bz2,fasta.gz,fasta</token> <xml name="edam_ontology"> <edam_topics>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt_action_crop.out Mon Jul 08 16:21:21 2024 +0000 @@ -0,0 +1,12 @@ +@prefix:1_13_573/1 +CGTCCGAANTAG ++ +)3%)&&&&!.1& +@prefix:1_13_1259/1 +AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT ++ +;<:&:A;A!9<<<,7:<=3=;:<&<?<?8<;=<& +@prefix:1_13_1440/1 +CAAGATCTNCCCTGCCACATTGCCCTAGTTAAAC ++ +<=A:A=57!7<';<6?5;;6:+:=)71>70<,=: