| Previous changeset 39:fe74900d6dc7 (2024-05-17) Next changeset 41:5eb7e84243f2 (2024-07-18) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 8bdd212b8708a9d080e87303dd543fb93bc05c2f |
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modified:
cutadapt.xml macros.xml |
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added:
test-data/cutadapt_action_crop.out |
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| diff -r fe74900d6dc7 -r aa784cb3810d cutadapt.xml --- a/cutadapt.xml Fri May 17 13:32:03 2024 +0000 +++ b/cutadapt.xml Mon Jul 08 16:21:21 2024 +0000 |
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| b'@@ -155,6 +155,13 @@\n --length=-$other_trimming_options.shorten_options.length\n #end if\n #end if\n+#if $paired and str($other_trimming_options.shorten_options_r2.shorten_values_r2) == \'True\':\n+ #if str($other_trimming_options.shorten_options_r2.shorten_end_r2) == \'3prime\'\n+ -L $other_trimming_options.shorten_options_r2.length2\n+ #else\n+ -L -$other_trimming_options.shorten_options_r2.length2\n+ #end if\n+#end if\n \n $filter_options.discard_trimmed\n $filter_options.discard_untrimmed\n@@ -278,6 +285,7 @@\n <option value="retain">Retain: the read is trimmed, but the adapter sequence is not removed</option>\n <option value="mask">Mask: mask adapters with \'N\' characters instead of trimming them</option>\n <option value="lowercase">Lowercase: convert to lowercase</option>\n+ <option value="crop">Crop: trim upstream and downstream sequences, i.e. retain adapter sequences only</option>\n <option value="none">None: leave unchanged</option>\n </param>\n <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)." />\n@@ -321,6 +329,21 @@\n <when value="False">\n </when>\n </conditional>\n+ <conditional name="shorten_options_r2">\n+ <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.">\n+ <option value="True">Separate shortening of R2 reads</option>\n+ <option value="False" selected="true">Treat R2 reads the same as R1 reads</option>\n+ </param>\n+ <when value="True">\n+ <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." />\n+ <param name="shorten_end_r2" type="select" label="End at which to apply the slice">\n+ <option value="3prime">3\' ends</option>\n+ <option value="5prime">5\' ends</option>\n+ </param>\n+ </when>\n+ <when value="False">\n+ </when>\n+ </conditional>\n </section>\n <!-- Filter Options -->\n <section name="filter_options" title="Read Filtering Options">\n@@ -886,6 +909,22 @@\n </repeat>\n </section>\n <section name="adapter_options">\n+ <param name="action" value="crop"/>\n+ </section>\n+ <output name="out1" file="cutadapt_action_crop.out" ftype="fastq"/>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <param name="type" value="single" />\n+ <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />\n+ <section name="r1">\n+ <repeat name="adapters">\n+ <conditional name="adapter_source">\n+ <param name="adapter_source_list" value="user"/>\n+ <param name="adapter" value="CGTCCGAANTAG"/>\n+ </conditional>\n+ </repeat>\n+ </section>\n+ <section name="adapter_options">\n <param name="action" value="none"/>\n </section>\n <output name="out1" file="cutadapt_action_none.out" ftype="fastq"/>\n@@ -907,7 +946,7 @@\n </section>\n <output name="out1" file="cutadapt_revcomp.out" ftype="fastq"/>\n </test>\n- <!-- Test minimum lenghth paired-reads -->\n+ <!-- Test minimum length paired-reads -->\n <test expect_num_outputs="2">\n <param name="type" value="paired" />\n <'..b' name="minimum_length" value="10"/>\n@@ -1020,14 +1051,6 @@\n </conditional>\n </repeat>\n </section>\n- <section name="r2">\n- <repeat name="adapters2">\n- <conditional name="adapter_source2">\n- <param name="adapter_source_list2" value="user"/>\n- <param name="adapter2" value="AGATCGGAAGAGC"/>\n- </conditional>\n- </repeat>\n- </section>\n <section name="filter_options">\n <param name="pair_filter" value="both"/>\n <param name="minimum_length" value="10"/>\n@@ -1089,6 +1112,67 @@\n </section>\n <output name="out1" file="cutadapt_shorten_5prime.out" ftype="fastq"/>\n </test>\n+ <test expect_num_outputs="2">\n+ <param name="type" value="paired" />\n+ <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />\n+ <section name="r1">\n+ <repeat name="adapters">\n+ <conditional name="adapter_source">\n+ <param name="adapter_source_list" value="user"/>\n+ <param name="adapter" value="AGCCGCTANGACG"/>\n+ </conditional>\n+ </repeat>\n+ </section>\n+ <section name="r2">\n+ <repeat name="adapters2">\n+ <conditional name="adapter_source">\n+ <param name="adapter_source_list" value="user"/>\n+ <param name="adapter" value="AGCCGCTANGACG"/>\n+ </conditional>\n+ </repeat>\n+ </section>\n+ <section name="other_trimming_options">\n+ <conditional name="shorten_options">\n+ <param name="shorten_values" value="True"/>\n+ <param name="shorten_end" value="3prime"/>\n+ <param name="length" value="10"/>\n+ </conditional>\n+ <conditional name="shorten_options_r2">\n+ <param name="shorten_values_r2" value="True"/>\n+ <param name="shorten_end_r2" value="5prime"/>\n+ <param name="length2" value="10"/>\n+ </conditional>\n+ </section>\n+ <section name="filter_options">\n+ <param name="minimum_length" value="0"/>\n+ </section>\n+ <output name="out1" file="cutadapt_shorten_3prime.out" ftype="fastq"/>\n+ <output name="out2" file="cutadapt_shorten_5prime.out" ftype="fastq"/>\n+ </test>\n+ <test expect_num_outputs="2">\n+ <param name="type" value="paired" />\n+ <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />\n+ <section name="r2">\n+ <repeat name="adapters2">\n+ <conditional name="adapter_source">\n+ <param name="adapter_source_list" value="user"/>\n+ <param name="adapter" value="AGCCGCTANGACG"/>\n+ </conditional>\n+ </repeat>\n+ </section>\n+ <section name="other_trimming_options">\n+ <conditional name="shorten_options_r2">\n+ <param name="shorten_values_r2" value="True"/>\n+ <param name="shorten_end_r2" value="3prime"/>\n+ <param name="length2" value="10"/>\n+ </conditional>\n+ </section>\n+ <section name="filter_options">\n+ <param name="minimum_length" value="0"/>\n+ </section>\n+ <output name="out1" file="cutadapt_small.fastq" ftype="fastq"/>\n+ <output name="out2" file="cutadapt_shorten_3prime.out" ftype="fastq"/>\n+ </test>\n <!-- Test max expected errors options -->\n <test expect_num_outputs="1">\n <param name="type" value="single" />\n' |
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| diff -r fe74900d6dc7 -r aa784cb3810d macros.xml --- a/macros.xml Fri May 17 13:32:03 2024 +0000 +++ b/macros.xml Mon Jul 08 16:21:21 2024 +0000 |
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| @@ -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> |
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| diff -r fe74900d6dc7 -r aa784cb3810d test-data/cutadapt_action_crop.out --- /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 |
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| @@ -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<,=: |