| Previous changeset 20:e4691e1589d3 (2019-04-08) Next changeset 22:093678460093 (2020-07-04) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96" |
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modified:
cutadapt.xml |
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| diff -r e4691e1589d3 -r 104d86c98776 cutadapt.xml --- a/cutadapt.xml Mon Apr 08 13:49:22 2019 -0400 +++ b/cutadapt.xml Thu Mar 05 06:45:31 2020 -0500 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="cutadapt" name="Cutadapt" version="1.16.6" profile="17.09">\n+<tool id="cutadapt" name="Cutadapt" version="1.16.7" profile="17.09">\n <description>Remove adapter sequences from Fastq/Fasta</description>\n <macros>\n <import>macros.xml</import>\n@@ -107,10 +107,10 @@\n \n $filter_options.discard\n $filter_options.discard_untrimmed\n-#if str($filter_options.min) != \'0\':\n+#if str($filter_options.min):\n --minimum-length=$filter_options.min\n #end if\n-#if str($filter_options.max) != \'0\':\n+#if str($filter_options.max):\n --maximum-length=$filter_options.max\n #end if\n #if $filter_options.max_n:\n@@ -197,10 +197,10 @@\n \n <!-- Filter Options -->\n <section name="filter_options" title="Filter Options">\n- <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!" />\n+ <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!" />\n <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." />\n- <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." />\n- <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." />\n+ <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." />\n+ <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." />\n <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." />\n <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">\n <option value="any" selected="True">any</option>\n@@ -330,6 +330,14 @@\n <param name="adapter2" value="AGATCGGAAGAGC"/>\n <output name="out1" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/>\n <output name="out2" decompress="True" file="cutadapt_out2.fq.gz" ftype="fastq.gz"/>\n+ <assert_command>\n+ <not_has_text text="--discard-trimmed"/>\n+ <not_has_text text="--discard-untrimmed"/>\n+ '..b'ce">\n- <param name="front_adapter_source_list" value="file"/>\n- <param name="front_adapter_file" ftype="fasta" value="barcodes.fasta" />\n- </conditional>\n- </repeat>\n- </section>\n- </conditional>\n- <param name="report" value="False" />\n- <param name="info_file" value="False" />\n- <param name="multiple_output" value="True" />\n- <output_collection name="split_output" type="list" count="3">\n- <element name="A1" decompress="True" file="A1.fastq.gz" ftype="fastq.gz">\n- </element>\n- <element name="A2" decompress="True" file="A2.fastq.gz" ftype="fastq.gz">\n- </element>\n- <element name="unknown" decompress="True" file="unknown.fastq.gz" ftype="fastq.gz">\n- </element>\n- </output_collection>\n- </test>\n+ <test>\n+ <conditional name="library">\n+ <param name="type" value="single" />\n+ <param name="input_1" ftype="fastq.gz" value="cutadapt_in_split.fastq.gz" />\n+ <section name="r1" >\n+ <repeat name="front_adapters">\n+ <conditional name="front_adapter_source">\n+ <param name="front_adapter_source_list" value="file"/>\n+ <param name="front_adapter_file" ftype="fasta" value="barcodes.fasta" />\n+ </conditional>\n+ </repeat>\n+ </section>\n+ </conditional>\n+ <param name="report" value="False" />\n+ <param name="info_file" value="False" />\n+ <param name="multiple_output" value="True" />\n+ <output_collection name="split_output" type="list" count="3">\n+ <element name="A1" decompress="True" file="A1.fastq.gz" ftype="fastq.gz">\n+ </element>\n+ <element name="A2" decompress="True" file="A2.fastq.gz" ftype="fastq.gz">\n+ </element>\n+ <element name="unknown" decompress="True" file="unknown.fastq.gz" ftype="fastq.gz">\n+ </element>\n+ </output_collection>\n+ </test>\n \n <!-- Ensure untrimmed file output works -->\n <test>\n@@ -493,6 +505,30 @@\n -->\n <output name="untrimmed_output" file="cutadapt_untrimmed.out.gz" compare="sim_size" delta="4000" ftype="fastq.gz"/>\n </test>\n+ <!-- same as 1st test with paired data + filter options (because of discard_untrimmed no comparison is done) -->\n+ <test>\n+ <param name="type" value="paired" />\n+ <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />\n+ <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />\n+ <param name="adapter_source_list" value="user"/>\n+ <param name="adapter" value="AGATCGGAAGAGC"/>\n+ <param name="adapter_source_list2" value="user"/>\n+ <param name="adapter2" value="AGATCGGAAGAGC"/>\n+ <section name="filter_options">\n+ <param name="discard_untrimmed" value="true"/>\n+ <param name="min" value="1"/>\n+ <param name="max" value="1000"/>\n+ <param name="max_n" value="1"/>\n+ <param name="pair_filter" value="both"/>\n+ </section>\n+ <assert_command>\n+ <has_text text="--discard-untrimmed"/>\n+ <has_text text="--minimum-length=1"/>\n+ <has_text text="--maximum-length=1000"/>\n+ <has_text text="--max-n=1"/>\n+ <has_text text="--pair-filter=both"/>\n+ </assert_command>\n+ </test>\n </tests>\n \n <help><![CDATA[\n' |