| Next changeset 1:40874f772ea1 (2024-08-26) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/ commit 138d7e0d844a783f1e8100d264d57540199f290f" |
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added:
adapter_removal.xml macros.xml test-data/reads1.fastq.gz test-data/reads2.fastq.gz |
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| diff -r 000000000000 -r 04d05400d3a6 adapter_removal.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/adapter_removal.xml Wed May 04 13:45:52 2022 +0000 |
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| b'@@ -0,0 +1,452 @@\n+<tool id="adapter_removal" name="AdapterRemoval: remove adapter sequences" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+ <description>from HTS data</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="bio_tools"/>\n+ <expand macro="requirements"/>\n+ <command detect_errors="exit_code"><![CDATA[\n+#import re\n+\n+#if $input_type_cond.input_type in [\'single\', \'pair\', \'interleaved\']:\n+ #set read1 = $input_type_cond.read1\n+ #if $input_type_cond.input_type == \'pair\':\n+ #set read2 = $input_type_cond.read2\n+ #end if\n+#else:\n+ #set read1 = $input_type_cond.reads_collection[\'forward\']\n+ #set read2 = $input_type_cond.reads_collection[\'reverse\']\n+#end if\n+\n+#set read1_identifier = \'read1\' + $read1.ext\n+ln -s \'${read1}\' \'${read1_identifier}\' &&\n+\n+#if $input_type_cond.input_type in ["pair", "paired"]:\n+ #set read2_identifier = \'read2\' + $read2.ext\n+ ln -s \'${read2}\' \'${read2_identifier}\' &&\n+#end if\n+\n+AdapterRemoval\n+--file1 \'${read1_identifier}\'\n+#if str($input_type_cond.input_type) == \'interleaved\':\n+ --interleaved\n+ --interleaved-input\n+ #if str($input_type_cond.interleaved_output) == \'yes\':\n+ --interleaved-output \'$output_interleaved_truncated\'\n+ #end if\n+ $input_type_cond.combined_output\n+#else if str($input_type_cond.input_type) in [\'pair\', \'paired\']:\n+ --file2 \'${read2_identifier}\'\n+ $input_type_cond.identify_adapters\n+ #if str($input_type_cond.interleaved_output) == \'yes\':\n+ --interleaved-output\n+ #end if\n+ $input_type_cond.combined_output\n+#end if\n+\n+--threads \\${GALAXY_SLOTS:-8}\n+\n+###### FASTQ Options\n+--qualitybase \'33\'\n+--qualitybase-output \'33\'\n+--qualitymax $fastq_options.qualitymax\n+\n+###### FASTQ Trimming Options\n+--adapter1 \'$fastq_trimming_options.adapter1\'\n+--adapter2 \'$fastq_trimming_options.adapter2\'\n+#if $fastq_trimming_options.adapter_list:\n+ --adapter-list \'$fastq_trimming_options.adapter_list\'\n+#end if\n+--minadapteroverlap $fastq_trimming_options.minadapteroverlap\n+--mm $fastq_trimming_options.mm\n+--shift $fastq_trimming_options.shift\n+#if str($fastq_trimming_options.trim5p_cond.trim5p_param) == \'yes\':\n+ --trim5p $fastq_trimming_options.trim5p_cond.trim5p_mate1 $fastq_trimming_options.trim5p_cond.trim5p_mate2\n+#end if\n+#if str($fastq_trimming_options.trim3p_cond.trim3p_param) == \'yes\':\n+ --trim3p $fastq_trimming_options.trim3p_cond.trim3p_mate1 $fastq_trimming_options.trim3p_cond.trim3p_mate2\n+#end if\n+$fastq_trimming_options.trimns\n+--maxns $fastq_trimming_options.maxns\n+$fastq_trimming_options.trimqualities\n+#if str($fastq_trimming_options.sliding_window_cond.sliding_window_param) == \'yes\':\n+ --trimwindows $fastq_trimming_options.sliding_window_cond.window_size\n+#end if\n+--minquality $fastq_trimming_options.minquality\n+$fastq_trimming_options.preserve5p\n+--minlength $fastq_trimming_options.minlength\n+--maxlength $fastq_trimming_options.maxlength\n+\n+###### FASTQ Merging Options\n+$fastq_merging_options.collapse\n+--minalignmentlength $fastq_merging_options.minalignmentlength\n+$fastq_merging_options.collapse_deterministic\n+$fastq_merging_options.collapse_conservatively\n+\n+###### Output Options\n+--settings \'$output_settings\'\n+#if str($input_type_cond.input_type) == \'single\':\n+ --output1 \'$output_truncated\'\n+#else if str($input_type_cond.input_type) in [\'pair\', \'paired\']:\n+ #if str($input_type_cond.interleaved_output) == \'no\':\n+ --output1 \'$output_forward_truncated\'\n+ --output2 \'$output_reverse_truncated\'\n+ #else:\n+ --output1 \'$output_interleaved_truncated\'\n+ #end if\n+#end if\n+\n+###### Outputs\n+#if \'output_singleton\' in $output_select:\n+ --singleton \'$output_singleton_truncated\'\n+#end if\n+#if \'output_collapsed\' in $output_select:\n+ --outputcollapsed \'$output_collapsed\'\n+#end if\n+#if \'output_collapsed_truncated\' in $output_select:\n+ --outputcollapsedtruncated \'$output_collapsed_truncated\'\n+#end if'..b's in single-end mode, while ensuring that all possible adapter contamination is trimmed.\n+ * **The fraction of mismatches allowed in the aligned region** - The allowed fraction of mismatches allowed in the aligned region. If the value is less than 1, then the value is used directly. If --mismatchrate is greater than 1, the rate is set to 1 / --mismatchrate. The default setting is 3 when trimming adapters, corresponding to a maximum mismatch rate of 1/3, and 10 when using --identify-adapters.\n+ * **Slip the alignment by this number of bases in the 5\' end to allow for missing bases in the 5\' end of the read** - To allow for missing bases in the 5\' end of the read, the program can let the alignment slip --shift bases in the 5\' end. This corresponds to starting the alignment maximum --shift nucleotides into read2 (for paired-end) or the adapter (for single-end).\n+ * **Trim the 5\' of reads by a fixed amount after removing adapters, but before carrying out quality based trimming** - Trim the 5\' of reads by a fixed amount after removing adapters, but before carrying out quality based trimming. Specify one value to trim mate 1 and mate 2 reads the same amount, or two values separated by a space to trim each mate different amounts.\n+ * **Trim the 3\' of reads by a fixed amount after removing adapters, but before carrying out quality based trimming** - Trim the 3\' of reads by a fixed amount. See the descriptiuon of thetrim5p parameter immediately above.\n+ * **Trim consecutive Ns from the 5\' and 3\' termini** - If quality trimming is also enabled (--trimqualities), then stretches of mixed low-quality bases and/or Ns are trimmed.\n+ * **Window based quality trimming** - If window_size is greater than or equal to 1, that number is used as the window size for all reads. If window_size is greater than or equal to 0 and less than 1, then that number is multiplied by the length of individual reads to determine the window size. If the window length is zero or is greater than the current read length, then the read length is used instead. Reads are trimmed as follows for a given window size:\n+\n+ 1. The new 5\' is determined by locating the first window where both the average quality and the quality of the first base in the window is greater than --minquality.\n+ 2. The new 3\' is located by sliding the first window right, until the average quality becomes less than or equal to --minquality. The new 3\' is placed at the last base in that window where the quality is greater than or equal to --minquality.\n+ 3. If no 5\' position could be determined, the read is discarded.\n+\n+**FASTQ Merging Options**\n+\n+ * **Output complete reads with an \'M\\_\' name prefix and trimmed reads with an \'MT\\_\' name prefix** - In paired-end mode, merge overlapping mates into a single and recalculate the quality scores. In single-end mode, attempt to identify templates for which the entire sequence is available. In both cases, complete "collapsed" reads are written with a \'M\\_\' name prefix, and "collapsed" reads which are trimmed due to quality settings are written with a \'MT\\_\' name prefix. The overlap needs to be at least --minalignmentlength nucleotides, with a maximum number of mismatches determined by --mm.\n+ * **Collapse deterministically** - Enable deterministic mode; currently only affects --collapse, different overlapping bases with equal quality are set to N quality 0, instead of being randomly sampled. Setting this option also sets --collapse.\n+ * **Collapse conservatively** - Alternative merging algorithm inspired by FASTQ-join: For matching overlapping bases, the highest quality score is used. For mismatching overlapping bases, the highest quality base is used and the quality is set to the absolute difference in Phred-score between the two bases. For mismatching bases with identical quality scores, the base is set to \'N\' and the quality score to 0 (Phred-encoded). Setting this option also sets --collapse.\n+ </help>\n+ <expand macro="citations"/>\n+</tool>\n' |
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| diff -r 000000000000 -r 04d05400d3a6 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed May 04 13:45:52 2022 +0000 |
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| @@ -0,0 +1,44 @@ +<macros> + <token name="@TOOL_VERSION@">2.3.3</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">20.09</token> + <token name="@DATATYPES@">fastqsanger.gz,fastqsanger</token> + <xml name="bio_tools"> + <xrefs> + <xref type="bio.tools">adapterremoval</xref> + </xrefs> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">adapterremoval</requirement> + </requirements> + </xml> + <xml name="interleaved_output_param"> + <param argument="--interleaved_output" type="select" label="Write paired-end reads to a single file, interleaving mate 1 and mate 2 reads?"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + </xml> + <xml name="identify_adapters_param"> + <param argument="--identify_adapters" type="boolean" truevalue="--identify-adapters" falsevalue="" checked="false" label="Attempt to build a consensus adapter sequence from fully overlapping pairs of paired-end reads?" help="No trimming is performed in this mode"/> + </xml> + <xml name="combined_output_param"> + <param argument="--combined_output" type="boolean" truevalue="--combined-output" falsevalue="" checked="false" label="Output trimmed reads such that the sequences of reads discarded due to quality filters or read merging are replaced with a single 'N' with Phred score 0?"/> + </xml> + <xml name="sanitizer"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'" /> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1186/s13104-016-1900-2</citation> + </citations> + </xml> +</macros> + |
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| diff -r 000000000000 -r 04d05400d3a6 test-data/reads1.fastq.gz |
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| diff -r 000000000000 -r 04d05400d3a6 test-data/reads2.fastq.gz |
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| Binary file test-data/reads2.fastq.gz has changed |