| Previous changeset 0:988729b728f0 (2018-03-09) Next changeset 2:415fd81b85d3 (2018-07-10) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 |
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modified:
fastp.xml macros.xml |
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| diff -r 988729b728f0 -r f44e93b4529c fastp.xml --- a/fastp.xml Fri Mar 09 20:21:51 2018 -0500 +++ b/fastp.xml Tue Mar 20 04:24:38 2018 -0400 |
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| b'@@ -8,7 +8,6 @@\n </requirements>\n <version_command>fastp --version | tail -n 1</version_command>\n <command detect_errors="exit_code"><![CDATA[\n-\n ## Link input files\n \n #if $in1.is_of_type(\'fastq.gz\')\n@@ -24,10 +23,19 @@\n #end if\n \n \n+## Set filename for output report\n+\n+#import re\n+#set $filename = re.sub(\'[^\\w\\-\\s]\', \'_\', str($in1.element_identifier))\n+\n+\n ## Run fastp\n \n fastp\n \n+--thread \\${GALAXY_SLOTS:-1}\n+--report_title \'fastp report for $filename\'\n+\n #if $in1.is_of_type(\'fastqillumina\', \'fastqsolexa\', \'fastqillumina.gz\', \'fastqsolexa.gz\'):\n --phred64\n #end if\n@@ -40,7 +48,8 @@\n -O second.$ext\n #end if\n \n-## Adapter trimming options\n+\n+## Adapter Trimming Options\n \n $single_paired.adapter_trimming_options.disable_adapter_trimming\n \n@@ -55,7 +64,7 @@\n #end if\n \n \n-## Global trimming options\n+## Global Trimming Options\n \n #if str($single_paired.global_trimming_options.trim_front1):\n -f $single_paired.global_trimming_options.trim_front1\n@@ -75,76 +84,6 @@\n #end if\n \n \n-## PolyG tail trimming, useful for NextSeq/NovaSeq data\n-\n-#if $polyg_tail_trimming.trimming_select in [\'\', \'-g\']:\n- #if str($polyg_tail_trimming.poly_g_min_len):\n- --poly_g_min_len $polyg_tail_trimming.poly_g_min_len\n- #end if\n- $polyg_tail_trimming.trimming_select\n-#end if\n-\n-## Per read cutting by quality options\n-\n-#if $cutting_by_quality_options.cut_by_quality5 or $cutting_by_quality_options.cut_by_quality3:\n-\n- $cutting_by_quality_options.cut_by_quality5\n-\n- $cutting_by_quality_options.cut_by_quality3\n-\n- #if str($cutting_by_quality_options.cut_window_size):\n- -W $cutting_by_quality_options.cut_window_size\n- #end if\n- #if str($cutting_by_quality_options.cut_mean_quality):\n- -M $cutting_by_quality_options.cut_mean_quality\n- #end if\n-#end if\n-\n-\n-## Quality filtering options\n-\n-$quality_filtering_options.disable_quality_filtering\n-\n-#if str($quality_filtering_options.qualified_quality_phred):\n- -q $quality_filtering_options.qualified_quality_phred\n-#end if\n-#if str($quality_filtering_options.unqualified_percent_limit):\n- -u $quality_filtering_options.unqualified_percent_limit\n-#end if\n-#if str($quality_filtering_options.n_base_limit):\n- -n $quality_filtering_options.n_base_limit\n-#end if\n-\n-\n-## Length filtering options\n-\n-$length_filtering_options.disable_length_filtering\n-\n-#if str($length_filtering_options.length_required):\n- -l $length_filtering_options.length_required\n-#end if\n-\n-\n-## Base correction by overlap analysis options\n-\n-$base_correction_options.correction\n-\n-\n-## UMI processing\n-\n-#if $umi_processing.umi:\n- $umi_processing.umi\n- #if str($umi_processing.umi_loc):\n- --umi_loc \'$umi_processing.umi_loc\'\n- #end if\n- #if str($umi_processing.umi_len):\n- --umi_len $umi_processing.umi_len\n- #end if\n- #if str($umi_processing.umi_prefix):\n- --umi_prefix \'$umi_processing.umi_prefix\'\n- #end if\n-#end if\n-\n ## Overrepresented sequence analysis\n \n $overrepresented_sequence_analysis.overrepresentation_analysis\n@@ -154,8 +93,94 @@\n #end if\n \n \n-## Thread options\n---thread \\${GALAXY_SLOTS:-1}\n+## Filter Options\n+\n+## Quality filtering options\n+\n+$filter_options.quality_filtering_options.disable_quality_filtering\n+\n+#if str($filter_options.quality_filtering_options.qualified_quality_phred):\n+ -q $filter_options.quality_filtering_options.qualified_quality_phred\n+#end if\n+#if str($filter_options.quality_filtering_options.unqualified_percent_limit):\n+ -u $filter_options.quality_filtering_options.unqualified_percent_limit\n+#end if\n+#if str($filter_options.quality_filtering_options.n_base_limit):\n+ -n $filter_options.quality_filtering_options.n_base_limit\n+#end if\n+\n+\n+## Length filtering options\n+\n+$filter_options.length_filtering_options.disable_length_filtering\n+\n+#if str($filter_options.length_filtering_options.length_required):\n+ -l $filter_options.length_filtering_options.length_required\n+#end if\n+\n+## Low complexity fil'..b' <output name="out2" ftype="fastq" file="out_bwa_umi_read2_2.fq"/>\n </test>\n- <test>\n- <param name="in1" value="R1.fq" ftype="fastq"/>\n+ <!-- Ensure JSON report output works -->\n+ <test expect_num_outputs="2">\n+ <param name="in1" ftype="fastqsanger" value="R1.fq"/>\n <param name="single_paired_selector" value="single"/>\n- <output name="out1" file="out1.fq" ftype="fastq"/>\n- <output name="report_html">\n+ <param name="report_html" value="False"/>\n+ <param name="report_json" value="True"/>\n+ <output name="out1" ftype="fastqsanger" file="out1.fq"/>\n+ <output name="report_json">\n <assert_contents>\n <has_text text="fastp report"/>\n </assert_contents>\n </output>\n </test>\n- <test>\n- <param name="in1" value="R1.fq.gz" ftype="fastq.gz"/>\n+ <!-- Ensure polyG trimming works -->\n+ <test expect_num_outputs="2">\n+ <param name="in1" ftype="fastq.gz" value="R1.fq.gz"/>\n <param name="single_paired_selector" value="single"/>\n <param name="trimming_select" value="-g"/>\n <param name="poly_g_min_len" value="10"/>\n- <output name="out1" file="out1.fq.gz" ftype="fastq.gz" compare="sim_size"/>\n- <output name="report_html">\n- <assert_contents>\n- <has_text text="fastp report"/>\n- </assert_contents>\n- </output>\n+ <output name="out1" ftype="fastq.gz" decompress="True" file="out1.fq.gz"/>\n </test>\n </tests>\n <help><![CDATA[\n@@ -366,23 +434,25 @@\n \n 1. Filter out bad reads (too low quality, too short, or too many N...)\n \n-2. Cut low quality bases for per read in its 5\' and 3\' by evaluating the mean quality from a sliding window (like Trimmomatic but faster).\n+2. Cut low quality bases for per read in its 5\' and 3\' by evaluating the mean quality from a sliding window (like Trimmomatic but faster)\n \n 3. Trim all reads in front and tail\n \n-4. Cut adapters. Adapter sequences can be automatically detected,which means you don\'t have to input the adapter sequences to trim them.\n+4. Cut adapters. Adapter sequences can be automatically detected, which means you don\'t have to input the adapter sequences to trim them.\n+\n+5. Correct mismatched base pairs in overlapped regions of paired end reads, if one base is with high quality while the other is with ultra-low quality\n \n-5. Correct mismatched base pairs in overlapped regions of paired end reads, if one base is with high quality while the other is with ultra low quality\n+6. Trim polyG in 3\' ends, which is commonly seen in NovaSeq/NextSeq data. Trim polyX in 3\' ends to remove unwanted polyX tailing (i.e. polyA tailing for mRNA-Seq data)\n \n-6. Preprocess unique molecular identifer (UMI) enabled data, shift UMI to sequence name.\n+7. Preprocess unique molecular identifer (UMI) enabled data, shift UMI to sequence name\n \n-7. Report JSON format result for further interpreting.\n+8. Report JSON format result for further interpreting\n \n-8. Visualize quality control and filtering results on a single HTML page (like FASTQC but faster and more informative).\n+9. Visualize quality control and filtering results on a single HTML page (like FASTQC but faster and more informative)\n \n-9. Split the output to multiple files (0001.R1.gz, 0002.R1.gz...) to support parallel processing. Two modes can be used, limiting the total split file number, or limitting the lines of each split file.\n+10. Split the output to multiple files (0001.R1.gz, 0002.R1.gz...) to support parallel processing. Two modes can be used, limiting the total split file number, or limitting the lines of each split file (*Not enabled in this Galaxy tool*)\n \n-10. Support long reads (data from PacBio / Nanopore devices).\n+11. Support long reads (data from PacBio / Nanopore devices)\n \n -----\n \n' |
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| diff -r 988729b728f0 -r f44e93b4529c macros.xml --- a/macros.xml Fri Mar 09 20:21:51 2018 -0500 +++ b/macros.xml Tue Mar 20 04:24:38 2018 -0400 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@WRAPPER_VERSION@">0.12.4</token> + <token name="@WRAPPER_VERSION@">0.12.5</token> <xml name="adapter_sequence1"> <param name="adapter_sequence1" argument="--adapter_sequence" type="text" optional="true" label="Adapter sequence for input 1" @@ -21,5 +21,4 @@ <param name="poly_g_min_len" argument="--poly_g_min_len" type="integer" optional="true" label="PolyG minimum length" help="The minimum length to detect polyG in the read tail. 10 by default."/> </xml> - </macros> |