Mercurial > repos > pjbriggs > trimmomatic
diff trimmomatic.xml @ 16:9a38087e3bfd draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic commit ab36e4731731f12cce0e7d7cc3b50ba6a0bab1ef
author | iuc |
---|---|
date | Sun, 14 Jan 2024 11:00:33 +0000 |
parents | 32f1f56bd970 |
children | b9aaed85cbd1 |
line wrap: on
line diff
--- a/trimmomatic.xml Thu Mar 02 15:24:24 2023 +0000 +++ b/trimmomatic.xml Sun Jan 14 11:00:33 2024 +0000 @@ -10,7 +10,7 @@ See similar fix for snpSift https://github.com/galaxyproject/tools-iuc/commit/b5e2080a7afdea9fa476895693b6115824c6fbb9 --> - <requirement type="package" version="8.25">coreutils</requirement> + <requirement type="package" version="9.4">coreutils</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ @CONDA_TRIMMOMATIC_JAR_PATH@ && @@ -38,7 +38,7 @@ SE -threads \${GALAXY_SLOTS:-6} fastq_in.'$fastq_in.extension' fastq_out.'$fastq_in.extension' #end if ## ILLUMINACLIP option - #if $illuminaclip.do_illuminaclip + #if $illuminaclip.do_illuminaclip == "yes" #if $illuminaclip.adapter_type.standard_or_custom == "custom" #if $readtype.single_or_paired in ["pair_of_files","collection"] ILLUMINACLIP:$adapter_file_from_text:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold:$illuminaclip.min_adapter_len:$illuminaclip.keep_both_reads @@ -134,7 +134,10 @@ </when> </conditional> <conditional name="illuminaclip"> - <param name="do_illuminaclip" type="boolean" label="Perform initial ILLUMINACLIP step?" help="Cut adapter and other illumina-specific sequences from the read" truevalue="yes" falsevalue="no" checked="False" /> + <param name="do_illuminaclip" type="select" label="Perform initial ILLUMINACLIP step?" help="Cut adapter and other illumina-specific sequences from the read"> + <option value="no" selected="true">no</option> + <option value="yes">yes</option> + </param> <when value="yes"> <conditional name="adapter_type"> <param name="standard_or_custom" type="select" label="Select standard adapter sequences or provide custom?"> @@ -252,7 +255,7 @@ </data> </outputs> <tests> - <test> + <test expect_num_outputs="3"> <!-- Single-end example --> <conditional name="readtype"> <param name="single_or_paired" value="se" /> @@ -263,16 +266,16 @@ <param name="output_err" value="yes" /> <output name="fastq_out" file="trimmomatic_se_out1.fastq" /> <output name="log_file" file="trimmomatic_se_out1.log" /> - <output name="err_file" file="trimmomatic_se_out1.err" /> + <output name="err_file" compare="re_match" file="trimmomatic_se_out1.err.re_match" /> </test> - <test> + <test expect_num_outputs="1"> <!-- Single-end example - gzipped --> <param name="single_or_paired" value="se" /> <param name="fastq_in" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" /> <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> <output name="fastq_out" file="trimmomatic_se_out1.fastq.gz" /> </test> - <test> + <test expect_num_outputs="4"> <!-- Paired-end example - gzipped --> <param name="single_or_paired" value="pair_of_files" /> <param name="fastq_r1_in" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" /> @@ -283,7 +286,7 @@ <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq.gz" /> <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq.gz" /> </test> - <test> + <test expect_num_outputs="4"> <!-- Paired-end example --> <param name="single_or_paired" value="pair_of_files" /> <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> @@ -294,7 +297,7 @@ <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" /> <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq" /> </test> - <test> + <test expect_num_outputs="4"> <!-- Paired-end Illumina 1.3-1.7 quality encoding --> <param name="single_or_paired" value="pair_of_files" /> <param name="fastq_r1_in" value="Illumina_SG_R1.fastqillumina" ftype="fastqillumina" /> @@ -305,7 +308,7 @@ <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastqillumina" /> <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastqillumina" /> </test> - <test> + <test expect_num_outputs="4"> <!-- Paired-end Solexa quality encoding --> <param name="single_or_paired" value="pair_of_files" /> <param name="fastq_r1_in" value="Illumina_SG_R1.fastqsolexa" ftype="fastqsolexa" /> @@ -316,7 +319,7 @@ <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastqsolexa" /> <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastqsolexa" /> </test> - <test> + <test expect_num_outputs="1"> <!-- Single-end example (cropping) --> <param name="single_or_paired" value="se" /> <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> @@ -324,7 +327,7 @@ <param name="operations_0|operation|crop" value="10" /> <output name="fastq_out" file="trimmomatic_se_out2.fastq" /> </test> - <test> + <test expect_num_outputs="6"> <!-- Paired-end with dataset collection --> <param name="single_or_paired" value="collection" /> <param name="fastq_pair"> @@ -343,7 +346,7 @@ <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq" /> </output_collection> </test> - <test> + <test expect_num_outputs="6"> <!-- Paired-end with dataset collection - gzipped --> <param name="single_or_paired" value="collection" /> <param name="fastq_pair"> @@ -362,7 +365,7 @@ <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq.gz" /> </output_collection> </test> - <test> + <test expect_num_outputs="1"> <!-- Single-end using AVGQUAL --> <param name="single_or_paired" value="se" /> <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> @@ -370,7 +373,7 @@ <param name="operations_0|operation|avgqual" value="30" /> <output name="fastq_out" file="trimmomatic_avgqual.fastq" /> </test> - <test> + <test expect_num_outputs="1"> <!-- Single-end using MAXINFO --> <param name="single_or_paired" value="se" /> <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> @@ -379,12 +382,12 @@ <param name="operations_0|operation|strictness" value="0.8" /> <output name="fastq_out" file="trimmomatic_maxinfo.fastq" /> </test> - <test> + <test expect_num_outputs="4"> <!-- Paired-end ILLUMINACLIP - this does not check valid clipping --> <param name="single_or_paired" value="pair_of_files" /> <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" /> - <param name="do_illuminaclip" value="true"/> + <param name="do_illuminaclip" value="yes"/> <param name="adapter_fasta" value="TruSeq2-PE.fa"/> <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1_clip.fastq" /> @@ -392,12 +395,12 @@ <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" /> <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1_clip.fastq" /> </test> - <test> + <test expect_num_outputs="4"> <!-- Paired-end ILLUMINACLIP providing 'custom' adapters - this does not check valid clipping --> <param name="single_or_paired" value="pair_of_files" /> <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" /> - <param name="do_illuminaclip" value="true"/> + <param name="do_illuminaclip" value="yes"/> <param name="standard_or_custom" value="custom"/> <param name="adapter_text" value=">PrefixPE/1 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT >PrefixPE/2 CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT >PCR_Primer1 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT >PCR_Primer1_rc AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT >PCR_Primer2 CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT >PCR_Primer2_rc AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG >FlowCell1 TTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC >FlowCell2 TTTTTTTTTTCAAGCAGAAGACGGCATACGA "/> @@ -408,7 +411,7 @@ <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" /> <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1_clip.fastq" /> </test> - <test> + <test expect_num_outputs="3"> <!-- Quality score test --> <conditional name="readtype"> <param name="single_or_paired" value="se" /> @@ -420,7 +423,7 @@ <param name="quality_score" value="-phred33"/> <output name="fastq_out" file="trimmomatic_se_out1.fastq" /> <output name="log_file" file="trimmomatic_se_out1.log" /> - <output name="err_file" file="trimmomatic_se_out2.err" /> + <output name="err_file" compare="re_match" file="trimmomatic_se_out2.err.re_match" /> </test> </tests> <help><![CDATA[ @@ -499,9 +502,11 @@ **Credits** -This Galaxy tool has been developed within the Bioinformatics Core Facility at the -University of Manchester, with contributions from Peter van Heusden, Marius -van den Beek, Jelle Scholtalbers, Charles Girardot, Matthias Bernt and Cristóbal Gallardo. +This Galaxy tool was originally developed within the Bioinformatics Core +Facility at the University of Manchester, with contributions from Peter van +Heusden, Marius van den Beek, Jelle Scholtalbers, Charles Girardot, Matthias +Bernt and Cristóbal Gallardo. It is now maintained as part of the IUC tool +collection. It runs the Trimmomatic program which has been developed within Bjorn Usadel's group at RWTH Aachen university.