Mercurial > repos > dave > lofreq_indelqual
changeset 0:8d8ee5939303 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
| author | dave |
|---|---|
| date | Wed, 27 Nov 2019 15:25:08 +0000 |
| parents | |
| children | |
| files | lofreq_indelqual.xml macros.xml test-data/alnqual-out1.bam test-data/alnqual-out2.bam test-data/alnqual-out3.bam test-data/alnqual-out4.bam test-data/alnqual-out5.bam test-data/call-out1.vcf test-data/indelqual-out1.bam test-data/indelqual-out2.bam test-data/indelqual-out3.bam test-data/lofreq-in1.bam test-data/pBR322.fa test-data/viterbi-out1.bam test-data/viterbi-out2.bam tool-data/fasta_indexes.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 17 files changed, 275 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lofreq_indelqual.xml Wed Nov 27 15:25:08 2019 +0000 @@ -0,0 +1,99 @@ +<tool id="lofreq_indelqual" name="Insert indel qualities" version="@WRAPPER_VERSION@0"> + <description>into a BAM file</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + #if $strategy.selector == 'dindel' + #if str($strategy.reference_source.ref_selector) == 'history': + #set $reference_fasta_fn = 'reference.fa' + ln -s '$strategy.reference_source.ref' $reference_fasta_fn && + lofreq faidx $reference_fasta_fn 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 && + #else + #set $reference_fasta_fn = str($strategy.reference_source.ref.fields.path) + #end if + #end if + lofreq indelqual + #if $strategy.selector == 'dindel' + --dindel + --ref $reference_fasta_fn + #else + #if $strategy.deletions + --uniform $strategy.insertions,$strategy.deletions + #else + --uniform $strategy.insertions + #end if + #end if + -o output.bam $reads + ]]></command> + <inputs> + <param type="data" name="reads" format="bam" /> + <conditional name="strategy" label="Indel calculation approach"> + <param name="selector" type="select"> + <option value="uniform">Uniform</option> + <option value="dindel">Dindel</option> + </param> + <when value="uniform"> + <param name="insertions" type="integer" value="30" label="Indel quality to add" help="Should probably not be left at the default value" /> + <param name="deletions" type="integer" optional="true" label="Separate deletion quality" help="Leave blank to use the same values for insertions and deletions" /> + </when> + <when value="dindel"> + <expand macro="reference_interface" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="output" format="bam" from_work_dir="output.bam" label="Add indel qualities to data ${reads.dataset.hid}" /> + </outputs> + <tests> + <test> + <param name="reads" ftype="bam" value="lofreq-in1.bam" /> + <param name="selector" value="uniform" /> + <param name="insertions" value="20" /> + <param name="deletions" value="30" /> + <output name="output" file="indelqual-out1.bam" /> + </test> + <test> + <param name="reads" ftype="bam" value="lofreq-in1.bam" /> + <param name="selector" value="dindel" /> + <param name="ref_selector" value="history" /> + <param name="ref" ftype="fasta" value="pBR322.fa" /> + <output name="output" file="indelqual-out2.bam" /> + </test> + <test> + <param name="reads" ftype="bam" value="lofreq-in1.bam" /> + <param name="selector" value="uniform" /> + <param name="insertions" value="20" /> + <output name="output" file="indelqual-out3.bam" /> + </test> + </tests> + <help><![CDATA[ + lofreq indelqual: Insert indel qualities into BAM file (required for indel predictions) + +Usage: lofreq indelqual [options] in.bam +Options: + -u | --uniform INT[,INT] Add this indel quality uniformly to all bases. + Use two comma separated values to specify + insertion and deletion quality separately. + (clashes with --dindel) + --dindel Add Dindel's indel qualities (Illumina specific) + (clashes with -u; needs --ref) + -f | --ref Reference sequence used for mapping + (Only required for --dindel) + -o | --out FILE Output BAM file [- = stdout = default] + --verbose Be verbose + +The preferred way of inserting indel qualities should be via GATK's BQSR (>=2) If that's not possible, use this subcommand. +The command has two modes: 'uniform' and 'dindel': +- 'uniform' will assign a given value uniformly, whereas +- 'dindel' will insert indel qualities based on Dindel (PMID 20980555). +Both will overwrite any existing values. +Do not realign your BAM file afterwards! + + + ]]></help> + <expand macro="citations"> + <citation type="doi">10.1101/gr.112326.110</citation> + </expand> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Nov 27 15:25:08 2019 +0000 @@ -0,0 +1,47 @@ +<macros> + <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy</token> + <token name="@TOOL_VERSION@">2.1.3.1</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">lofreq</requirement> + <requirement type="package" version="1.9">samtools</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/nar/gks918</citation> + <yield /> + </citations> + </xml> + <token name="@PREPARE_REF@"><![CDATA[ + #if str($reference_source.ref_selector) == 'history': + #set $reference_fasta_fn = 'reference.fa' + ln -s '$reference_source.ref' $reference_fasta_fn && + lofreq faidx $reference_fasta_fn 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 && + #else + #set $reference_fasta_fn = str($reference_source.ref.fields.path) + #end if + ]]></token> + <xml name="reference_interface"> + <conditional name="reference_source"> + <param name="ref_selector" type="select" + label="Choose the source for the reference genome"> + <option value="cached">Locally cached</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param argument="--ref" type="select" + label="Reference genome"> + <options from_data_table="fasta_indexes"> + <filter type="data_meta" column="dbkey" key="dbkey" ref="reads" /> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" /> + </options> + </param> + </when> + <when value="history"> + <param argument="--ref" type="data" format="fasta" label="Reference" help="Reference sequence" /> + </when> + </conditional> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/call-out1.vcf Wed Nov 27 15:25:08 2019 +0000 @@ -0,0 +1,19 @@ +##fileformat=VCFv4.0 +##fileDate=20191125 +##source=lofreq call --ref reference.fa --no-default-filter -r pBR322:1-2180 -o /tmp/lofreq2_call_parallel3mrmthi_/0.vcf.gz alignments.bam +##reference=reference.fa +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth"> +##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> +##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position"> +##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant)."> +##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position"> +##FILTER=<ID=min_snvqual_38,Description="Minimum SNV Quality (Phred) 38"> +##FILTER=<ID=min_indelqual_20,Description="Minimum Indel Quality (Phred) 20"> +##FILTER=<ID=min_dp_10,Description="Minimum Coverage 10"> +##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000"> +##FILTER=<ID=min_snvqual_38,Description="Minimum SNV Quality (Phred) 38"> +##FILTER=<ID=min_indelqual_20,Description="Minimum Indel Quality (Phred) 20"> +#CHROM POS ID REF ALT QUAL FILTER INFO +pBR322 1134 . C T 49314 PASS DP=1767;AF=1.000000;SB=0;DP4=0,0,910,857
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pBR322.fa Wed Nov 27 15:25:08 2019 +0000 @@ -0,0 +1,74 @@ +>pBR322 +TTCTCATGTTTGACAGCTTATCATCGATAAGCTTTAATGCGGTAGTTTATCACAGTTAAA +TTGCTAACGCAGTCAGGCACCGTGTATGAAATCTAACAATGCGCTCATCGTCATCCTCGG +CACCGTCACCCTGGATGCTGTAGGCATAGGCTTGGTTATGCCGGTACTGCCGGGCCTCTT +GCGGGATATCGTCCATTCCGACAGCATCGCCAGTCACTATGGCGTGCTGCTAGCGCTATA +TGCGTTGATGCAATTTCTATGCGCACCCGTTCTCGGAGCACTGTCCGACCGCTTTGGCCG +CCGCCCAGTCCTGCTCGCTTCGCTACTTGGAGCCACTATCGACTACGCGATCATGGCGAC +CACACCCGTCCTGTGGATCCTCTACGCCGGACGCATCGTGGCCGGCATCACCGGCGCCAC +AGGTGCGGTTGCTGGCGCCTATATCGCCGACATCACCGATGGGGAAGATCGGGCTCGCCA +CTTCGGGCTCATGAGCGCTTGTTTCGGCGTGGGTATGGTGGCAGGCCCCGTGGCCGGGGG +ACTGTTGGGCGCCATCTCCTTGCATGCACCATTCCTTGCGGCGGCGGTGCTCAACGGCCT +CAACCTACTACTGGGCTGCTTCCTAATGCAGGAGTCGCATAAGGGAGAGCGTCGACCGAT +GCCCTTGAGAGCCTTCAACCCAGTCAGCTCCTTCCGGTGGGCGCGGGGCATGACTATCGT +CGCCGCACTTATGACTGTCTTCTTTATCATGCAACTCGTAGGACAGGTGCCGGCAGCGCT +CTGGGTCATTTTCGGCGAGGACCGCTTTCGCTGGAGCGCGACGATGATCGGCCTGTCGCT +TGCGGTATTCGGAATCTTGCACGCCCTCGCTCAAGCCTTCGTCACTGGTCCCGCCACCAA +ACGTTTCGGCGAGAAGCAGGCCATTATCGCCGGCATGGCGGCCGACGCGCTGGGCTACGT +CTTGCTGGCGTTCGCGACGCGAGGCTGGATGGCCTTCCCCATTATGATTCTTCTCGCTTC +CGGCGGCATCGGGATGCCCGCGTTGCAGGCCATGCTGTCCAGGCAGGTAGATGACGACCA +TCAGGGACAGCTTCAAGGATCGCTCGCGGCTCTTACCAGCCTAACTTCGATCACTGGACC +GCTGATCGTCACGGCGATTTATGCCGCCTCGGCGAGCACATGGAACGGGTTGGCATGGAT +TGTAGGCGCCGCCCTATACCTTGTCTGCCTCCCCGCGTTGCGTCGCGGTGCATGGAGCCG +GGCCACCTCGACCTGAATGGAAGCCGGCGGCACCTCGCTAACGGATTCACCACTCCAAGA +ATTGGAGCCAATCAATTCTTGCGGAGAACTGTGAATGCGCAAACCAACCCTTGGCAGAAC +ATATCCATCGCGTCCGCCATCTCCAGCAGCCGCACGCGGCGCATCTCGGGCAGCGTTGGG +TCCTGGCCACGGGTGCGCATGATCGTGCTCCTGTCGTTGAGGACCCGGCTAGGCTGGCGG +GGTTGCCTTACTGGTTAGCAGAATGAATCACCGATACGCGAGCGAACGTGAAGCGACTGC +TGCTGCAAAACGTCTGCGACCTGAGCAACAACATGAATGGTCTTCGGTTTCCGTGTTTCG +TAAAGTCTGGAAACGCGGAAGTCAGCGCCCTGCACCATTATGTTCCGGATCTGCATCGCA +GGATGCTGCTGGCTACCCTGTGGAACACCTACATCTGTATTAACGAAGCGCTGGCATTGA +CCCTGAGTGATTTTTCTCTGGTCCCGCCGCATCCATACCGCCAGTTGTTTACCCTCACAA +CGTTCCAGTAACCGGGCATGTTCATCATCAGTAACCCGTATCGTGAGCATCCTCTCTCGT +TTCATCGGTATCATTACCCCCATGAACAGAAATCCCCCTTACACGGAGGCATCAGTGACC +AAACAGGAAAAAACCGCCCTTAACATGGCCCGCTTTATCAGAAGCCAGACATTAACGCTT +CTGGAGAAACTCAACGAGCTGGACGCGGATGAACAGGCAGACATCTGTGAATCGCTTCAC +GACCACGCTGATGAGCTTTACCGCAGCTGCCTCGCGCGTTTCGGTGATGACGGTGAAAAC +CTCTGACACATGCAGCTCCCGGAGACGGTCACAGCTTGTCTGTAAGCGGATGCCGGGAGC +AGACAAGCCCGTCAGGGCGCGTCAGCGGGTGTTGGCGGGTGTCGGGGCGCAGCCATGACC +CAGTCACGTAGCGATAGCGGAGTGTATACTGGCTTAACTATGCGGCATCAGAGCAGATTG +TACTGAGAGTGCACCATATGCGGTGTGAAATACCGCACAGATGCGTAAGGAGAAAATACC +GCATCAGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGC +GGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTATCCACAGAATCAGGGGATA +ACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCG +CGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCT +CAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAA +GCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTC +TCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGT +AGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCG +CCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGG +CAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCT +TGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGC +TGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCG +CTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTC +AAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTT +AAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAA +AATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAAT +GCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCT +GACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTG +CAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAG +CCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTA +ATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTG +CCATTGCTGCAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCG +GTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCT +CCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTA +TGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTG +GTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCC +CGGCGTCAACACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTG +GAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGA +TGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTG +GGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAAT +GTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTC +TCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCA +CATTTCCCCGAAAAGTGCCACCTGACGTCTAAGAAACCATTATTATCATGACATTAACCT +ATAAAAATAGGCGTATCACGAGGCCCTTTCGTCTTCAAGAA \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Wed Nov 27 15:25:08 2019 +0000 @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Nov 27 15:25:08 2019 +0000 @@ -0,0 +1,7 @@ +<tables> + <!-- Location of SAMTools indexes for FASTA files --> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> +</tables>