Mercurial > repos > iuc > samtools_view
view macros.xml @ 8:bf328cec6a42 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
author | iuc |
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date | Wed, 02 Sep 2020 15:29:22 -0400 |
parents | b01db2684fa5 |
children | 350bbc5c2ffd |
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<macros> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">samtools</requirement> <yield/> </requirements> </xml> <token name="@TOOL_VERSION@">1.9</token> <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token> <token name="@PREPARE_IDX@"><![CDATA[ ##prepare input and indices ln -s '$input' infile && #if $input.is_of_type('bam'): #if str( $input.metadata.bam_index ) != "None": ln -s '${input.metadata.bam_index}' infile.bai && #else: samtools index infile infile.bai && #end if #elif $input.is_of_type('cram'): #if str( $input.metadata.cram_index ) != "None": ln -s '${input.metadata.cram_index}' infile.crai && #else: samtools index infile infile.crai && #end if #end if ]]></token> <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[ ##prepare input and indices #for $i, $bam in enumerate( $input_bams ): ln -s '$bam' '${i}' && #if $bam.is_of_type('bam'): #if str( $bam.metadata.bam_index ) != "None": ln -s '${bam.metadata.bam_index}' '${i}.bai' && #else: samtools index '${i}' '${i}.bai' && #end if #elif $bam.is_of_type('cram'): #if str( $bam.metadata.cram_index ) != "None": ln -s '${bam.metadata.cram_index}' '${i}.crai' && #else: samtools index '${i}' '${i}.crai' && #end if #end if #end for ]]></token> <token name="@PREPARE_FASTA_IDX@"><![CDATA[ ##checks for reference data ($addref_cond.addref_select=="history" or =="cached") ##and sets the -t/-T parameters accordingly: ##- in case of history a symbolic link is used because samtools (view) will generate ## the index which might not be possible in the directory containing the fasta file ##- in case of cached the absolute path is used which allows to read the cram file ## without specifying the reference #if $addref_cond.addref_select == "history": ln -s '${addref_cond.ref}' reference.fa && samtools faidx reference.fa && #set reffa="reference.fa" #set reffai="reference.fa.fai" #elif $addref_cond.addref_select == "cached": #set reffa=str($addref_cond.ref.fields.path) #set reffai=str($addref_cond.ref.fields.path)+".fai" #else #set reffa=None #set reffai=None #end if ]]></token> <token name="@ADDTHREADS@"><![CDATA[ ##compute the number of ADDITIONAL threads to be used by samtools (-@) addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) && ]]></token> <token name="@ADDMEMORY@"><![CDATA[ ##compute the number of memory available to samtools sort (-m) ##use only 75% of available: https://github.com/samtools/samtools/issues/831 addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ]]></token> <xml name="seed_input"> <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> </xml> <xml name="flag_options"> <option value="1">Read is paired</option> <option value="2">Read is mapped in a proper pair</option> <option value="4">Read is unmapped</option> <option value="8">Mate is unmapped</option> <option value="16">Read is mapped to the reverse strand of the reference</option> <option value="32">Mate is mapped to the reverse strand of the reference</option> <option value="64">Read is the first in a pair</option> <option value="128">Read is the second in a pair</option> <option value="256">Alignment of the read is not primary</option> <option value="512">Read fails platform/vendor quality checks</option> <option value="1024">Read is a PCR or optical duplicate</option> <option value="2048">Alignment is supplementary</option> </xml> <!-- region specification macros and tokens for tools that allow the specification of region by bed file / space separated list of regions --> <token name="@REGIONS_FILE@"><![CDATA[ #if $cond_region.select_region == 'tab': -t '$cond_region.targetregions' #end if ]]></token> <token name="@REGIONS_MANUAL@"><![CDATA[ #if $cond_region.select_region == 'text': #for $i, $x in enumerate($cond_region.regions_repeat): '${x.region}' #end for #end if ]]></token> <xml name="regions_macro"> <conditional name="cond_region"> <param name="select_region" type="select" label="Filter by regions" help="restricts output to only those alignments which overlap the specified region(s)"> <option value="no" selected="True">No</option> <option value="text">Manualy specify regions</option> <option value="tab">Regions from tabular file</option> </param> <when value="no"/> <when value="text"> <repeat name="regions_repeat" min="1" default="1" title="Regions"> <param name="region" type="text" label="region" help="format chr:from-to"> <validator type="regex" message="Required format: CHR[:FROM[-TO]]; where CHR: string containing any character except quotes, whitespace and colon; FROM and TO: any integer">^[^\s'\":]+(:\d+(-\d+){0,1}){0,1}$</validator> </param> </repeat> </when> <when value="tab"> <param name="targetregions" argument="-t/--target-regions" type="data" format="tabular" label="Target regions file" help="Do stats in these regions only. Tab-delimited file chr,from,to (1-based, inclusive)" /> </when> </conditional> </xml> <xml name="citations"> <citations> <citation type="bibtex"> @misc{SAM_def, title={Definition of SAM/BAM format}, url = {https://samtools.github.io/hts-specs/},} </citation> <citation type="doi">10.1093/bioinformatics/btp352</citation> <citation type="doi">10.1093/bioinformatics/btr076</citation> <citation type="doi">10.1093/bioinformatics/btr509</citation> <citation type="bibtex"> @misc{Danecek_et_al, Author={Danecek, P., Schiffels, S., Durbin, R.}, title={Multiallelic calling model in bcftools (-m)}, url = {http://samtools.github.io/bcftools/call-m.pdf},} </citation> <citation type="bibtex"> @misc{Durbin_VCQC, Author={Durbin, R.}, title={Segregation based metric for variant call QC}, url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} </citation> <citation type="bibtex"> @misc{Li_SamMath, Author={Li, H.}, title={Mathematical Notes on SAMtools Algorithms}, url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} </citation> <citation type="bibtex"> @misc{SamTools_github, title={SAMTools GitHub page}, url = {https://github.com/samtools/samtools},} </citation> </citations> </xml> <xml name="version_command"> <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command> </xml> <xml name="stdio"> <stdio> <exit_code range="1:" level="fatal" description="Error" /> </stdio> </xml> </macros>