samtools_view: samtools_view.xml comparison

comparison samtools_view.xml @ 7:b01db2684fa5 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"

author	iuc
date	Tue, 21 Jan 2020 07:40:18 -0500
parents	ff313de5f7f4
children	bf328cec6a42

comparison

equal deleted inserted replaced

-:ff313de5f7f4
+:b01db2684fa5
-<tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@">
+<tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy1">
-<description>reformat, filter, or subsample</description>
+<description>- reformat, filter, or subsample SAM, BAM or CRAM</description>
 <macros>
 <import>macros.xml</import>
+<token name="@REF_DATA@">
+## additional reference data
+#if $reffa!=None:
+-T '$reffa'
+-t '$reffai'
+#end if
+</token>
+<xml name="read_output_formatting">
+<yield />
+<section name="adv_output" title="Read Reformatting Options" expanded="false">
+<repeat name="readtags" title="Strip read tags from output">
+<param name="readtag" type="text" argument="-x" label="Read tag to strip" help="Read tag to exclude from output."/>
+</repeat>
+<param name="collapsecigar" type="boolean" argument="-B" truevalue="-B" falsevalue="" checked="false" label="Collapse backward CIGAR operation" help="Collapse the backward CIGAR operation." />
+</section>
+</xml>
+<xml name="output_format_selector">
+<conditional name="output_format">
+<param name="oformat" type="select" label="Output format">
+<option value="sam">SAM</option>
+<option value="bam" selected="True">BAM (-b)</option>
+<option value="cram">CRAM (-C)</option>
+</param>
+<when value="sam">
+<yield />
+<param name="fmtopt" type="hidden" value="" />
+</when>
+<when value="bam">
+<param name="fmtopt" type="hidden" value="-b" />
+</when>
+<when value="cram">
+<param name="fmtopt" type="hidden" value="-C" />
+</when>
+</conditional>
+</xml>
 </macros>
 <expand macro="requirements">
 <requirement type="package">gawk</requirement>
 </expand>
 <expand macro="stdio"/>
 <command><![CDATA[
 @ADDTHREADS@
 ## prepare reference data
 @PREPARE_FASTA_IDX@
 @PREPARE_IDX@
-#if $cond_subsample.select_subsample == 'target':
-##this must be done before the main command because we don't know the total # reads until execution time
+#if str($mode.outtype) == 'header':
-#if str($cond_subsample.seed) == '':
+## call samtools view and be done
-#set seed_expr="int(rand() * 32768)"
+samtools view
-#else
+-H ${mode.output_options.output_format.fmtopt} -o outfile
-#set seed_expr=$cond_subsample.seed
+@REF_DATA@
+infile
+#else:
+## are filtering and/or subsampling in effect?
+#set $with_filtering = False
+#set $with_subsampling = False
+#if str($mode.outtype) == 'selected_reads':
+#set $with_filtering = True
+#if str($mode.subsample_config.subsampling_mode.select_subsample) != 'fraction' or $mode.subsample_config.subsampling_mode.factor > 1:
+#set $with_subsampling = True
+#end if
 #end if
-#if $input.is_of_type('sam'):
-sample_fragment=`samtools view -c infile | awk '{s=\$1} END {frac=$cond_subsample.target/s; print(frac < 1 ? "-s "  $seed_expr+frac : "")}'` &&
+## are we producing one or two outputs?
-#else
+#if str($mode.outtype) == 'selected_reads' and str($mode.output_options.reads_report_type) != 'count' and str($mode.output_options.complementary_output) == 'yes':
-sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {frac=$cond_subsample.target/s; print(frac < 1 ? "-s " $seed_expr+frac : "")}'` &&
+#set $with_non_selected_reads_output = True
+#else:
+#set $with_non_selected_reads_output = False
+	    #end if
+#set $std_filters = ''
+#set $reg_filters = ''
+#if $with_filtering:
+## build string of all user-configured filter options
+#if str($mode.filter_config.cond_region.select_region) == 'bed':
+#set std_filters = $std_filters + " -L '%s'" % str($mode.filter_config.cond_region.bedfile)
+#elif str($mode.filter_config.cond_region.select_region) == 'text':
+#set $reg_filters = "'%s'" % str($mode.filter_config.cond_region.regions).strip()
+#end if
+#if $mode.filter_config.cond_rg.select_rg == 'text':
+#set $std_filters = $std_filters + " -r '%s'" % str($mode.filter_config.cond_rg.readgr)
+#else if $mode.filter_config.cond_rg.select_rg == 'file':
+#set $std_filters = $std_filters + " -R '%s'" % str($mode.filter_config.cond_rg.rgfile)
+#end if
+#if str($mode.filter_config.quality) != '' and int($mode.filter_config.quality) > 0:
+#set $std_filters = $std_filters + " -q %s" % str($mode.filter_config.quality)
+#end if
+#if str($mode.filter_config.library):
+#set $std_filters = $std_filters + " -l '%s'" % str($mode.filter_config.library)
+#end if
+#if str($mode.filter_config.cigarcons):
+#set $std_filters = $std_filters + " -m %s" % str($mode.filter_config.cigarcons)
+#end if
+#if str($mode.filter_config.inclusive_filter) != 'None':
+#set $filter = str($mode.filter_config.inclusive_filter)
+@FLAGS@
+#set $std_filters = $std_filters + " -f %s" % str($flags)
+#end if
+#if str($mode.filter_config.exclusive_filter) != 'None':
+#set $filter = str($mode.filter_config.exclusive_filter)
+@FLAGS@
+#set $std_filters = $std_filters + " -F %s" % str($flags)
+#end if
+#if str($mode.filter_config.exclusive_filter_all) != 'None':
+#set $filter = str($mode.filter_config.exclusive_filter_all)
+@FLAGS@
+#set $std_filters = $std_filters + " -G %s" % str($flags)
+#end if
 #end if
-#end if
-##call samtools view
+#if $with_subsampling:
-samtools view
+## handle seed and fraction calculation for subsampling
--@ \$addthreads
+#import random
+#if str($mode.subsample_config.subsampling_mode.seed):
-#if $outtype == 'count':
+#set $seed = int($mode.subsample_config.subsampling_mode.seed)
--c
+#else:
-#elif $outtype == 'bam':
+#set $seed = random.randrange(32768)
--b
+#end if
-#elif $outtype == 'cram':
--C
+#if $mode.subsample_config.subsampling_mode.select_subsample == 'target':
-#end if
+##this must be done before the main command because we don't know the total # reads until execution time
+#if $input.is_of_type('sam') or $std_filters or $reg_filters:
-## filter options (regions filter is the last parameter)
+## There is no index or we cannot use it because we are
-#if $cond_filter.select_filter == 'yes':
+## not dealing with all of the reads in the indexed
-#if $cond_filter.cond_region.select_region == 'bed' and str( $cond_filter.cond_region.bedfile ) != 'None'
+## file. We have to do an extra pass over the input to
--L '$cond_filter.cond_region.bedfile'
+## count the reads to subsample.
+sample_fragment=`samtools view -c $std_filters infile $reg_filters | awk '{s=\$1} END {frac=${mode.subsample_config.subsampling_mode.target}/s; print(frac < 1 ? $seed+frac : ".0")}'` &&
+#else:
+## We can get the count of reads to subsample using
+## an inexpensive call to idxstats.
+sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {frac=${mode.subsample_config.subsampling_mode.target}/s; print(frac < 1 ? $seed+frac : ".0")}'` &&
+#end if
+#end if
 #end if
-#if $cond_filter.cond_rg.select_rg == 'text':
--r '$cond_filter.cond_rg.readgr'
+## call samtools view
-#else if $cond_filter.cond_rg.select_rg == 'file':
+samtools view
--R '$cond_filter.cond_rg.rgfile'
+-@ \$addthreads
+#if str($mode.output_options.reads_report_type) == 'count':
+-c
+#else:
+${mode.output_options.output_format.fmtopt}
 #end if
-#if str($cond_filter.quality) != '' and int( $cond_filter.quality ) > 0
--q $cond_filter.quality
+## filter options (except regions filter, which is the last parameter)
+$std_filters
+#if $with_subsampling:
+#if str($mode.subsample_config.subsampling_mode.select_subsample) == "target":
+##this is calculated at execution time before the main samtools command
+-s \${sample_fragment}
+#else:
+#set $fraction = $seed + 1 / float($mode.subsample_config.subsampling_mode.factor)
+-s $fraction
+#end if
 #end if
-#if str( $cond_filter.library ) != ''
--l '$cond_filter.library'
+## output options
+#if str($mode.output_options.reads_report_type) == 'count':
+-o outfile
+#else:
+## output options
+#if str($mode.output_options.output_format.oformat) == 'sam':
+${mode.output_options.output_format.with_header}
+#end if
+${mode.output_options.adv_output.collapsecigar}
+#for $s in $mode.output_options.adv_output.readtags:
+-x '${s.readtag}'
+#end for
+#if str($mode.output_options.reads_report_type) == 'retained'
+-o outfile
+#if $with_non_selected_reads_output:
+-U inv_outfile
+#end if
+#else:
+-U outfile
+#if $with_non_selected_reads_output:
+-o inv_outfile
+#else:
+-o /dev/null
+#end if
+#end if
+##currently reference based CRAM is disabled (see https://github.com/galaxyproject/tools-iuc/pull/1963)
+#if $mode.output_options.output_format.oformat == 'cram':
+--output-fmt-option no_ref
+#end if
 #end if
-#if str( $cond_filter.cigarcons ) != ''
--m $cond_filter.cigarcons
+@REF_DATA@
+infile
+## region filter needs to be at the end
+$reg_filters
+#if str($mode.output_options.reads_report_type) != 'count':
+## if data is converted from an unsorted file (SAM, CRAM, or unsorted BAM) to BAM
+## then sort the output by coordinate,
+#if not $input.is_of_type('bam') and str($mode.output_options.output_format.oformat) == 'bam':
+&& samtools sort
+-@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
+-O bam
+-o tmpsam
+outfile
+&& mv tmpsam outfile
+#if $with_non_selected_reads_output:
+&& samtools sort
+-@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
+-O bam
+-o tmpsam
+inv_outfile
+&& mv tmpsam inv_outfile
+#end if
+#end if
 #end if
-#if str($cond_filter.inclusive_filter) != 'None':
-#set $filter = $cond_filter.inclusive_filter
+##end of reads and count-specific section
-@FLAGS@
--f $flags
-#end if
-#if str($cond_filter.exclusive_filter) != 'None':
-#set $filter = $cond_filter.exclusive_filter
-@FLAGS@
--F $flags
-#end if
-#if str($cond_filter.exclusive_filter_all) != 'None':
-#set $filter = $cond_filter.exclusive_filter_all
-@FLAGS@
--G $flags
-#end if
-#for $i, $s in enumerate($cond_filter.readtags)
--x '${s.readtag}'
-#end for
-#end if
-#if $cond_subsample.select_subsample != 'no':
-#if $cond_subsample.select_subsample == "target":
-##this is calculated at execution time before the main samtools command
-"\${sample_fragment}"
-#else
-#set fraction=str($cond_subsample.fraction).split('.')[1]
-#if  str($cond_subsample.seed) == '':
--s "\${RANDOM}".$fraction
-#else
--s $cond_subsample.seed.$fraction
-#end if
-#end if
-#end if
-## output options
-$adv_output.header
-$adv_output.collapsecigar
-#if $adv_output.outputpassing == 'yes'
--U inv_outfile
-#end if
--o outfile
-## additional reference data
-#if $reffa!=None:
--T '$reffa'
--t '$reffai'
-#end if
-##currently reference based CRAM is disabled (see https://github.com/galaxyproject/tools-iuc/pull/1963)
-#if $outtype=='cram':
---output-fmt-option no_ref
-#end if
-infile
-## region filter need to be at the end
-#if $cond_filter.select_filter == 'yes' and $cond_filter.cond_region.select_region == 'text':
-'$cond_filter.cond_region.regions'
-#end if
-## if data is converted from an unsorted file (SAM, CRAM, or unsorted BAM) to BAM
-## then sort the output by coordinate,
-#if not $input.is_of_type('bam') and $outtype == 'bam':
-&& samtools sort
--@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
--O bam
--o 'tmpsam'
-outfile
-&& mv tmpsam outfile
-#if $adv_output.outputpassing == 'yes':
-&& samtools sort
--@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
--O bam
--o 'tmpsam'
-inv_outfile
-&& mv tmpsam inv_outfile
-#end if
 #end if
 ]]></command>
 <inputs>
 <!-- note unsorted bam includes all derived bam types (inlcuding bam which is sorted) -->
 <param name="input" format="sam,unsorted.bam,cram" type="data" label="SAM/BAM/CRAM data set" />
-<param name="outtype" type="select" argument="-b/-C/-c" label="Output type">
+<conditional name="mode">
-<help>Select output type. In case of counts only the total number of alignments is returned. All filters are taken into account</help>
+<param name="outtype" type="select" label="What would you like to look at?">
-<option value="sam">SAM</option>
+<option value="all_reads">All reads in the input dataset</option>
-<option value="bam">BAM (-b)</option>
+<option value="selected_reads">A filtered/subsampled selection of reads</option>
-<option value="cram">CRAM (-C)</option>
+<option value="header">Just the input header (-H)</option>
-<option value="count">Count of alignments (-c)</option>
-</param>
-<conditional name="cond_filter">
-<param name="select_filter" type="select" label="Filter alignment">
-<option value="yes">Yes</option>
-<option value="no" selected="True">No</option>
 </param>
-<when value="yes">
+<when value="all_reads">
-<conditional name="cond_region">
+<conditional name="output_options">
-<param name="select_region" type="select" label="Filter by regions">
+<param name="reads_report_type" type="select" label="What would you like to have reported?">
-<option value="no" selected="True">No</option>
+<option value="retained">The actual reads</option>
-<option value="text">Manualy specify regions</option>
+<option value="count">The count of reads (-c)</option>
-<option value="bed">Regions from BED file</option>
 </param>
-<when value="no"/>
+<when value="retained">
-<when value="text">
+<expand macro="read_output_formatting" />
-<param name="regions" type="text" optional="false" label="Filter by regions" help="One or more space-separated region specifications to restrict output to only those alignments which overlap the specified region(s)."/>
+<expand macro="output_format_selector">
+<param name="with_header" type="boolean" truevalue="-h" falsevalue="" checked="True"
+label="Include SAM header in the output?" />
+</expand>
 </when>
-<when value="bed">
+<when value="count" />
-<param name="bedfile" format="bed" argument="-L" optional="false" type="data" label="Filter by intervals in a bed file" help="Only output alignments overlapping the intervals in the input bed file." />
+</conditional>
+</when>
+<when value="selected_reads">
+<section name="filter_config" title="Configure filters" expanded="false">
+<conditional name="cond_region">
+<param name="select_region" type="select" label="Filter by regions">
+<option value="no" selected="True">No</option>
+<option value="text">Manualy specify regions</option>
+<option value="bed">Regions from BED file</option>
+</param>
+<when value="no"/>
+<when value="text">
+<param name="regions" type="text" optional="false" label="Filter by regions" help="One or more space-separated region specifications to restrict output to only those alignments which overlap the specified region(s)."/>
+</when>
+<when value="bed">
+<param name="bedfile" format="bed" argument="-L" optional="false" type="data" label="Filter by intervals in a bed file" help="Only output alignments overlapping the intervals in the input bed file." />
+</when>
+</conditional>
+<conditional name="cond_rg">
+<param name="select_rg" type="select" label="Filter by readgroup">
+<option value="no" selected="True">No</option>
+<option value="text">Single read group </option>
+<option value="file">Read groups from file</option>
+</param>
+<when value="no"/>
+<when value="text">
+<param name="readgr" type="text" argument="-r" label="Filter by read group" help="Only output alignments in read group." />
+</when>
+<when value="file">
+<param name="rgfile" type="data" format="tabular" argument="-R" label="Filter by read groups in file" help="Output alignments in read groups listed in FILE." />
+</when>
+</conditional>
+<param name="quality" type="integer" argument="-q" optional="true" min="0" label="Filter by quality" help="Skip alignments with MAPQ smaller than INT." />
+<param name="library" type="text" argument="-l" optional="true" label="Filter by library" help="Only output alignments in library STR" />
+<param name="cigarcons" type="integer" argument="-m" optional="true" min="0" label="Filter by number of CIGAR bases consuming query sequence" help="Only output alignments with number of CIGAR bases consuming query sequence greater than or equal INT." />
+<param name="inclusive_filter" argument="-f" type="select" multiple="True" label="Require that these flags are set">
+<expand macro="flag_options" />
+</param>
+<param name="exclusive_filter" argument="-F" type="select" multiple="True" label="Exclude reads with any of the following flags set">
+<expand macro="flag_options" />
+</param>
+<param name="exclusive_filter_all" argument="-G" type="select" multiple="True" label="Exclude reads with all of the following flags set">
+<expand macro="flag_options" />
+</param>
+</section>
+<section name="subsample_config" title="Configure subsampling" expanded="false">
+<conditional name="subsampling_mode">
+<param name="select_subsample" type="select" argument="-s" label="Subsample alignment">
+<option value="fraction">Specify a downsampling factor</option>
+<option value="target">Specify a target # of reads</option>
+</param>
+<when value="fraction">
+<param name="factor" type="float" optional="False" value="1" min="1" label="Downsampling factor" help="The factor by which to downsample the input reads. A fraction of approx. 1/factor of the reads will be kept (default: 1 = no downsampling)." />
+<expand macro="seed_input" />
+</when>
+<when value="target">
+<param name="target" type="integer" optional="False" min="0" value="" label="Target # of reads" help="Sets the approx. target number of reads to subsample." />
+<expand macro="seed_input" />
+</when>
+</conditional>
+</section>
+<conditional name="output_options">
+<param name="reads_report_type" type="select"
+label="What would you like to have reported?"
+help="Hint: To invert all of the filtering/subsampling logic configured above, choose 'Reads dropped during filtering and subsampling'.">
+<option value="retained">All reads retained after filtering and subsampling</option>
+<option value="dropped">Reads dropped during filtering and subsampling</option>
+<option value="count">The count of retained reads (-c)</option>
+</param>
+<when value="retained">
+<expand macro="read_output_formatting">
+<param name="complementary_output" type="boolean" truevalue="yes" falsevalue="no" checked="false"
+label="Produce extra dataset with dropped reads?" />
+</expand>
+<expand macro="output_format_selector">
+<param name="with_header" type="boolean" truevalue="-h" falsevalue="" checked="True"
+label="Include SAM header in the output?" />
+</expand>
 </when>
-</conditional>
+<when value="dropped">
-<conditional name="cond_rg">
+<expand macro="read_output_formatting">
-<param name="select_rg" type="select" label="Filter by readgroup">
+<param name="complementary_output" type="boolean" truevalue="yes" falsevalue="no" checked="false"
-<option value="no" selected="True">No</option>
+label="Produce extra dataset with retained reads?" />
-<option value="text">Single read group </option>
+</expand>
-<option value="file">Read groups from file</option>
+<expand macro="output_format_selector">
+<param name="with_header" type="boolean" truevalue="-h" falsevalue="" checked="True"
+label="Include SAM header in the output?" />
+</expand>
+</when>
+<when value="count" />
+</conditional>
+</when>
+<when value="header">
+<conditional name="output_options">
+<param name="reads_report_type" type="select" label="What would you like to have reported?">
+<option value="">The header in ...</option>
 </param>
-<when value="no"/>
+<when value="">
-<when value="text">
+<expand macro="output_format_selector" />
-<param name="readgr" type="text" argument="-r" label="Filter by read group" help="Only output alignments in read group." />
 </when>
-<when value="file">
+</conditional>
-<param name="rgfile" type="data" format="tabular" argument="-R" label="Filter by read groups in file" help="Output alignments in read groups listed in FILE." />
-</when>
-</conditional>
-<param name="quality" type="integer" argument="-q" optional="true" min="0" label="Filter by quality" help="Skip alignments with MAPQ smaller than INT." />
-<param name="library" type="text" argument="-l" optional="true" label="Filter by library" help="Only output alignments in library STR" />
-<param name="cigarcons" type="integer" argument="-m" optional="true" min="0" label="Filter by number of CIGAR bases consuming query sequence" help="Only output alignments with number of CIGAR bases consuming query sequence greater than or equal INT." />
-<param name="inclusive_filter" argument="-f" type="select" multiple="True" label="Require that these flags are set">
-<expand macro="flag_options" />
-</param>
-<param name="exclusive_filter" argument="-F" type="select" multiple="True" label="Exclude reads with any of the following flags set">
-<expand macro="flag_options" />
-</param>
-<param name="exclusive_filter_all" argument="-G" type="select" multiple="True" label="Exclude reads with all of the following flags set">
-<expand macro="flag_options" />
-</param>
-<!-- TODO could also make this a text field (comma/space separated) -->
-<repeat name="readtags" title="Filter by read tags">
-<param name="readtag" type="text" argument="-x" label="Filter by read tag" help="Read tag to exclude from output."/>
-</repeat>
 </when>
-<when value="no"/>
-</conditional>
-<conditional name="cond_subsample">
-<param name="select_subsample" type="select" argument="-s" label="Subsample alignment">
-<option value="fraction">Specify a fraction to keep</option>
-<option value="target">Specify a target # of reads</option>
-<option value="no" selected="True">No downsampling</option>
-</param>
-<when value="fraction">
-<param name="fraction" type="float" optional="False" value="0.5" min="0" max="1" label="Subsampling fraction" help="sets the fraction of templates/pairs to subsample." />
-<expand macro="seed_input" />
-</when>
-<when value='target'>
-<param name="target" type="integer" optional="False" value="" min="0"  label="Target # of reads" help="sets the target number of reads to subsample." />
-<expand macro="seed_input" />
-</when>
-<when value="no"/>
 </conditional>
 <conditional name="addref_cond">
 <param name="addref_select" type="select" label="Reference data">
 <help>Reference data as fasta(.gz). Required for SAM input without @SQ headers and useful/required for writing CRAM output (see help).</help>
 <option value="no" selected="True">No, see help (-output-fmt-option no_ref)</option>
 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
 </options>
 </param>
 </when>
 </conditional>
-<section name="adv_output" title="Output Options" expanded="false">
-<param name="header" type="select" argument="-h/-H" label="Header options">
-<option value="-h" selected="True">Include header in SAM output (-h)</option>
-<option value="-H">Return header only (-H)</option>
-<option value="">Exclude header</option>
-</param>
-<param name="outputpassing" type="boolean" argument="-U" truevalue="yes" falsevalue="no" checked="false" label="Output alignments not passing the filter" help="Write alignments that are not selected by the various filter options to an extra data set. When this option is used, all alignments (or all alignments intersecting the regions specified) are written to either the output data set or this extra output data set, but never both." />
-<param name="collapsecigar" type="boolean" argument="-B" truevalue="-B" falsevalue="" checked="false" label="Collapse backward CIGAR operation" help="Collapse the backward CIGAR operation." />
-</section>
 </inputs>
 <outputs>
 <!-- TODO do I need an action for dbkey? -->
 <data name="outputsam" format_source="input" from_work_dir="outfile" label="${tool.name} on ${on_string}: filtered alignments">
-<filter>outtype != 'count'</filter>
+<filter>mode['outtype'] == 'header' or mode['output_options']['reads_report_type'] != 'count'</filter>
-<!-- TODO is change_format deprecated? how can I modify the type for the different bam types? -->
 <change_format>
-<when input="outtype" value="sam" format="sam" />
+<when input="mode.output_options.output_format.oformat" value="sam" format="sam" />
-<when input="outtype" value="bam" format="bam" />
+<when input="mode.output_options.output_format.oformat" value="bam" format="bam" />
-<when input="outtype" value="cram" format="cram" />
+<when input="mode.output_options.output_format.oformat" value="cram" format="cram" />
 </change_format>
 </data>
 <data name="invoutputsam" format_source="input" from_work_dir="inv_outfile"  label="${tool.name} on ${on_string}: unfiltered alignments">
-<filter>adv_output['outputpassing'] == 'yes' and outtype != 'count'</filter>
+<filter>mode['outtype'] == 'selected_reads' and mode['output_options']['reads_report_type'] != 'count' and mode['output_options']['complementary_output']</filter>
 <change_format>
-<when input="outtype" value="sam" format="sam" />
+<when input="mode.output_options.output_format.oformat" value="sam" format="sam" />
-<when input="outtype" value="bam" format="bam" />
+<when input="mode.output_options.output_format.oformat" value="bam" format="bam" />
-<when input="outtype" value="cram" format="cram" />
+<when input="mode.output_options.output_format.oformat" value="cram" format="cram" />
 </change_format>
 </data>
 <data name="outputcnt" format="txt" from_work_dir="outfile" label="${tool.name} on ${on_string}: Counts">
-<filter>outtype == 'count'</filter>
+<filter>mode['outtype'] != 'header' and mode['output_options']['reads_report_type'] == 'count'</filter>
 </data>
 </outputs>
 <tests>
 <!-- sam to bam (copied from the sam_to_bam tool) -->
 <test>
 <param name="input" ftype="sam" value="sam_to_bam_in1.sam" />
-<param name="outtype" value="bam" />
+<output name="outputsam" ftype="bam" file="sam_to_bam_out1.bam" />
+</test>
+<test>
+<param name="input" ftype="sam" dbkey="equCab2" value="sam_to_bam_in1.sam" />
+<conditional name="addref_cond">
+<param name="addref_select" value="cached" />
+<param name="ref" value="equCab2chrM" />
+</conditional>
+<output name="outputsam" ftype="bam" file="sam_to_bam_out2.bam" />
+</test>
+<test>
+<param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
 <conditional name="addref_cond">
 <param name="addref_select" value="history" />
 <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" />
 </conditional>
-<output name="outputsam" ftype="bam" file="sam_to_bam_out1.bam" />
+<output name="outputsam" ftype="bam" file="sam_to_bam_out3.bam" />
 </test>
-<test>
+<!-- bam to cram + region filter (adapted from bam_to_cram tool)-->
-<param name="input" ftype="sam" dbkey="equCab2" value="sam_to_bam_in1.sam" />
+<test>
-<param name="outtype" value="bam" />
+<param name="input" value="test.bam" ftype="bam" />
+<conditional name="mode">
+<param name="outtype" value="selected_reads" />
+<section name="filter_config">
+<conditional name="cond_region">
+<param name="select_region" value="no"/>
+</conditional>
+</section>
+<conditional name="output_options">
+<conditional name="output_format">
+<param name="oformat" value="cram" />
+</conditional>
+</conditional>
+</conditional>
+<conditional name="addref_cond">
+<param name="addref_select" value="history" />
+<param name="ref" value="test.fa" />
+</conditional>
+<output name="outputsam" file="test.cram" ftype="cram" compare="sim_size" delta="250" />
+</test>
+<!-- count alignments -->
+<test>
+<param name="input" value="test.bam" ftype="bam" />
+<conditional name="mode">
+<param name="outtype" value="all_reads" />
+<conditional name="output_options">
+<param name="reads_report_type" value="count" />
+</conditional>
+</conditional>
+<output name="outputcnt" file="test_counts.tab" ftype="txt" />
+</test>
+<test>
+<param name="input" value="test.sam" ftype="sam" />
+<conditional name="mode">
+<param name="outtype" value="selected_reads" />
+<section name="filter_config">
+<conditional name="cond_region">
+<param name="select_region" value="no"/>
+</conditional>
+</section>
+<conditional name="output_options">
+<conditional name="output_format">
+<param name="oformat" value="cram" />
+</conditional>
+</conditional>
+</conditional>
+<conditional name="addref_cond">
+<param name="addref_select" value="history" />
+<param name="ref" value="test.fa" />
+</conditional>
+<output name="outputsam" file="test.cram" ftype="cram" compare="sim_size" delta="250" />
+</test>
+<test>
+<param name="input" value="test.bam" ftype="bam" />
+<conditional name="mode">
+<param name="outtype" value="selected_reads" />
+<section name="filter_config">
+<conditional name="cond_region">
+<param name="select_region" value="text"/>
+<param name="regions" value="CHROMOSOME_I" />
+</conditional>
+</section>
+<conditional name="output_options">
+<conditional name="output_format">
+<param name="oformat" value="cram" />
+</conditional>
+</conditional>
+</conditional>
+<conditional name="addref_cond">
+<param name="addref_select" value="history" />
+<param name="ref" value="test.fa" />
+</conditional>
+<output name="outputsam" file="test.cram" ftype="cram" compare="sim_size" delta="250" />
+</test>
+<!-- bam to sam + header options (adapted from bam_to_sam tool)-->
+<test>
+<param ftype="bam" name="input" value="bam_to_sam_in1.bam" />
+<conditional name="mode">
+<conditional name="output_options">
+<conditional name="output_format">
+<param name="oformat" value="sam" />
+<param name="with_header" value="true" />
+</conditional>
+</conditional>
+</conditional>
+<output file="bam_to_sam_out1.sam" ftype="sam" name="outputsam" />
+</test>
+<test>
+<param ftype="bam" name="input" value="bam_to_sam_in1.bam" />
+<conditional name="mode">
+<param name="outtype" value="header" />
+<conditional name="output_options">
+<conditional name="output_format">
+<param name="oformat" value="sam" />
+</conditional>
+</conditional>
+</conditional>
+<output file="bam_to_sam_out2.sam" ftype="sam" name="outputsam" />
+</test>
+<test>
+<param ftype="bam" name="input" value="bam_to_sam_in1.bam" />
+<conditional name="mode">
+<conditional name="output_options">
+<conditional name="output_format">
+<param name="oformat" value="sam" />
+<param name="with_header" value="false" />
+</conditional>
+</conditional>
+</conditional>
+<output file="bam_to_sam_out3.sam" ftype="sam" name="outputsam" />
+</test>
+<!-- cram to bam + region (adapted from cram_to_bam tool)-->
+<test>
+<param name="input" value="test.cram" ftype="cram" />
+<conditional name="addref_cond">
+<param name="addref_select" value="history" />
+<param name="ref" value="test.fa" />
+</conditional>
+<output name="outputsam" file="test.bam" ftype="bam" />
+</test>
+<test>
+<param name="input" value="test.cram" ftype="cram" />
+<conditional name="mode">
+<param name="outtype" value="selected_reads" />
+<section name="filter_config">
+<conditional name="cond_region">
+<param name="select_region" value="text"/>
+<param name="regions" value="CHROMOSOME_I" />
+</conditional>
+</section>
+<conditional name="output_options">
+<conditional name="output_format">
+<param name="oformat" value="bam" />
+</conditional>
+</conditional>
+</conditional>
+<conditional name="addref_cond">
+<param name="addref_select" value="history" />
+<param name="ref" value="test.fa" />
+</conditional>
+<output name="outputsam" file="test.bam" ftype="bam" />
+</test>
+<test>
+<param name="input" value="test.cram" ftype="cram" />
+<conditional name="mode">
+<param name="outtype" value="selected_reads" />
+<section name="filter_config">
+<conditional name="cond_region">
+<param name="select_region" value="bed" />
+<param name="bedfile" value="test.bed" ftype="bed" />
+</conditional>
+</section>
+<conditional name="output_options">
+<conditional name="output_format">
+<param name="oformat" value="bam" />
+</conditional>
+</conditional>
+</conditional>
+<conditional name="addref_cond">
+<param name="addref_select" value="history" />
+<param name="ref" value="test.fa" />
+</conditional>
+<output name="outputsam" file="test.bam" ftype="bam" />
+</test>
+<test>
+<param name="input" value="test2.cram" dbkey="equCab2" ftype="cram" />
+<conditional name="mode">
+<param name="outtype" value="selected_reads" />
+<section name="filter_config">
+<conditional name="cond_region">
+<param name="select_region" value="no"/>
+</conditional>
+</section>
+<conditional name="output_options">
+<conditional name="output_format">
+<param name="oformat" value="bam" />
+</conditional>
+</conditional>
+</conditional>
 <conditional name="addref_cond">
 <param name="addref_select" value="cached" />
 <param name="ref" value="equCab2chrM" />
 </conditional>
-<output name="outputsam" ftype="bam" file="sam_to_bam_out2.bam" />
+<output name="outputsam" file="sam_to_bam_out2.bam" ftype="bam" />
 </test>
-<test>
+<!-- sampling options-->
-<param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
+<test>
-<param name="outtype" value="bam" />
+<param name="input" value="test.sam" ftype="sam" />
-<conditional name="addref_cond">
+<conditional name="mode">
-<param name="addref_select" value="history" />
+<param name="outtype" value="selected_reads" />
-<param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" />
+<section name="subsample_config">
-</conditional>
+<conditional name="subsampling_mode">
-<output name="outputsam" ftype="bam" file="sam_to_bam_out3.bam" />
+<param name="select_subsample" value="target" />
-</test>
+<param name="target" value="2" />
-<!-- bam to cram + region filter (adapted from bam_to_cram tool)-->
+</conditional>
+</section>
+<conditional name="output_options">
+<conditional name="output_format">
+<param name="oformat" value="sam" />
+</conditional>
+</conditional>
+</conditional>
+<output name="outputsam" file="test_ds.sam" ftype="sam" compare="diff" lines_diff="6" />
+</test>
+<test>
+<param name="input" value="test.sam" ftype="sam" />
+<conditional name="mode">
+<param name="outtype" value="selected_reads" />
+<section name="subsample_config">
+<conditional name="subsampling_mode">
+<param name="select_subsample" value="target" />
+<param name="target" value="20" />
+</conditional>
+</section>
+<conditional name="output_options">
+<conditional name="output_format">
+<param name="oformat" value="sam" />
+</conditional>
+</conditional>
+</conditional>
+<output name="outputsam" file="test.sam" ftype="sam" />
+</test>
+<test>
+<param name="input" value="test.sam" ftype="sam" />
+<conditional name="mode">
+<param name="outtype" value="selected_reads" />
+<section name="subsample_config">
+<conditional name="subsampling_mode">
+<param name="select_subsample" value="target" />
+<param name="seed" value="7" />
+<param name="target" value="2" />
+</conditional>
+</section>
+<conditional name="output_options">
+<conditional name="output_format">
+<param name="oformat" value="sam" />
+</conditional>
+</conditional>
+</conditional>
+<output name="outputsam" file="test_ds.sam" ftype="sam" compare="diff" lines_diff="6" />
+</test>
 <test>
 <param name="input" value="test.bam" ftype="bam" />
-<param name="outtype" value="cram" />
+<conditional name="mode">
-<conditional name="addref_cond">
+<param name="outtype" value="selected_reads" />
-<param name="addref_select" value="history" />
+<section name="subsample_config">
-<param name="ref" value="test.fa" />
+<conditional name="subsampling_mode">
-</conditional>
+<param name="select_subsample" value="target" />
-<conditional name="cond_filter">
+<param name="seed" value="7" />
-<param name="select_filter" value="yes" />
+<param name="target" value="2" />
-<conditional name="cond_region">
+</conditional>
-<param name="select_region" value="no"/>
+</section>
-</conditional>
+<conditional name="output_options">
-</conditional>
+<conditional name="output_format">
-<output name="outputsam" file="test.cram" ftype="cram" compare="sim_size" delta="250" />
+<param name="oformat" value="bam" />
-</test>
+</conditional>
-<!-- count alignments -->
+</conditional>
-<test>
+</conditional>
+<output name="outputsam" file="test_ds.bam" ftype="bam" />
+</test>
+<test>
 <param name="input" value="test.bam" ftype="bam" />
-<param name="outtype" value="count" />
+<conditional name="mode">
-<output name="outputcnt" file="test_counts.tab" ftype="txt" />
+<param name="outtype" value="selected_reads" />
-</test>
+<section name="subsample_config">
-<test>
+<conditional name="subsampling_mode">
-<param name="input" value="test.sam" ftype="sam" />
+<param name="select_subsample" value="target" />
-<param name="outtype" value="cram" />
+<param name="seed" value="7" />
-<conditional name="addref_cond">
+<param name="target" value="20" />
-<param name="addref_select" value="history" />
+</conditional>
-<param name="ref" value="test.fa" />
+</section>
-</conditional>
+<conditional name="output_options">
-<conditional name="cond_filter">
+<conditional name="output_format">
-<param name="select_filter" value="yes" />
+<param name="oformat" value="bam" />
-<conditional name="cond_region">
+</conditional>
-<param name="select_region" value="no"/>
+</conditional>
 </conditional>
-</conditional>
+<output name="outputsam" file="test.bam" ftype="bam" />
-<output name="outputsam" file="test.cram" ftype="cram" compare="sim_size" delta="250" />
 </test>
 <test>
 <param name="input" value="test.bam" ftype="bam" />
-<param name="outtype" value="cram" />
+<conditional name="mode">
-<conditional name="addref_cond">
+<param name="outtype" value="selected_reads" />
-<param name="addref_select" value="history" />
+<section name="subsample_config">
-<param name="ref" value="test.fa" />
+<conditional name="subsampling_mode">
-</conditional>
+<param name="select_subsample" value="fraction" />
-<conditional name="cond_filter">
+<param name="seed" value="7" />
-<param name="select_filter" value="yes" />
+<param name="factor" value="5" />
-<conditional name="cond_region">
+</conditional>
-<param name="select_region" value="text"/>
+</section>
-<param name="regions" value="CHROMOSOME_I" />
+<conditional name="output_options">
-</conditional>
+<conditional name="output_format">
-</conditional>
+<param name="oformat" value="bam" />
-<output name="outputsam" file="test.cram" ftype="cram" compare="sim_size" delta="250" />
+</conditional>
-</test>
+</conditional>
-<!-- bam to sam + header options (adapted from bam_to_sam tool)-->
-<test>
-<param ftype="bam" name="input" value="bam_to_sam_in1.bam" />
-<param name="outtype" value="sam" />
-<param name="header" value="-h" />
-<output file="bam_to_sam_out1.sam" ftype="sam" name="outputsam" />
-</test>
-<test>
-<param ftype="bam" name="input" value="bam_to_sam_in1.bam" />
-<param name="outtype" value="sam" />
-<param name="header" value="-H" />
-<output file="bam_to_sam_out2.sam" ftype="sam" name="outputsam" />
-</test>
-<test>
-<param ftype="bam" name="input" value="bam_to_sam_in1.bam" />
-<param name="outtype" value="sam" />
-<param name="header" value="" />
-<output file="bam_to_sam_out3.sam" ftype="sam" name="outputsam" />
-</test>
-<!-- cram to bam + region (adapted from cram_to_bam tool)-->
-<test>
-<param name="input" value="test.cram" ftype="cram" />
-<param name="outtype" value="bam" />
-<conditional name="addref_cond">
-<param name="addref_select" value="history" />
-<param name="ref" value="test.fa" />
-</conditional>
-<output name="outputsam" file="test.bam" ftype="bam" />
-</test>
-<test>
-<param name="input" value="test.cram" ftype="cram" />
-<param name="outtype" value="bam" />
-<conditional name="addref_cond">
-<param name="addref_select" value="history" />
-<param name="ref" value="test.fa" />
-</conditional>
-<param name="target_region" value="region" />
-<param name="region_string" value="CHROMOSOME_I" />
-<output name="outputsam" file="test.bam" ftype="bam" />
-</test>
-<test>
-<param name="input" value="test.cram" ftype="cram" />
-<param name="outtype" value="bam" />
-<conditional name="addref_cond">
-<param name="addref_select" value="history" />
-<param name="ref" value="test.fa" />
-</conditional>
-<param name="target_region" value="regions_bed_file" />
-<param name="regions_bed_file" value="test.bed" ftype="bed" />
-<output name="outputsam" file="test.bam" ftype="bam" />
-</test>
-<test>
-<param name="input" value="test2.cram" dbkey="equCab2" ftype="cram" />
-<param name="outtype" value="bam" />
-<conditional name="addref_cond">
-<param name="addref_select" value="cached" />
-<param name="ref" value="equCab2chrM" />
-</conditional>
-<conditional name="cond_region">
-<param name="select_region" value="no"/>
-</conditional>
-<output name="outputsam" file="sam_to_bam_out2.bam" ftype="bam" />
-</test>
-<!-- sampling options-->
-<test>
-<param name="input" value="test.sam" ftype="sam" />
-<param name="outtype" value="sam" />
-<conditional name="cond_subsample">
-<param name="select_subsample" value="target" />
-<param name="target" value="2" />
-</conditional>
-<output name="outputsam" file="test_ds.sam" ftype="sam" compare="diff" lines_diff="6" />
-</test>
-<test>
-<param name="input" value="test.sam" ftype="sam" />
-<param name="outtype" value="sam" />
-<conditional name="cond_subsample">
-<param name="select_subsample" value="target" />
-<param name="seed" value="7" />
-<param name="target" value="2" />
-</conditional>
-<output name="outputsam" file="test_ds.sam" ftype="sam" compare="diff" lines_diff="6" />
-</test>
-<test>
-<param name="input" value="test.bam" ftype="bam" />
-<param name="outtype" value="bam" />
-<conditional name="cond_subsample">
-<param name="select_subsample" value="target" />
-<param name="seed" value="7" />
-<param name="target" value="2" />
 </conditional>
 <output name="outputsam" file="test_ds.bam" ftype="bam" />
 </test>
 <test>
 <param name="input" value="test.bam" ftype="bam" />
-<param name="outtype" value="bam" />
+<conditional name="mode">
-<conditional name="cond_subsample">
+<param name="outtype" value="selected_reads" />
-<param name="select_subsample" value="fraction" />
+<section name="subsample_config">
-<param name="seed" value="7" />
+<conditional name="subsampling_mode">
-<param name="fraction" value=".2" />
+<param name="select_subsample" value="fraction" />
+<param name="seed" value="7" />
+<param name="factor" value="1.25" />
+</conditional>
+</section>
+<conditional name="output_options">
+<param name="reads_report_type" value="dropped" />
+<conditional name="output_format">
+<param name="oformat" value="bam" />
+</conditional>
+</conditional>
 </conditional>
 <output name="outputsam" file="test_ds.bam" ftype="bam" />
 </test>
 </tests>
 <help>
 **What it does**
 Samtools view can:
-1. filter alignments according to various criteria
+1. convert between alignment formats (SAM, BAM, CRAM)
-2. convert between alignment formats (SAM, BAM, CRAM)
+2. filter and subsample alignments according to user-specified criteria
+3. count the reads in the input dataset or those retained after filtering
-With no options or regions specified, prints all alignments in the specified input alignment file (in SAM, BAM, or CRAM format) to standard output in SAM format (with no header).
+and subsampling
+4. obtain just the header of the input in any supported format
+In addition, the tool has (limited) options to modify read records during conversion and/or filtering by:
+- stripping them of user-specified tags
+- collapsing backward CIGAR operations if they are specified in their CIGAR
+fields
+With default settings, the tool generates a BAM dataset with the header and
+reads found in the input dataset (which can be in SAM, BAM, or CRAM format).
 **Alignment format conversion**
+By changing the *Output format* it is possible to convert an input dataset to
+another format.
 Inputs of type SAM, BAM, and CRAM are accepted and can be converted to each of these formats (alternatively alignment counts can be computed) by selecting the appropriate "Output type".
 .. class:: infomark
-samtools view allows to specify a reference sequence. This is required for SAM input with missing @SQ headers (which include sequence names, length, md5, etc) and useful (and sometimes necessary) for CRAM input and output. In the following the use of reference sequence in the CRAM format is detailed.
+The tool allows you to specify a reference sequence. This is required for SAM input with missing @SQ headers (which include sequence names, length, md5, etc) and useful (and sometimes necessary) for CRAM input and output. In the following the use of the reference sequence in the CRAM format is detailed.
-CRAM is (intended as a primarily) a reference-based compressed format, i.e. only differences between the stored sequences and the reference are stored. As a consequence the reference that was used to generate the alignemnts is always needed in order to interpret the alignments (a checksum stored in the CRAM file is used to verify that the only the correct sequence can be used), i.e. the CRAM file on its own is not useful per default. This allows for a more space efficient storage compared to BAM.
+CRAM is (primarily) a reference-based compressed format, i.e. only sequence differences between aligned reads and the reference are stored. As a consequence, the reference that was used during read mapping is needed in order to interpret the alignment records (a checksum stored in the CRAM file is used to verify that only the correct reference sequence can be used). This allows for more space-efficient storage than with BAM format, but such a CRAM file is not usable without its reference.
-But it is also possible to use CRAM without a reference with the disadvantage that the reference is stored explicitely (as in SAM and BAM).
+It is also possible, however, to use CRAM without a reference with the disadvantage that the reference sequence gets stored then explicitely (as in SAM and BAM).
 The Galaxy tool **currently generates only CRAM without reference sequence**.
 For reference based CRAM input the correct refernce sequence needs to be specified.
 **Filtering alignments**
-samtools view allows to filter alignements based on various criteria, i.e. the output will contain only alignemnts matching all criteria (an additional output containing the remaining alignments can be created additionally, see "Output alignments not passing the filter" in "output options"): e.g. by regions (see below), alignment quality (see below), and tags or flags set in the alignments.
+If you ask for *A filtered/subsampled selection of reads*, the tool will allow
+you to specify filter conditions and/or to choose a subsampling strategy, and
+the output will contain one of the following depending on your choice under
+*What would you like to have reported?*:
+- All reads retained after filtering and subsampling
+- Reads dropped during filtering and subsampling
+If instead you want to *split* the input reads based on your criteria and
+obtain *two* datasets, one with the retained and one with the dropped reads, check
+the *Produce extra dataset with dropped/retained reads?* option.
 **Filtering by regions**
 You may specify one or more space-separated region specifications after the input filename to restrict output to only those alignments which overlap the specified region(s). Use of region specifications requires a coordinate-sorted and indexed input file (in BAM or CRAM format).
 Regions can be specified as: RNAME[:STARTPOS[-ENDPOS]] and all position coordinates are 1-based.
-Important note: when multiple regions are given, some alignments may be output multiple times if they overlap more than one of the specified regions.
+.. class:: Warning mark
+When multiple regions are given, some alignments may be output multiple times if they overlap more than one of the specified regions.
 Examples of region specifications:
-- chr1 Output all alignments mapped to the reference sequence named 'chr1' (i.e. @SQ SN:chr1).
+``chr1``
-- chr2:1000000 The region on chr2 beginning at base position 1,000,000 and ending at the end of the chromosome.
+Output all alignments mapped to the reference sequence named 'chr1' (i.e. @SQ SN:chr1).
-- chr3:1000-2000 The 1001bp region on chr3 beginning at base position 1,000 and ending at base position 2,000 (including both end positions).
-- '*' Output the unmapped reads at the end of the file. (This does not include any unmapped reads placed on a reference sequence alongside their mapped mates.)
+``chr2:1000000``
-- . Output all alignments. (Mostly unnecessary as not specifying a region at all has the same effect.)
+The region on chr2 beginning at base position 1,000,000 and ending at the end of the chromosome.
+``chr3:1000-2000``
+The 1001bp region on chr3 beginning at base position 1,000 and ending at base position 2,000 (including both end positions).
+``*``
+Output the unmapped reads at the end of the file. (This does not include any unmapped reads placed on a reference sequence alongside their mapped mates.)
+``.``
+Output all alignments. (Mostly unnecessary as not specifying a region at all has the same effect.)
 **Filtering by quality**
-This filters based on the MAPQ column of the SAM format which gives an estimate about the correct placement of the alignemnt. Note that aligners do not follow a consistent definition.
+This filters based on the MAPQ column of the SAM format which gives an estimate about the correct placement of the alignment. Note that aligners do not follow a consistent definition.
-The -x, -B, and -s options modify the data which is contained in each alignment.
 </help>
 <expand macro="citations"/>
 </tool>

Mercurial > repos > iuc > samtools_view

comparison samtools_view.xml @ 7:b01db2684fa5 draft