Mercurial > repos > devteam > samtools_bedcov
changeset 4:46c6639921f1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
| author | iuc |
|---|---|
| date | Tue, 28 Sep 2021 16:11:43 +0000 |
| parents | 9149ad20699a |
| children | 6856f8a01905 |
| files | macros.xml samtools_bedcov.xml test-data/samtools_bedcov_out7.tab test-data/samtools_depth_out5.tab test-data/samtools_depth_out6.tab |
| diffstat | 5 files changed, 128 insertions(+), 23 deletions(-) [+] |
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--- a/macros.xml Mon Jul 29 08:47:23 2019 -0400 +++ b/macros.xml Tue Sep 28 16:11:43 2021 +0000 @@ -5,10 +5,16 @@ <yield/> </requirements> </xml> - <token name="@TOOL_VERSION@">1.9</token> - <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token> + <token name="@TOOL_VERSION@">1.13</token> + <token name="@PROFILE@">20.05</token> + <token name="@FLAGS@"><![CDATA[ + #set $flags = 0 + #if $filter + #set $flags = sum(map(int, str($filter).split(','))) + #end if + ]]></token> <token name="@PREPARE_IDX@"><![CDATA[ - ##prepare input and indices + ##prepare input and indices ln -s '$input' infile && #if $input.is_of_type('bam'): #if str( $input.metadata.bam_index ) != "None": @@ -25,7 +31,7 @@ #end if ]]></token> <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[ - ##prepare input and indices + ##prepare input and indices #for $i, $bam in enumerate( $input_bams ): ln -s '$bam' '${i}' && #if $bam.is_of_type('bam'): @@ -63,6 +69,51 @@ #set reffai=None #end if ]]></token> + + <xml name="optional_reference"> + <conditional name="addref_cond"> + <param name="addref_select" type="select" label="Use a reference sequence"> + <help>@HELP@</help> + <option value="no">No</option> + <option value="history">Use a genome/index from the history</option> + <option value="cached">Use a built-in genome</option> + </param> + <when value="no"/> + <when value="history"> + <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/> + </when> + <when value="cached"> + <param name="ref" argument="@ARGUMENT@" type="select" label="Reference"> + <options from_data_table="fasta_indexes"> + <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/> + </options> + <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset"/> + </param> + </when> + </conditional> + </xml> + <xml name="mandatory_reference" token_help="" token_argument=""> + <conditional name="addref_cond"> + <param name="addref_select" type="select" label="Use a reference sequence"> + <help>@HELP@</help> + <option value="history">Use a genome/index from the history</option> + <option value="cached">Use a built-in genome</option> + </param> + <when value="history"> + <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/> + </when> + <when value="cached"> + <param name="ref" argument="@ARGUMENT@" type="select" label="Reference"> + <options from_data_table="fasta_indexes"> + <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/> + <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" /> + </options> + </param> + </when> + </conditional> + </xml> + + <token name="@ADDTHREADS@"><![CDATA[ ##compute the number of ADDITIONAL threads to be used by samtools (-@) addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) && @@ -70,28 +121,28 @@ <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=\${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." /> + <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 reverse strand</option> - <option value="32">mate reverse strand</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 or 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">supplementary alignment</option> + <xml name="flag_options" token_s1="false" token_s2="false" token_s4="false" token_s8="false" token_s16="false" token_s32="false" token_s64="false" token_s128="false" token_s256="false" token_s512="false" token_s1024="false" token_s2048="false"> + <option value="1" selected="@S1@">Read is paired</option> + <option value="2" selected="@S2@">Read is mapped in a proper pair</option> + <option value="4" selected="@S4@">Read is unmapped</option> + <option value="8" selected="@S8@">Mate is unmapped</option> + <option value="16" selected="@S16@">Read is mapped to the reverse strand of the reference</option> + <option value="32" selected="@S32@">Mate is mapped to the reverse strand of the reference</option> + <option value="64" selected="@S64@">Read is the first in a pair</option> + <option value="128" selected="@S128@">Read is the second in a pair</option> + <option value="256" selected="@S256@">Alignment of the read is not primary</option> + <option value="512" selected="@S512@">Read fails platform/vendor quality checks</option> + <option value="1024" selected="@S1024@">Read is a PCR or optical duplicate</option> + <option value="2048" selected="@S2048@">Alignment is supplementary</option> </xml> - <!-- region specification macros and tokens for tools that allow the specification + <!-- 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':
--- a/samtools_bedcov.xml Mon Jul 29 08:47:23 2019 -0400 +++ b/samtools_bedcov.xml Tue Sep 28 16:11:43 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="samtools_bedcov" name="BedCov" version="2.0.2"> +<tool id="samtools_bedcov" name="Samtools bedcov" version="2.0.3" profile="@PROFILE@"> <description>calculate read depth for a set of genomic intervals</description> <macros> <import>macros.xml</import> @@ -14,44 +14,89 @@ -Q $mapq #end if $countdel + #set $filter = $additional_options.required_flags + @FLAGS@ + -g $flags + #set $filter = $additional_options.skipped_flags + @FLAGS@ + -G $flags + #if $depth_thresh: + -d $depth_thresh + #end if '${input_bed}' - #for $i in range(len( $input_bams )): + #for $i in range(len($input_bams)): '${i}' #end for > '${output}' ]]></command> <inputs> - <param name="input_bed" type="data" format="bed" label="Genemic intervals (in BED format)" /> + <param name="input_bed" type="data" format="bed" label="Genetic intervals (in BED format)" /> <param name="input_bams" type="data" format="bam" multiple="true" label="BAM file(s)" /> <param name="mapq" argument="-Q" type="integer" value="" optional="true" label="Minimum MAPQ" help="Only count reads with mapping quality greater than this value" /> <param name="countdel" argument="-j" type="boolean" checked="false" truevalue="-j" falsevalue="" label="Exclude deletions and ref skips" help=" Do not include deletions (D) and ref skips (N) in bedcov computation" /> + <param name="depth_thresh" argument="-d" type="integer" value="" min="0" optional="true" label="Depth threshold" help="Number of reference bases with coverage above and including this value will be displayed in a separate column." /> + + <section name="additional_options" title="Additional Filter Options"> + <param name="required_flags" argument="-g" type="select" multiple="True" label="Require that these flags are set."> + <expand macro="flag_options" /> + </param> + + <param name="skipped_flags" argument="-G" type="select" multiple="True" label="Exclude reads with any of the following flags set (the default set is UNMAP,SECONDARY,QCFAIL,DUP or 0x704)."> + <expand macro="flag_options" s4="true" s256="true" s512="true" s1024="true"/> + </param> + </section> </inputs> <outputs> <data name="output" format="tabular" label="${tool.name} on ${on_string}" /> </outputs> <tests> + <!-- 1) --> <test> <param name="input_bed" value="eboVir3.1.bed" ftype="bed" /> <param name="input_bams" value="eboVir3.bam" ftype="bam" /> <output name="output" file="samtools_bedcov_out1.tab" /> </test> + <!-- 2) --> <test> <param name="input_bed" value="eboVir3.1.bed" ftype="bed" /> <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" /> <output name="output" file="samtools_bedcov_out2.tab" /> </test> + <!-- 3) --> <test> <param name="input_bed" value="eboVir3.1.bed" ftype="bed" /> <param name="input_bams" value="eboVir3.bam" ftype="bam" /> <param name="mapq" value="40"/> <output name="output" file="samtools_bedcov_out1.tab" /> </test> + <!-- 4) --> <test> <param name="input_bed" value="eboVir3.1.bed" ftype="bed" /> <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" /> <param name="countdel" value="-j" /> <output name="output" file="samtools_bedcov_out2.tab" /> </test> + <!-- 5) Testing argument -g --> + <test> + <param name="input_bed" value="eboVir3.1.bed" ftype="bed" /> + <param name="input_bams" value="eboVir3.bam" ftype="bam" /> + <param name="required_flags" value="2,16,64" /> + <output name="output" file="samtools_depth_out5.tab" /> + </test> + <!-- 6) Testing argument -G --> + <test> + <param name="input_bed" value="eboVir3.1.bed" ftype="bed" /> + <param name="input_bams" value="eboVir3.bam" ftype="bam" /> + <param name="skipped_flags" value="2,16,64" /> + <output name="output" file="samtools_depth_out6.tab" /> + </test> + <!-- 7) Testing depth threshold -d --> + <test> + <param name="input_bed" value="eboVir3.1.bed" ftype="bed" /> + <param name="input_bams" value="eboVir3.bam" ftype="bam" /> + <param name="depth_thresh" value="10" /> + <output name="output" file="samtools_bedcov_out7.tab" /> + </test> </tests> <help> **What it does**
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_bedcov_out7.tab Tue Sep 28 16:11:43 2021 +0000 @@ -0,0 +1,3 @@ +eboVir3 500 1500 7919 229 +eboVir3 1500 2000 3009 9 +eboVir3 1500 3000 9986 122