Mercurial > repos > devteam > bamtools_filter
diff bamtools-filter.xml @ 4:3213c223678c draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_filter commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
| author | devteam |
|---|---|
| date | Wed, 18 Jan 2017 11:47:29 -0500 |
| parents | 29ba2103739c |
| children | bd735cae4ce6 |
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--- a/bamtools-filter.xml Fri Jan 13 11:02:24 2017 -0500 +++ b/bamtools-filter.xml Wed Jan 18 11:47:29 2017 -0500 @@ -1,215 +1,212 @@ -<tool id="bamFilter" name="Filter" version="0.0.2"> - <description>BAM datasets on a variety of attributes</description> - <requirements> - <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement> - </requirements> - <command> - cat $script_file > $out_file2; - - #for $bam_count, $input_bam in enumerate( $input_bams ): - ln -s "${input_bam}" "localbam_${bam_count}.bam" && - ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" && - #end for - - bamtools - filter - -script $script_file - - #for $bam_count, $input_bam in enumerate( $input_bams ): - -in "localbam_${bam_count}.bam" - #end for - -out $out_file1 - </command> - <inputs> - <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/> - <repeat name="conditions" title="Condition" min="1"> - <repeat name="filters" title="Filter" min="1"> - <conditional name="bam_property"> - <param name="bam_property_selector" type="select" label="Select BAM property to filter on"> - <option value="alignmentFlag"/> - <option value="cigar"/> - <option value="insertSize"/> - <option value="isDuplicate"/> - <option value="isFailedQC"/> - <option value="isFirstMate"/> - <option value="isMapped"/> - <option value="isMateMapped"/> - <option value="isMateReverseStrand"/> - <option value="isPaired"/> - <option value="isPrimaryAlignment"/> - <option value="isProperPair"/> - <option value="isReverseStrand"/> - <option value="isSecondMate"/> - <option selected="True" value="mapQuality"/> - <option value="matePosition"/> - <option value="mateReference"/> - <option value="name"/> - <option value="position"/> - <option value="queryBases"/> - <option value="reference"/> - <option value="tag"/> - </param> - <!-- would be fanstastic to have AND and OR constructs in when statements --> - <when value="alignmentFlag"> - <param name="bam_property_value" type="integer" value="3" label="Filter on this alignment flag" help="Default (3) is for a paired read mapped in a proper pair"/> - </when> - <when value="cigar"> - <param name="bam_property_value" type="text" value="101M" label="Filter on this CIGAR string" help="Default (101M) is for 101 continuously matched bases"/> - </when> - <when value="insertSize"> - <param name="bam_property_value" type="text" value=">=250" label="Filter on insert size" help="You can use >, <, =, and ! (not) in your expression. E.g., to select pairs with insert size above 250 nt use ">=250""> - <sanitizer invalid_char=""> - <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/><add value="-"/></valid> - </sanitizer> - </param> - </when> - <when value="isDuplicate"> - <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads makwed as duplicates" help="Checked = Read IS Duplicate, Empty = Read is NOT Duplicate" /> - </when> - <when value="isFailedQC"> - <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads failing QC" help="Checked = Failed QC, Empty = Passed QC"/> - </when> - <when value="isFirstMate"> - <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select first mate in a read pair" help="Checked = is first mate, Empty = is NOT first mate"/> - </when> - <when value="isMapped"> - <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Selected mapped reads" help="Checked = Mapped, Empty = NOT mapped"/> - </when> - <when value="isMateMapped"> - <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads with mapped mate" help="Checked = Mate IS mapped Empty = Mate is NOT mapped"/> - </when> - <when value="isMateReverseStrand"> - <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads with mate on the reverse strand" help="Checked = Mate IS on reverse strand, Empty = Mate is NOT on the reverse strand"/> - </when> - <when value="isPaired"> - <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select paired reads" help="Checked = Read IS paired, Empty = Read is NOT paired"/> - </when> - <when value="isPrimaryAlignment"> - <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select BAM records for primary alignments" help="Checked = Alignment IS primary, Empty = Alignment is NOT primary"/> - </when> - <when value="isProperPair"> - <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select properly paired reads" help="Checked = Read IS in proper pair, Empty = Read is NOT in the proper pair"/> - </when> - <when value="isReverseStrand"> - <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads in the reverse strand only" help="Checked = Read IS on the reverse strand, Empty = Read is NOT on the reverse strand"/> - </when> - <when value="isSecondMate"> - <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select second mate in a read pair" help="Checked = Read IS second mate, Empty = Read is NOT second mate"/> - </when> - <when value="mapQuality"> - <param name="bam_property_value" type="text" value="20" label="Filter on read mapping quality (phred scale)" help="You can use >, <, =, and ! (not) in your expression. E.g., to select reads with mapping quality of at least 30 use ">=30""> - <sanitizer invalid_char=""> - <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> - </sanitizer> - </param> - </when> - <when value="matePosition"> - <param name="bam_property_value" type="text" value="1000000" label="Filter on the position of the mate" help="You can use >, <, =, and ! (not) in your expression. E.g., to select reads with mate (second end) mapping after position 1,000,000 use ">1000000""> - <sanitizer invalid_char=""> - <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> - </sanitizer> - </param> - </when> - <when value="mateReference"> - <param name="bam_property_value" type="text" value="chr22" label="Filter on reference name for the mate" help="You can use = and ! (not) in your expression. E.g., to select reads with mates mapping to chrM use "chr22""> - <sanitizer invalid_char=""> - <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> - </sanitizer> - </param> - </when> - <when value="name"> - <param name="bam_property_value" type="text" label="Filter on read name" help="You can use = and ! (not) in your expression."> - <sanitizer invalid_char=""> - <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> - </sanitizer> - </param> - </when> - <when value="position"> - <param name="bam_property_value" type="text" value="500000" label="Filter on the position of the read" help="You can use >, <, =, and ! (not) in your expression. E.g., to select reads mapping after position 5,000 use ">5000""> - <sanitizer invalid_char=""> - <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> - </sanitizer> - </param> - </when> - <when value="queryBases"> - <param name="bam_property_value" type="text" value="ttagggttagg" label="Filter on a sequence motif" help="You can use ! (not) in your expression"> - <sanitizer invalid_char=""> - <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> - </sanitizer> - </param> - </when> - <when value="reference"> - <param name="bam_property_value" type="text" value="chr22" label="Filter on the reference name for the read" help="You can use ! (not) in your expression"> - <sanitizer invalid_char=""> - <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> - </sanitizer> - </param> - </when> - <when value="tag"> - <param name="bam_property_value" type="text" value="NM:>1" label="Filter on a particular tag" help="You can use >, <, =, and ! (not). - Tag name and its value must be separated by ":". E.g., to obtain reads with at least one mismatch use "NM:>1""> - <sanitizer invalid_char=""> - <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value=":!="/></valid> - </sanitizer> - </param> - </when> +<tool id="bamFilter" name="Filter" version="2.4.0"> + <description>BAM datasets on a variety of attributes</description> + <requirements> + <requirement type="package" version="2.4.0">bamtools</requirement> + </requirements> + <command> + <![CDATA[ + cat $script_file > $out_file2; + #for $bam_count, $input_bam in enumerate( $input_bams ): + ln -s "${input_bam}" "localbam_${bam_count}.bam" && + ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" && + #end for + bamtools + filter + -script $script_file + #for $bam_count, $input_bam in enumerate( $input_bams ): + -in "localbam_${bam_count}.bam" + #end for + -out $out_file1 + ]]> + </command> + <configfiles> + <configfile name="script_file"> + ##Sets up a json configfile for bamtools filter + ##If there is more than one condition prints brackets and "filters:" + #if len( $conditions ) > 1 + { + "filters": + [ + #end if + #for $i, $c in enumerate( $conditions, start=1 ) + { "id": "$i", + #for $j, $s in enumerate( $c.filters, start=1 ) + ##The if below takes care of the comma at the end of last condition within group + #if $j != len( $c.filters) + "${s.bam_property.bam_property_selector}":"${s.bam_property.bam_property_value}", + #else + "${s.bam_property.bam_property_selector}":"${s.bam_property.bam_property_value}" + #end if + #end for + ##The if below takes care of the comma at the end of last condition within group + #if $i != len( $conditions ) + }, + #else + } + #end if + #end for + #if len( $conditions ) > 1 + #if str( $rule_configuration.rules_selector ) == "True": + ], + "rule" : "${rule_configuration.rules}" + #else + ] + #end if + } + #end if + </configfile> + </configfiles> + <inputs> + <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/> + <repeat name="conditions" title="Condition" min="1"> + <repeat name="filters" title="Filter" min="1"> + <conditional name="bam_property"> + <param name="bam_property_selector" type="select" label="Select BAM property to filter on"> + <option value="alignmentFlag"/> + <option value="cigar"/> + <option value="insertSize"/> + <option value="isDuplicate"/> + <option value="isFailedQC"/> + <option value="isFirstMate"/> + <option value="isMapped"/> + <option value="isMateMapped"/> + <option value="isMateReverseStrand"/> + <option value="isPaired"/> + <option value="isPrimaryAlignment"/> + <option value="isProperPair"/> + <option value="isReverseStrand"/> + <option value="isSecondMate"/> + <option selected="True" value="mapQuality"/> + <option value="matePosition"/> + <option value="mateReference"/> + <option value="name"/> + <option value="position"/> + <option value="queryBases"/> + <option value="reference"/> + <option value="tag"/> + </param> + <!-- would be fanstastic to have AND and OR constructs in when statements --> + <when value="alignmentFlag"> + <param name="bam_property_value" type="integer" value="3" label="Filter on this alignment flag" help="Default (3) is for a paired read mapped in a proper pair"/> + </when> + <when value="cigar"> + <param name="bam_property_value" type="text" value="101M" label="Filter on this CIGAR string" help="Default (101M) is for 101 continuously matched bases"/> + </when> + <when value="insertSize"> + <param name="bam_property_value" type="text" value=">=250" label="Filter on insert size" help="You can use >, <, =, and ! (not) in your expression. E.g., to select pairs with insert size above 250 nt use ">=250""> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/><add value="-"/></valid> + </sanitizer> + </param> + </when> + <when value="isDuplicate"> + <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads makwed as duplicates" help="Checked = Read IS Duplicate, Empty = Read is NOT Duplicate" /> + </when> + <when value="isFailedQC"> + <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads failing QC" help="Checked = Failed QC, Empty = Passed QC"/> + </when> + <when value="isFirstMate"> + <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select first mate in a read pair" help="Checked = is first mate, Empty = is NOT first mate"/> + </when> + <when value="isMapped"> + <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Selected mapped reads" help="Checked = Mapped, Empty = NOT mapped"/> + </when> + <when value="isMateMapped"> + <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads with mapped mate" help="Checked = Mate IS mapped Empty = Mate is NOT mapped"/> + </when> + <when value="isMateReverseStrand"> + <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads with mate on the reverse strand" help="Checked = Mate IS on reverse strand, Empty = Mate is NOT on the reverse strand"/> + </when> + <when value="isPaired"> + <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select paired reads" help="Checked = Read IS paired, Empty = Read is NOT paired"/> + </when> + <when value="isPrimaryAlignment"> + <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select BAM records for primary alignments" help="Checked = Alignment IS primary, Empty = Alignment is NOT primary"/> + </when> + <when value="isProperPair"> + <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select properly paired reads" help="Checked = Read IS in proper pair, Empty = Read is NOT in the proper pair"/> + </when> + <when value="isReverseStrand"> + <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads in the reverse strand only" help="Checked = Read IS on the reverse strand, Empty = Read is NOT on the reverse strand"/> + </when> + <when value="isSecondMate"> + <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select second mate in a read pair" help="Checked = Read IS second mate, Empty = Read is NOT second mate"/> + </when> + <when value="mapQuality"> + <param name="bam_property_value" type="text" value="20" label="Filter on read mapping quality (phred scale)" help="You can use >, <, =, and ! (not) in your expression. E.g., to select reads with mapping quality of at least 30 use ">=30""> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> + </sanitizer> + </param> + </when> + <when value="matePosition"> + <param name="bam_property_value" type="text" value="1000000" label="Filter on the position of the mate" help="You can use >, <, =, and ! (not) in your expression. E.g., to select reads with mate (second end) mapping after position 1,000,000 use ">1000000""> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> + </sanitizer> + </param> + </when> + <when value="mateReference"> + <param name="bam_property_value" type="text" value="chr22" label="Filter on reference name for the mate" help="You can use = and ! (not) in your expression. E.g., to select reads with mates mapping to chrM use "chr22""> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> + </sanitizer> + </param> + </when> + <when value="name"> + <param name="bam_property_value" type="text" label="Filter on read name" help="You can use = and ! (not) in your expression."> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> + </sanitizer> + </param> + </when> + <when value="position"> + <param name="bam_property_value" type="text" value="500000" label="Filter on the position of the read" help="You can use >, <, =, and ! (not) in your expression. E.g., to select reads mapping after position 5,000 use ">5000""> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> + </sanitizer> + </param> + </when> + <when value="queryBases"> + <param name="bam_property_value" type="text" value="ttagggttagg" label="Filter on a sequence motif" help="You can use ! (not) in your expression"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> + </sanitizer> + </param> + </when> + <when value="reference"> + <param name="bam_property_value" type="text" value="chr22" label="Filter on the reference name for the read" help="You can use ! (not) in your expression"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value="!="/></valid> + </sanitizer> + </param> + </when> + <when value="tag"> + <param name="bam_property_value" type="text" value="NM:>1" label="Filter on a particular tag" help="You can use >, <, =, and ! (not). Tag name and its value must be separated by ":". E.g., to obtain reads with at least one mismatch use "NM:>1""> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value=":!="/></valid> + </sanitizer> + </param> + </when> + </conditional> + </repeat> + </repeat> + <conditional name="rule_configuration"> + <param name="rules_selector" type="boolean" truevalue="true" falsevalue="false" label="Would you like to set rules?" help="Allows complex logical constructs. See Example 4 below." /> + <when value="false"/> + <when value="true"> + <param name="rules" type="text" label="Enter rules here" help="This option can only be used with at least two conditions. Read help below (Example 4) to understand how it works." > + <sanitizer invalid_char=""> + <valid initial="string.printable"/> + </sanitizer> + </param> + </when> </conditional> - </repeat> - </repeat> - <conditional name="rule_configuration"> - <param name="rules_selector" type="boolean" truevalue="true" falsevalue="false" label="Would you like to set rules?" help="Allows complex logical constructs. See Example 4 below." /> - <when value="true"> - <param name="rules" type="text" label="Enter rules here" help="This option can only be used with at least two conditions. Read help below (Example 4) to understand how it works." > - <sanitizer invalid_char=""> - <valid initial="string.printable"/> - </sanitizer> - </param> - </when> - </conditional> - </inputs> - - <configfiles> - <configfile name="script_file"> - ##Sets up a json configfile for bamtools filter - ##If there is more than one condition prints brackets and "filters:" - #if len( $conditions ) > 1 - { - "filters": - [ - #end if - #for $i, $c in enumerate( $conditions, start=1 ) - { "id": "$i", - #for $j, $s in enumerate( $c.filters, start=1 ) - ##The if below takes care of the comma at the end of last condition within group - #if $j != len( $c.filters) - "${s.bam_property.bam_property_selector}":"${s.bam_property.bam_property_value}", - #else - "${s.bam_property.bam_property_selector}":"${s.bam_property.bam_property_value}" - #end if - #end for - ##The if below takes care of the comma at the end of last condition within group - #if $i != len( $conditions ) - }, - #else - } - #end if - #end for - #if len( $conditions ) > 1 - #if str( $rule_configuration.rules_selector ) == "True": - ], - "rule" : "${rule_configuration.rules}" - #else - ] - #end if - } - #end if - </configfile> - </configfiles> - - <outputs> - <data format="txt" name="out_file2" /> - <data format="bam" name="out_file1" /> - </outputs> + </inputs> + <outputs> + <data format="txt" name="out_file2" /> + <data format="bam" name="out_file1" /> + </outputs> <tests> <test> <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/> @@ -218,7 +215,7 @@ <output name="out_file1" file="bamtools-test1.bam" ftype="bam"/> </test> </tests> -<help> + <help> **What is does** BAMTools filter is a very powerful utility to perform complex filtering of BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools). @@ -318,8 +315,8 @@ Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki -</help> - <citations> - <citation type="doi">10.1093/bioinformatics/btr174</citation> - </citations> + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btr174</citation> + </citations> </tool>