Mercurial > repos > devteam > bamtools_filter
changeset 6:82658c080fd0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 36169ce65193faaace8e8b999f83adf0c3d5aeba
| author | iuc |
|---|---|
| date | Tue, 05 Jun 2018 15:29:04 -0400 |
| parents | bd735cae4ce6 |
| children | 4fe8a75334c8 |
| files | bamtools-filter.xml macros.xml |
| diffstat | 2 files changed, 29 insertions(+), 13 deletions(-) [+] |
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--- a/bamtools-filter.xml Thu May 25 11:49:34 2017 -0400 +++ b/bamtools-filter.xml Tue Jun 05 15:29:04 2018 -0400 @@ -1,9 +1,10 @@ <tool id="bamFilter" name="Filter" version="2.4.1"> <description>BAM datasets on a variety of attributes</description> - <requirements> - <requirement type="package" version="2.4.0">bamtools</requirement> - </requirements> - <command> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"> <![CDATA[ cp '$script_file' '$out_file2' && ln -s '${input_bam}' localbam.bam && @@ -26,7 +27,7 @@ $(config[ 'filters' ].append( $filter )) #end for #if str( $rule_configuration.rules_selector ) == "true": - #set $config[ 'rule' ] = $rule_configuration.rules + #set $config[ 'rule' ] = str( $rule_configuration.rules ) #end if #end if $json.dumps( $config, indent=4 ) @@ -70,7 +71,7 @@ <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""> + <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> @@ -110,7 +111,7 @@ <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""> + <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> @@ -159,9 +160,9 @@ </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""> + <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> + <valid initial="string.letters,string.digits"><add value=">"/><add value="<"/><add value=":!=+-"/></valid> </sanitizer> </param> </when> @@ -188,11 +189,12 @@ <test> <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/> <param name="bam_property_selector" value="mapQuality"/> - <param name="bam_property_value" value=">20"/> + <param name="bam_property_value" value=">20"/> <output name="out_file1" ftype="bam" file="bamtools-test1.bam" /> </test> </tests> <help> +<![CDATA[ **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). @@ -250,7 +252,7 @@ For example, suppose get all reads that (**1**) do NOT map to mitochondria and either (**2**) have mapping quality over 20, or (**3**) are in properly mapped pairs. The logical rule to enable such filtering will look like this:: - !(1) & (2 | 3) + !(1) & (2 | 3) Here, numbers 1, 2, and 3 represent conditions. The following screenshot illustrates how to do this in Galaxy: @@ -290,8 +292,7 @@ .. class:: infomark Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki - - +]]> </help> <citations> <citation type="doi">10.1093/bioinformatics/btr174</citation>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Jun 05 15:29:04 2018 -0400 @@ -0,0 +1,15 @@ +<?xml version="1.0"?> +<macros> + <token name="@VERSION@">2.4.0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">bamtools</requirement> + <requirement type="package" version="1.4.1">samtools</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btr174</citation> + </citations> + </xml> +</macros> \ No newline at end of file