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BAMqc.xml |
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| diff -r 5bfcc6c131ed -r bee9673b8f46 BAMqc.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BAMqc.xml Wed Mar 30 12:14:36 2016 -0400 |
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| @@ -0,0 +1,109 @@ +<tool id="cshl_BAMqc" name="ezBAMQC" version="0.6.7" > + + <description> + performs QC on BAM files for gene abundances and sample correlation + </description> + + <requirements> + <requirement type="package">BAMqc</requirement> + <requirement type="package">samtools</requirement> + <requirement type="package">R</requirement> + </requirements> + + <command interpreter="sh"> + + BAMqc.sh + + -r '${refdb}' + + -f '${attrID}' + + -R '${rRNAdb}' + + -s '$stranded' + + -o "$output" + + #set $core = len($files) + + -p $core + + #if str($cond_adv_options.adv_options) == 'yes': + -q '$cond_adv_options.mapq' + #end if + + #for $file in $files + '$file.input' + '$file.input.tag' + #end for + + </command> + + <inputs> + <repeat name="files" title="BAM files" min="1"> + <param format="bam" name="input" type="data" label="Files for QC" /> + </repeat> + + <param name="refdb" type="select" label="Reference gene model (GTF)"> + <options from_data_table="gene_GTF_database" /> + </param> + + <param name="attrID" type="text" size="50" value="gene_id" label="Feature ID name" help="Summing reads based on gene (gene_id) or transcript (transcript_id."> + <sanitizer> + <valid initial="none"> + <add value="ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz01234567890_-." /> + </valid> + </sanitizer> + </param> + + <param name="rRNAdb" type="select" label="Ribosomal RNA locations (BED)"> + <options from_data_table="rRNA_BED_database" /> + </param> + + <param name="stranded" type="select" label="Strandedness"> + <option value="yes">Yes - Read from stranded library</option> + <option value="no">No - Reads from unstranded library</option> + <option value="reverse">Reverse - reverse-stranded library (e.g. NSR)</option> + </param> + + <conditional name="cond_adv_options"> + <param name="adv_options" type="select" label="Set advanced options"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + + <when value="yes"> + <param name="mapq" type="integer" value="30" label="Minimum mapping quality for an alignment to be called uniquely mapped" /> + </when> + + <when value="no" /> + </conditional> + + </inputs> + + <outputs> + <data format="html" name="output" label="BAM QC on $on_tag_string" /> + <data format="txt" name="log" from_work_dir="bamqc.log" label="ezBAMQC log output" hidden="True" /> + </outputs> + + <help> + +**What it does** + +This tool takes the mapping results from RNA-Seq libraries (BAM), and performs rapid gene abundance quantification. If multiple files are provided, it will calculate and display correlation between each sample. + +----- + +The Galaxy wrapper for this tool is written by the `Cold Spring Harbor Laboratory`_ `Bioinformatics Shared Resources`_. + +ezBAMQC_ is written by the `Molly Hammell Laboratory`_ and the `Bioinformatics Shared Resources`_ at CSHL_. + +.. _CSHL: `Cold Spring Harbor Laboratory`_ +.. _ezBAMQC: http://hammelllab.labsites.cshl.edu/software#ezBAMQC +.. _`Molly Hammell Laboratory`: http://hammelllab.labsites.cshl.edu/ +.. _`Cold Spring Harbor Laboratory`: http://www.cshl.edu/ +.. _`Bioinformatics Shared Resources`: http://bioinfo.cshl.edu/index.html + + </help> +</tool> + |