Mercurial > repos > boris > filter_on_md
changeset 10:5108a91b93fe
Uploaded
author | boris |
---|---|
date | Fri, 20 Apr 2012 15:23:31 -0400 |
parents | 20b654fe58e2 |
children | 8a56e45f925f |
files | MDtag_filter.xml |
diffstat | 1 files changed, 35 insertions(+), 9 deletions(-) [+] |
line wrap: on
line diff
--- a/MDtag_filter.xml Fri Apr 20 15:23:12 2012 -0400 +++ b/MDtag_filter.xml Fri Apr 20 15:23:31 2012 -0400 @@ -1,13 +1,28 @@ <tool id="MDtag_filter" name="Filter mapped reads"> <description>on MD tag string</description> - <command interpreter="python">MDtag_filter.py $in_sam $n $m $out_sam</command> + <command interpreter="python">MDtag_filter.py $in_sam $n $m $out_sam ${create.choice} $discarded_sam</command> <inputs> <param format="sam" name="in_sam" type="data" label="Input SAM file"/> - <param name="n" type="integer" value='0' label="Number of bases to look at the start of the mapped read (n)"/> - <param name="m" type="integer" value='0' label="Number of bases to look at the end of the mapped read (m)"/> + <param name="n" type="integer" value='0' label="5' end window (n)" help="Any number of mismatches within this window will cause the read to be discarded"/> + <param name="m" type="integer" value='0' label="3' end window (m)" help="Any number of mismatches within this window will cause the read to be discarded"/> + <conditional name="create"> + <param name="choice" type="select" label="Create additional SAM file for discarded reads?"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + <!-- do nothing here --> + </when> + <when value="yes"> + <!-- do nothing here --> + </when> + </conditional> </inputs> <outputs> - <data format="sam" name="out_sam" metadata_source="in_sam" /> + <data format="sam" name="out_sam" label="MDtag_filter_(selected)_from_${in_sam.name}" metadata_source="in_sam"/> + <data format="sam" name="discarded_sam" label="MDtag_filter_(discarded)_from_${in_sam.name}" metadata_source="in_sam"> + <filter> (create['choice']=='yes') </filter> + </data> </outputs> <tests> <test> @@ -16,11 +31,20 @@ <param name="m" value="5"/> <output name="out_sam" file="test_md_filtered.sam"/> </test> + <test> + <param name="in_sam" value="test_for_md_filter.sam"/> + <param name="n" value="5"/> + <param name="m" value="5"/> + <param name="choice" value="yes"/> + <output name="out_sam" file="test_md_selected.sam"/> + <output name="discarded_sam" file="test_md_discarded.sam"/> + </test> </tests> <help> -Mismatches at the start and end of a mapped read are most likely sequencing errors. -This tool aims to control the variation noise due to sequencing errors. + +Mismatches at either end of a mapped read are most likely sequencing errors. +This tool aims to control the variation noise due to potential sequencing errors. ----- @@ -28,8 +52,10 @@ **What it does** -This tool reads the MD tag string of mapped reads. It discards mapped reads that contain variation at either end. -The user defines n and m. The mapped read is discarded if it contains any number of mismatches within **n** bases of the read start and within **m** bases of the read end. +This tool reads the MD tag of mapped reads (see SAM format specification). The user defines the 5' and 3' windows **n** and **m** (in bp), respectively. +The mapped read is discarded if it contains any number of mismatches within **n** bases of the read 5' end and within **m** bases of the read 3' end. +The resulting SAM file is enriched for mapped reads that show internal variation (if any) over reads whose variation is found within the read ends. +The user might also want to keep the discarded reads in an additional file. ----- @@ -37,7 +63,7 @@ **Note** -Mapped reads without an MD tag will be removed from the output SAM file. +Mapped reads without an MD tag will be removed from the output SAM file(s). -----