Mercurial > repos > iuc > seqtk
diff seqtk_fqchk.xml @ 0:e0a0fd938de4 draft
Uploaded
| author | iuc |
|---|---|
| date | Thu, 05 Feb 2015 11:52:40 -0500 |
| parents | |
| children | f73729b62b51 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqtk_fqchk.xml Thu Feb 05 11:52:40 2015 -0500 @@ -0,0 +1,58 @@ +<?xml version="1.0"?> +<tool id="seqtk_fqchk" name="seqtk_fqchk" version="@WRAPPER_VERSION@.0"> + <description>fastq QC (base/quality summary)</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <command><![CDATA[seqtk fqchk +-q $q +$in_file | awk '{if(NR<4){print "#"$0}else{print $0}}' +> $default]]></command> + <inputs> + <expand macro="in_fq"/> + <param name="q" type="integer" value="20" label="quality values" help="use 0 to get the distribution of all quality values (-q)"/> + </inputs> + <outputs> + <data format="tabular" hidden="false" name="default" label="Quality information for $in_file.name"/> + </outputs> + <tests> + <test> + <param name="in_file" value="seqtk_fqchk.fq"/> + <output name="default" file="seqtk_fqchk.out" ftype="tabular"/> + </test> + </tests> + <help><![CDATA[ +**What it does** + +Returns quality score information base-by-base. + +:: + + @SEQ_ID1 + GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT + + + !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65 + +each based is examined individually and information reported: + +:: + + #min_len: 60; max_len: 60; avg_len: 60.00; 15 distinct quality values + #POS #bases %A %C %G %T %N avgQ errQ %low %high + #ALL 60 31.7 16.7 18.3 33.3 0.0 15.1 8.7 66.7 33.3 + 1 1 0.0 0.0 100.0 0.0 0.0 0.0 3.0 100.0 0.0 + 2 1 100.0 0.0 0.0 0.0 0.0 6.0 6.0 100.0 0.0 + 3 1 0.0 0.0 0.0 100.0 0.0 6.0 6.0 100.0 0.0 + 4 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0 + 5 1 0.0 0.0 0.0 100.0 0.0 7.0 7.0 100.0 0.0 + 6 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0 + 7 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0 + 8 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0 + 9 1 0.0 0.0 100.0 0.0 0.0 9.0 9.0 100.0 0.0 + 10 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0 + +@ATTRIBUTION@ +]]></help> +</tool>