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view samtools_flagstat.xml @ 8:5fd05c7b42f8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty
author | iuc |
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date | Sun, 28 Jul 2019 14:47:58 -0400 |
parents | 5d3100bf5357 |
children | 5fbe9dcaef98 |
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<tool id="samtools_flagstat" name="Samtools flagstat" version="2.0.2"> <description>tabulate descriptive stats for BAM datset</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ @ADDTHREADS@ samtools flagstat -@ \$addthreads '$input1' > '$output1' ]]></command> <inputs> <param name="input1" type="data" format="sam,bam,cram" label="BAM File to report statistics of" /> </inputs> <outputs> <data name="output1" format="txt" /> </outputs> <tests> <test> <param name="input1" value="samtools_flagstat_input1.bam" ftype="bam" /> <output name="output1" file="samtools_flagstat_out1.txt" /> </test> </tests> <help><![CDATA[ **What it does** Uses ``samtools flagstat`` command to print descriptive information for a BAM dataset. Here is an example of such information:: 200 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 25 + 0 mapped (12.50%:nan%) 200 + 0 paired in sequencing 100 + 0 read1 100 + 0 read2 0 + 0 properly paired (0.00%:nan%) 0 + 0 with itself and mate mapped 25 + 0 singletons (12.50%:nan%) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5) ]]></help> <expand macro="citations"/> </tool>