Mercurial > repos > jeltje > samtools_1_18_mpileup
changeset 3:a3cf6bfdd81d draft
Uploaded
| author | jeltje |
|---|---|
| date | Mon, 12 Jan 2015 14:48:20 -0500 |
| parents | 862b189568c7 |
| children | 117867d6f99e |
| files | samtools_flagstat.xml samtools_mpileup.xml |
| diffstat | 2 files changed, 27 insertions(+), 37 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_flagstat.xml Mon Jan 12 14:48:20 2015 -0500 @@ -0,0 +1,27 @@ +<tool id="samtools_0_1_18_flagstat" name="flagstat" version="1.0.0"> + <requirements> + <requirement type="package" version="0.1.18">samtools</requirement> + </requirements> + <description>provides simple stats on BAM files</description> + <command>samtools flagstat "$input1" > "$output1" + </command> + <inputs> + <param name="input1" type="data" format="bam" label="BAM File" /> + </inputs> + <outputs> + <data name="output1" format="txt" /> + </outputs> +<!-- + <tests> + <test> + <param name="input1" value="unsorted.bam" ftype="bam" /> + <output name="output1" file="samtools_flagstat_out1.txt" /> + </test> + </tests> +--> + <help> + +This tool runs the flagstat command of samtools 0.1.18 to produce simple stats on a BAM file. + + </help> +</tool>
--- a/samtools_mpileup.xml Mon Jan 12 14:47:27 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ -<tool id="samtools_1_18_mpileup" name=mpileup" version="1.0.0"> - <requirements> - <requirement type="package" version="0.1.18">samtools</requirement> - </requirements> - <description>runs basic mpileup on input control and tumor files</description> - <command>samtools mpileup "$bamc" "$bamt"> "$output1" -<!-- - <command>samtools mpileup -q 1 -B "$index" "$bamc" "$bamt"> "$output1" ---> - </command> - <inputs> - <param name="bamc" type="data" format="bam" label="BAM file (control)" /> - <param name="bamt" type="data" format="bam" label="BAM file (tumor)" /> -<!-- - <param name="index" type="select"> - <options from_data_table="picard_index" /> ---> - </param> - </inputs> - <outputs> - <data name="output1" format="txt" /> - </outputs> -<!-- - <tests> - <test> - <param name="input1" value="unsorted.bam" ftype="bam" /> - <output name="output1" file="samtools_flagstat_out1.txt" /> - </test> - </tests> ---> - <help> - -This tool runs the mpileup command of samtools 0.1.18 -with flags -q 1 -B - - </help> -</tool>