Mercurial > repos > jeltje > samtools_0_1_18_flagstat
changeset 1:b469f90740f8 draft
Uploaded
| author | jeltje |
|---|---|
| date | Mon, 12 Jan 2015 14:45:02 -0500 |
| parents | a381e8c76e58 |
| children | 1bf4de6596f1 |
| files | samtools_flagstat.xml samtools_mpileup.xml |
| diffstat | 2 files changed, 37 insertions(+), 27 deletions(-) [+] |
line wrap: on
line diff
--- a/samtools_flagstat.xml Fri Jan 09 18:40:34 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27 +0,0 @@ -<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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_mpileup.xml Mon Jan 12 14:45:02 2015 -0500 @@ -0,0 +1,37 @@ +<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>