Mercurial > repos > xuebing > sharplabtool
comparison tools/samtools/bam_to_sam.xml @ 0:9071e359b9a3
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| children |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 <tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.3"> | |
| 2 <requirements> | |
| 3 <requirement type="package">samtools</requirement> | |
| 4 </requirements> | |
| 5 <description>converts BAM format to SAM format</description> | |
| 6 <command interpreter="python"> | |
| 7 bam_to_sam.py | |
| 8 --input1=$input1 | |
| 9 --output1=$output1 | |
| 10 $header | |
| 11 </command> | |
| 12 <inputs> | |
| 13 <param name="input1" type="data" format="bam" label="BAM File to Convert" /> | |
| 14 <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" label="Include header in output" /> | |
| 15 </inputs> | |
| 16 <outputs> | |
| 17 <data format="sam" name="output1" label="${tool.name} on ${on_string}: converted SAM" /> | |
| 18 </outputs> | |
| 19 <tests> | |
| 20 <test> | |
| 21 <!-- | |
| 22 Bam-to-Sam command: | |
| 23 samtools view -o bam_to_sam_out1.sam test-data/bam_to_sam_in1.bam | |
| 24 bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam | |
| 25 --> | |
| 26 <param name="input1" value="bam_to_sam_in1.bam" ftype="bam" /> | |
| 27 <param name="header" value="" /> | |
| 28 <output name="output1" file="bam_to_sam_out1.sam" sorted="True" /> | |
| 29 </test> | |
| 30 <test> | |
| 31 <!-- | |
| 32 Bam-to-Sam command: | |
| 33 samtools view -o bam_to_sam_out2.sam test-data/bam_to_sam_in2.bam | |
| 34 bam_to_sam_in2.bam can be created from bam_to_sam_in2.sam | |
| 35 --> | |
| 36 <param name="input1" value="bam_to_sam_in2.bam" ftype="bam" /> | |
| 37 <param name="header" value="" /> | |
| 38 <output name="output1" file="bam_to_sam_out2.sam" sorted="True" /> | |
| 39 </test> | |
| 40 <test> | |
| 41 <!-- | |
| 42 Bam-to-Sam command: | |
| 43 samtools view -h -o bam_to_sam_out3.sam test-data/bam_to_sam_in1.bam | |
| 44 bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam | |
| 45 --> | |
| 46 <param name="input1" value="bam_to_sam_in1.bam" ftype="bam" /> | |
| 47 <param name="header" value="--header" /> | |
| 48 <output name="output1" file="bam_to_sam_out3.sam" sorted="True" lines_diff="6" /><!-- header param not working in func tests so won't produce correct 6-line header (fine in browser) --> | |
| 49 </test> | |
| 50 </tests> | |
| 51 <help> | |
| 52 | |
| 53 **What it does** | |
| 54 | |
| 55 This tool uses the SAMTools_ toolkit to produce a SAM file from a BAM file. | |
| 56 | |
| 57 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml | |
| 58 | |
| 59 </help> | |
| 60 </tool> |