Mercurial > repos > devteam > bam_to_sam
annotate bam_to_sam.xml @ 1:38859774da87 draft
Uploaded tool and dependency definition that specifies samtools version 0.1.19.
| author | devteam |
|---|---|
| date | Thu, 27 Mar 2014 14:02:29 -0400 |
| parents | c9e926d9d87e |
| children | 6eebf8420e31 |
| rev | line source |
|---|---|
|
1
38859774da87
Uploaded tool and dependency definition that specifies samtools version 0.1.19.
devteam
parents:
0
diff
changeset
|
1 <tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.4"> |
| 0 | 2 <requirements> |
|
1
38859774da87
Uploaded tool and dependency definition that specifies samtools version 0.1.19.
devteam
parents:
0
diff
changeset
|
3 <requirement type="package" version="0.1.19">samtools</requirement> |
| 0 | 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 ------ | |
| 60 | |
| 61 **Citation** | |
| 62 | |
| 63 For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ | |
| 64 | |
| 65 </help> | |
| 66 </tool> |