| Previous changeset 3:c1419fa820c6 (2015-03-18) Next changeset 5:f57df915aa10 (2017-05-09) |
|
Commit message:
Uploaded |
|
modified:
bam_to_sam.xml macros.xml test-data/bam_to_sam_out1.sam test-data/bam_to_sam_out2.sam test-data/bam_to_sam_out3.sam |
| b |
| diff -r c1419fa820c6 -r af7c50162f0b bam_to_sam.xml --- a/bam_to_sam.xml Wed Mar 18 15:44:51 2015 -0400 +++ b/bam_to_sam.xml Tue Apr 21 14:36:15 2015 -0400 |
| [ |
| @@ -1,20 +1,23 @@ -<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.6"> +<tool id="bam_to_sam" name="BAM-to-SAM" version="2.0"> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"></expand> <expand macro="version_command"></expand> <expand macro="stdio"></expand> - <description>converts BAM format to SAM format</description> + <description>convert BAM to SAM</description> <command> <![CDATA[ - samtools sort -O bam -@ \${GALAXY_SLOTS:-1} "$input1" -o sorted_input.bam -T temp && - samtools view sorted_input.bam $header -o $output1 -@ \${GALAXY_SLOTS:-1} + samtools view -o "${output1}" ${header} "${input1}" ]]> </command> <inputs> <param format="bam" label="BAM File to Convert" name="input1" type="data" /> - <param checked="False" falsevalue="" label="Include header in output" name="header" truevalue="-h" type="boolean" /> + <param name="header" label="Header options" type="select" help="Allows to choose between seeing the entire dataset with the header, header only, or data only."> + <option value="-h">Include header in SAM output (-h)</option> + <option value="-H">Print header only (-H)</option> + <option value="">Exclude header</option> + </param> </inputs> <outputs> <data format="sam" label="${tool.name} on ${on_string}: converted SAM" name="output1" /> @@ -22,17 +25,17 @@ <tests> <test> <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" /> - <param name="header" value="" /> + <param name="header" value="-h" /> <output file="bam_to_sam_out1.sam" name="output1" sorted="True" /> </test> <test> - <param ftype="bam" name="input1" value="bam_to_sam_in2.bam" /> - <param name="header" value="" /> + <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" /> + <param name="header" value="-H" /> <output file="bam_to_sam_out2.sam" name="output1" sorted="True" /> </test> <test> <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" /> - <param name="header" value="True" /> + <param name="header" value="" /> <output file="bam_to_sam_out3.sam" name="output1" sorted="True" /> </test> </tests> @@ -41,9 +44,10 @@ **What it does** -This tool uses the SAMTools_ toolkit to produce a SAM file from a BAM file. +Converts BAM dataset to SAM using ``samtools view`` command:: -.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml + samtools view -o [OUTPUT SAM] [-h|-H] [INPUT BAM] + ]]> </help> <expand macro="citations"></expand> |
| b |
| diff -r c1419fa820c6 -r af7c50162f0b macros.xml --- a/macros.xml Wed Mar 18 15:44:51 2015 -0400 +++ b/macros.xml Tue Apr 21 14:36:15 2015 -0400 |
| b |
| @@ -7,7 +7,37 @@ </xml> <xml name="citations"> <citations> + <citation type="bibtex"> + @misc{SAM_def, + title={Definition of SAM/BAM format}, + url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} + </citation> <citation type="doi">10.1093/bioinformatics/btp352</citation> + <citation type="doi">10.1093/bioinformatics/btr076</citation> + <citation type="doi">10.1093/bioinformatics/btr509</citation> + <citation type="bibtex"> + @misc{Danecek_et_al, + Author={Danecek, P., Schiffels, S., Durbin, R.}, + title={Multiallelic calling model in bcftools (-m)}, + url = {http://samtools.github.io/bcftools/call-m.pdf},} + </citation> + <citation type="bibtex"> + @misc{Durbin_VCQC, + Author={Durbin, R.}, + title={Segregation based metric for variant call QC}, + url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} + </citation> + <citation type="bibtex"> + @misc{Li_SamMath, + Author={Li, H.}, + title={Mathematical Notes on SAMtools Algorithms}, + url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} + </citation> + <citation type="bibtex"> + @misc{SamTools_github, + title={SAMTools GitHub page}, + url = {https://github.com/samtools/samtools},} + </citation> </citations> </xml> <xml name="version_command"> @@ -18,4 +48,23 @@ <exit_code range="1:" level="fatal" description="Error" /> </stdio> </xml> + <token name="@no-chrom-options@"> +----- + +.. class:: warningmark + +**No options available? How to re-detect metadata** + +If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps: + +1. Click on the **pencil** icon adjacent to the dataset in the history +2. A new menu will appear in the center pane of the interface +3. Click **Datatype** tab +4. Set **New Type** to **BAM** +5. Click **Save** + +The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. + + </token> + </macros> |
| b |
| diff -r c1419fa820c6 -r af7c50162f0b test-data/bam_to_sam_out1.sam --- a/test-data/bam_to_sam_out1.sam Wed Mar 18 15:44:51 2015 -0400 +++ b/test-data/bam_to_sam_out1.sam Tue Apr 21 14:36:15 2015 -0400 |
| b |
| @@ -1,3 +1,9 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:101 +@SQ SN:chr7 LN:404 +@SQ SN:chr8 LN:202 +@RG ID:0 SM:Hi,Mom! +@PG ID:1 PN:Hey! VN:2.0 both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 |
| b |
| diff -r c1419fa820c6 -r af7c50162f0b test-data/bam_to_sam_out2.sam --- a/test-data/bam_to_sam_out2.sam Wed Mar 18 15:44:51 2015 -0400 +++ b/test-data/bam_to_sam_out2.sam Tue Apr 21 14:36:15 2015 -0400 |
| b |
| @@ -1,18 +1,6 @@ -bar:record:4 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:6 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 -bar:record:1 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:3 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 -bar:record:1 141 chr1 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:7 77 chr1 20 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 -bar:record:8 77 chr1 30 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 -bar:record:4 141 chr1 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:5 77 chr1 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 -bar:record:6 141 chr1 50 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg2 -bar:record:2 77 chr2 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:2 141 chr2 30 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg2 -bar:record:3 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:8 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:5 141 chr3 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:9 77 chr4 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:7 141 chr4 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:9 141 chr4 60 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:101 +@SQ SN:chr7 LN:404 +@SQ SN:chr8 LN:202 +@RG ID:0 SM:Hi,Mom! +@PG ID:1 PN:Hey! VN:2.0 |
| b |
| diff -r c1419fa820c6 -r af7c50162f0b test-data/bam_to_sam_out3.sam --- a/test-data/bam_to_sam_out3.sam Wed Mar 18 15:44:51 2015 -0400 +++ b/test-data/bam_to_sam_out3.sam Tue Apr 21 14:36:15 2015 -0400 |
| b |
| @@ -1,9 +1,3 @@ -@HD VN:1.0 SO:coordinate -@SQ SN:chr1 LN:101 -@SQ SN:chr7 LN:404 -@SQ SN:chr8 LN:202 -@RG ID:0 SM:Hi,Mom! -@PG ID:1 PN:Hey! VN:2.0 both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 |