Mercurial > repos > devteam > bam_to_sam
annotate macros.xml @ 5:f57df915aa10 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
| author | iuc |
|---|---|
| date | Tue, 09 May 2017 11:18:39 -0400 |
| parents | af7c50162f0b |
| children | 88eedb4abea0 |
| rev | line source |
|---|---|
| 3 | 1 <macros> |
| 2 <xml name="requirements"> | |
| 3 <requirements> | |
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f57df915aa10
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
4
diff
changeset
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4 <requirement type="package" version="1.3.1">samtools</requirement> |
| 3 | 5 <yield/> |
| 6 </requirements> | |
| 7 </xml> | |
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f57df915aa10
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
4
diff
changeset
|
8 <token name="@TOOL_VERSION@">1.3.1</token> |
| 3 | 9 <xml name="citations"> |
| 10 <citations> | |
| 4 | 11 <citation type="bibtex"> |
| 12 @misc{SAM_def, | |
| 13 title={Definition of SAM/BAM format}, | |
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f57df915aa10
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
4
diff
changeset
|
14 url = {https://samtools.github.io/hts-specs/},} |
| 4 | 15 </citation> |
| 3 | 16 <citation type="doi">10.1093/bioinformatics/btp352</citation> |
| 4 | 17 <citation type="doi">10.1093/bioinformatics/btr076</citation> |
| 18 <citation type="doi">10.1093/bioinformatics/btr509</citation> | |
| 19 <citation type="bibtex"> | |
| 20 @misc{Danecek_et_al, | |
| 21 Author={Danecek, P., Schiffels, S., Durbin, R.}, | |
| 22 title={Multiallelic calling model in bcftools (-m)}, | |
| 23 url = {http://samtools.github.io/bcftools/call-m.pdf},} | |
| 24 </citation> | |
| 25 <citation type="bibtex"> | |
| 26 @misc{Durbin_VCQC, | |
| 27 Author={Durbin, R.}, | |
| 28 title={Segregation based metric for variant call QC}, | |
| 29 url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} | |
| 30 </citation> | |
| 31 <citation type="bibtex"> | |
| 32 @misc{Li_SamMath, | |
| 33 Author={Li, H.}, | |
| 34 title={Mathematical Notes on SAMtools Algorithms}, | |
| 35 url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} | |
| 36 </citation> | |
| 37 <citation type="bibtex"> | |
| 38 @misc{SamTools_github, | |
| 39 title={SAMTools GitHub page}, | |
| 40 url = {https://github.com/samtools/samtools},} | |
| 41 </citation> | |
| 3 | 42 </citations> |
| 43 </xml> | |
| 44 <xml name="version_command"> | |
|
5
f57df915aa10
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
4
diff
changeset
|
45 <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command> |
| 3 | 46 </xml> |
| 47 <xml name="stdio"> | |
| 48 <stdio> | |
| 49 <exit_code range="1:" level="fatal" description="Error" /> | |
| 50 </stdio> | |
| 51 </xml> | |
| 4 | 52 <token name="@no-chrom-options@"> |
| 53 ----- | |
| 54 | |
| 55 .. class:: warningmark | |
| 56 | |
| 57 **No options available? How to re-detect metadata** | |
| 58 | |
| 59 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: | |
| 60 | |
| 61 1. Click on the **pencil** icon adjacent to the dataset in the history | |
| 62 2. A new menu will appear in the center pane of the interface | |
| 63 3. Click **Datatype** tab | |
| 64 4. Set **New Type** to **BAM** | |
| 65 5. Click **Save** | |
| 66 | |
| 67 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. | |
| 68 </token> | |
| 3 | 69 </macros> |