Mercurial > repos > devteam > samtools_rmdup
annotate macros.xml @ 5:586f9e1cdb2b draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
author | iuc |
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date | Mon, 29 Jul 2019 08:45:55 -0400 |
parents | 9129584416e2 |
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rev | line source |
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2 | 1 <macros> |
2 <xml name="requirements"> | |
3 <requirements> | |
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9129584416e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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4 <requirement type="package" version="1.3.1">samtools</requirement> |
2 | 5 <yield/> |
6 </requirements> | |
7 </xml> | |
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9129584416e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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2
diff
changeset
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8 <token name="@TOOL_VERSION@">1.3.1</token> |
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586f9e1cdb2b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents:
4
diff
changeset
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9 <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token> |
586f9e1cdb2b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents:
4
diff
changeset
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10 <xml name="filter_options"> |
586f9e1cdb2b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents:
4
diff
changeset
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11 <option value="1">Read is paired</option> |
586f9e1cdb2b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents:
4
diff
changeset
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12 <option value="2">Read is mapped in a proper pair</option> |
586f9e1cdb2b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents:
4
diff
changeset
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13 <option value="4">The read is unmapped</option> |
586f9e1cdb2b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents:
4
diff
changeset
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14 <option value="8">The mate is unmapped</option> |
586f9e1cdb2b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents:
4
diff
changeset
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15 <option value="16">Read strand</option> |
586f9e1cdb2b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents:
4
diff
changeset
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16 <option value="32">Mate strand</option> |
586f9e1cdb2b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents:
4
diff
changeset
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17 <option value="48">Read is the first in a pair</option> |
586f9e1cdb2b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents:
4
diff
changeset
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18 <option value="64">Read is the second in a pair</option> |
586f9e1cdb2b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents:
4
diff
changeset
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19 <option value="256">The alignment or this read is not primary</option> |
586f9e1cdb2b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents:
4
diff
changeset
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20 <option value="512">The read fails platform/vendor quality checks</option> |
586f9e1cdb2b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents:
4
diff
changeset
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21 <option value="768">The read is a PCR or optical duplicate</option> |
586f9e1cdb2b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents:
4
diff
changeset
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22 <option value="1024">Supplementary alignment</option> |
586f9e1cdb2b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
parents:
4
diff
changeset
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23 </xml> |
2 | 24 <xml name="citations"> |
25 <citations> | |
26 <citation type="bibtex"> | |
27 @misc{SAM_def, | |
28 title={Definition of SAM/BAM format}, | |
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9129584416e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
2
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changeset
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29 url = {https://samtools.github.io/hts-specs/},} |
2 | 30 </citation> |
31 <citation type="doi">10.1093/bioinformatics/btp352</citation> | |
32 <citation type="doi">10.1093/bioinformatics/btr076</citation> | |
33 <citation type="doi">10.1093/bioinformatics/btr509</citation> | |
34 <citation type="bibtex"> | |
35 @misc{Danecek_et_al, | |
36 Author={Danecek, P., Schiffels, S., Durbin, R.}, | |
37 title={Multiallelic calling model in bcftools (-m)}, | |
38 url = {http://samtools.github.io/bcftools/call-m.pdf},} | |
39 </citation> | |
40 <citation type="bibtex"> | |
41 @misc{Durbin_VCQC, | |
42 Author={Durbin, R.}, | |
43 title={Segregation based metric for variant call QC}, | |
44 url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} | |
45 </citation> | |
46 <citation type="bibtex"> | |
47 @misc{Li_SamMath, | |
48 Author={Li, H.}, | |
49 title={Mathematical Notes on SAMtools Algorithms}, | |
50 url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} | |
51 </citation> | |
52 <citation type="bibtex"> | |
53 @misc{SamTools_github, | |
54 title={SAMTools GitHub page}, | |
55 url = {https://github.com/samtools/samtools},} | |
56 </citation> | |
57 </citations> | |
58 </xml> | |
59 <xml name="version_command"> | |
4
9129584416e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
2
diff
changeset
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60 <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command> |
2 | 61 </xml> |
62 <xml name="stdio"> | |
63 <stdio> | |
64 <exit_code range="1:" level="fatal" description="Error" /> | |
65 </stdio> | |
66 </xml> | |
67 <token name="@no-chrom-options@"> | |
68 ----- | |
69 | |
70 .. class:: warningmark | |
71 | |
72 **No options available? How to re-detect metadata** | |
73 | |
74 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: | |
75 | |
76 1. Click on the **pencil** icon adjacent to the dataset in the history | |
77 2. A new menu will appear in the center pane of the interface | |
78 3. Click **Datatype** tab | |
79 4. Set **New Type** to **BAM** | |
80 5. Click **Save** | |
81 | |
82 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. | |
83 </token> | |
84 </macros> |