Mercurial > repos > devteam > samtools_mpileup
annotate macros.xml @ 9:fa7ad9b89f4a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
author | iuc |
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date | Mon, 03 Sep 2018 13:10:02 -0400 |
parents | 583abf29fc8e |
children | 8da515fbc1bf |
rev | line source |
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4 | 1 <macros> |
2 <xml name="requirements"> | |
3 <requirements> | |
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fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
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4 <requirement type="package" version="@TOOL_VERSION@">samtools</requirement> |
4 | 5 <yield/> |
6 </requirements> | |
7 </xml> | |
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fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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8 <token name="@TOOL_VERSION@">1.9</token> |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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9 <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token> |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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10 <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[ |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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11 ##prepare input and indices |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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12 #for $i, $bam in enumerate( $input_bams ): |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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13 ln -s '$bam' '${i}' && |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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14 #if $bam.is_of_type('bam'): |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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15 #if str( $bam.metadata.bam_index ) != "None": |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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16 ln -s '${bam.metadata.bam_index}' '${i}.bai' && |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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17 #else: |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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18 samtools index '${i}' '${i}.bai' && |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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19 #end if |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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20 #elif $bam.is_of_type('cram'): |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
parents:
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diff
changeset
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21 #if str( $bam.metadata.cram_index ) != "None": |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
parents:
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diff
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22 ln -s '${bam.metadata.cram_index}' '${i}.crai' && |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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23 #else: |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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24 samtools index '${i}' '${i}.crai' && |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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25 #end if |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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26 #end if |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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27 #end for |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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28 ]]></token> |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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diff
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29 <xml name="flag_options"> |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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30 <option value="1">read is paired</option> |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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31 <option value="2">read is mapped in a proper pair</option> |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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32 <option value="4">read is unmapped</option> |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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33 <option value="8">mate is unmapped</option> |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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34 <option value="16">read reverse strand</option> |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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35 <option value="32">mate reverse strand</option> |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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36 <option value="64">read is the first in a pair</option> |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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37 <option value="128">read is the second in a pair</option> |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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38 <option value="256">alignment or read is not primary</option> |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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39 <option value="512">read fails platform/vendor quality checks</option> |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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40 <option value="1024">read is a PCR or optical duplicate</option> |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
iuc
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41 <option value="2048">supplementary alignment</option> |
fa7ad9b89f4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
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42 </xml> |
4 | 43 <xml name="citations"> |
44 <citations> | |
45 <citation type="bibtex"> | |
46 @misc{SAM_def, | |
47 title={Definition of SAM/BAM format}, | |
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583abf29fc8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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48 url = {https://samtools.github.io/hts-specs/},} |
4 | 49 </citation> |
50 <citation type="doi">10.1093/bioinformatics/btp352</citation> | |
51 <citation type="doi">10.1093/bioinformatics/btr076</citation> | |
52 <citation type="doi">10.1093/bioinformatics/btr509</citation> | |
53 <citation type="bibtex"> | |
54 @misc{Danecek_et_al, | |
55 Author={Danecek, P., Schiffels, S., Durbin, R.}, | |
56 title={Multiallelic calling model in bcftools (-m)}, | |
57 url = {http://samtools.github.io/bcftools/call-m.pdf},} | |
58 </citation> | |
59 <citation type="bibtex"> | |
60 @misc{Durbin_VCQC, | |
61 Author={Durbin, R.}, | |
62 title={Segregation based metric for variant call QC}, | |
63 url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} | |
64 </citation> | |
65 <citation type="bibtex"> | |
66 @misc{Li_SamMath, | |
67 Author={Li, H.}, | |
68 title={Mathematical Notes on SAMtools Algorithms}, | |
69 url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} | |
70 </citation> | |
71 <citation type="bibtex"> | |
72 @misc{SamTools_github, | |
73 title={SAMTools GitHub page}, | |
74 url = {https://github.com/samtools/samtools},} | |
75 </citation> | |
76 </citations> | |
77 </xml> | |
78 <xml name="version_command"> | |
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583abf29fc8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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79 <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command> |
4 | 80 </xml> |
81 <xml name="stdio"> | |
82 <stdio> | |
83 <exit_code range="1:" level="fatal" description="Error" /> | |
84 </stdio> | |
85 </xml> | |
86 <token name="@no-chrom-options@"> | |
87 ----- | |
88 | |
89 .. class:: warningmark | |
90 | |
91 **No options available? How to re-detect metadata** | |
92 | |
93 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: | |
94 | |
95 1. Click on the **pencil** icon adjacent to the dataset in the history | |
96 2. A new menu will appear in the center pane of the interface | |
97 3. Click **Datatype** tab | |
98 4. Set **New Type** to **BAM** | |
99 5. Click **Save** | |
100 | |
101 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. | |
102 </token> | |
103 </macros> |