Mercurial > repos > iuc > bax2bam
comparison bax2bam.xml @ 0:4445939cacc9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
author | iuc |
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date | Sat, 12 Oct 2019 06:52:23 -0400 |
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children | ee356d7a5518 |
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1 <?xml version="1.0"?> | |
2 <tool id="bax2bam" name="bax2bam" version="@TOOL_VERSION@+@WRAPPER_VERSION@"> | |
3 <description>converts PacBio basecall format (bax.h5) into BAM</description> | |
4 <macros> | |
5 <import>macros.xml</import> | |
6 </macros> | |
7 <expand macro="requirements"/> | |
8 <stdio></stdio> | |
9 <command detect_errors="exit_code"><![CDATA[ | |
10 bax2bam | |
11 #for $file in $files | |
12 '$file' | |
13 #end for | |
14 -o output | |
15 $readtype | |
16 #if $pulsefeatures | |
17 --pulsefeatures=$pulsefeatures | |
18 #end if | |
19 $losslessframes | |
20 $internal | |
21 ]]></command> | |
22 <inputs> | |
23 <param name="files" type="data" format="h5" multiple="true" label="Files" help="Should be from the same movie."/> | |
24 <param name="readtype" type="select" label="Output read type" help=""> | |
25 <option value="--subread">subread</option> | |
26 <option value="--hqregion">hqregion</option> | |
27 <option value="--polymeraseread">polymeraseread</option> | |
28 </param> | |
29 <param argument="--pulsefeatures" type="select" multiple="true" label="Select pulse features in the output BAM." help=""> | |
30 <option value="DeletionQV" selected="true">dq - DeletionQV</option> | |
31 <option value="DeletionTag" selected="true">dt - DeletionTag</option> | |
32 <option value="InsertionQV" selected="true">iq - InsertionQV</option> | |
33 <option value="IPD" selected="true">ip - IPD</option> | |
34 <option value="PulseWidth" selected="true">pw - PulseWidth</option> | |
35 <option value="MergeQV" selected="true">mq - MergeQV</option> | |
36 <option value="SubstitutionQV" selected="true">sq - SubstitutionQV</option> | |
37 <option value="SubstitutionTag" selected="false">st - SubstitutionTag</option> | |
38 </param> | |
39 <param argument="--losslessframes" type="boolean" truevalue="--losslessframes" falsevalue="" checked="false" label="Store full, 16-bit IPD/PulseWidth data" help="Instead of (default) downsampled, 8-bit encoding."/> | |
40 <param argument="--internal" type="boolean" truevalue="--internal" falsevalue="" checked="false" label="Output BAMs in internal mode." help="Currently this indicates that non-sequencing ZMWs should be included in the output scraps BAM file, if applicable."/> | |
41 </inputs> | |
42 | |
43 <outputs> | |
44 <data name="output_scrap" from_work_dir="output.scraps.bam" format="bam" label="${tool.name} on ${on_string}: scraps"> | |
45 <filter>readtype == '--subread'</filter> | |
46 </data> | |
47 <data name="output_subread" from_work_dir="output.subreads.bam" format="bam" label="${tool.name} on ${on_string}: subreads"> | |
48 <filter>readtype == '--subread'</filter> | |
49 </data> | |
50 <data name="output_hqregion" from_work_dir="output.hqregions.bam" format="bam" label="${tool.name} on ${on_string}: hqregions"> | |
51 <filter>readtype == '--hqregion'</filter> | |
52 </data> | |
53 <data name="output_lqregion" from_work_dir="output.lqregions.bam" format="bam" label="${tool.name} on ${on_string}: lqregions"> | |
54 <filter>readtype == '--hqregion'</filter> | |
55 </data> | |
56 <data name="output_polymeraseread" from_work_dir="output.polymerase.bam" format="bam" label="${tool.name} on ${on_string}: polymerase"> | |
57 <filter>readtype == '--polymeraseread'</filter> | |
58 </data> | |
59 </outputs> | |
60 | |
61 <tests> | |
62 <!-- source of test data: https://github.com/PacificBiosciences/PacBioTestData/tree/master/data/HdfSubreadSet/Analysis_Results/ --> | |
63 <!-- #1: read type: subread --> | |
64 <test> | |
65 <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/> | |
66 <param name="readtype" value="--subread"/> | |
67 <output name="output_scrap" file="scraps.bam" compare="sim_size" delta="100"/> | |
68 <output name="output_subread" file="subreads.bam" compare="sim_size" delta="100"/> | |
69 </test> | |
70 <!-- #2: read type: hqregion --> | |
71 <test> | |
72 <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/> | |
73 <param name="readtype" value="--hqregion"/> | |
74 <output name="output_hqregion" file="hqregions.bam" compare="sim_size" delta="100"/> | |
75 <output name="output_hqregion" file="lqregions.bam" compare="sim_size" delta="100"/> | |
76 </test> | |
77 <!-- #3: read type: polymeraseread --> | |
78 <test> | |
79 <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/> | |
80 <param name="readtype" value="--polymeraseread" compare="sim_size" delta="100"/> | |
81 <output name="output_polymeraseread" file="polymerase.bam" compare="sim_size" delta="100"/> | |
82 </test> | |
83 <!-- #4: read type: subread, custom parameters --> | |
84 <test> | |
85 <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/> | |
86 <param name="readtype" value="--subread"/> | |
87 <param name="pulsefeatures" value="SubstitutionTag"/> | |
88 <param name="losslessframes" value="true"/> | |
89 <param name="internal" value="true"/> | |
90 <output name="output_scrap" file="scraps_custom.bam" compare="sim_size" delta="100"/> | |
91 <output name="output_subread" file="subreads_custom.bam" compare="sim_size" delta="100"/> | |
92 </test> | |
93 </tests> | |
94 <help><![CDATA[ | |
95 | |
96 .. class:: infomark | |
97 | |
98 **What it does** | |
99 | |
100 bax2bam converts the legacy PacBio basecall format (bax.h5) into the BAM basecall format. | |
101 | |
102 **Input** | |
103 | |
104 bax.h5 files that should be from the same movie. | |
105 | |
106 **Output** | |
107 | |
108 A single BAM file. | |
109 | |
110 .. class:: infomark | |
111 | |
112 **References** | |
113 | |
114 More information can be found on the github repositories `bax2bam <https://github.com/pacificbiosciences/bax2bam/>`_ and `PacBio Bioconda <https://github.com/PacificBiosciences/pbbioconda>`_. | |
115 ]]></help> | |
116 <citations> | |
117 <citation type="bibtex"> | |
118 @misc{PacificBiosciences2018, | |
119 author = {Pacific Biosciences}, | |
120 year = {2018}, | |
121 title = {bax2bam}, | |
122 publisher = {GitHub}, | |
123 journal = {GitHub repository}, | |
124 url = {https://github.com/pacificbiosciences/bax2bam/}, | |
125 } | |
126 </citation> | |
127 </citations> | |
128 </tool> |