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comparison bax2bam.xml @ 0:413d28ca0b6f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
author iuc
date Sat, 12 Oct 2019 06:50:34 -0400
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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>