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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 958bbd9e30ae4d320f872f1ab5e1bacfb28b1a00"
author iuc
date Sat, 17 Apr 2021 10:40:28 +0000
parents bbed92d5d4d9
children
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1:bbed92d5d4d9 2:0cd3f1c577de
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="bax2bam" name="bax2bam" version="@TOOL_VERSION@+@WRAPPER_VERSION@"> 2 <tool id="bax2bam" name="bax2bam" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
3 <description>converts PacBio basecall format (bax.h5) into BAM</description> 3 <description>converts PacBio basecall format (bax.h5) into BAM</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <token name="@TOOL_VERSION@">0.0.11</token>
6 <token name="@VERSION_SUFFIX@">0</token>
6 </macros> 7 </macros>
7 <expand macro="requirements"/> 8 <edam_topics>
8 <stdio></stdio> 9 <edam_topic>topic_3168</edam_topic> <!-- Topic - Laboratory techniques - Sequencing -->
10 </edam_topics>
11 <edam_operations>
12 <edam_operation>operation_3434</edam_operation> <!-- Operation - Conversion -->
13 </edam_operations>
14 <requirements>
15 <requirement type="package" version="@TOOL_VERSION@">bax2bam</requirement>
16 </requirements>
17 <version_command><![CDATA[bax2bam --version]]></version_command>
9 <command detect_errors="exit_code"><![CDATA[ 18 <command detect_errors="exit_code"><![CDATA[
10 bax2bam 19 ## skipped -h/--help, --xml, -f, --output-xml, --ccs (see https://github.com/PacificBiosciences/pbbioconda/issues/215)
11 #for $file in $files 20
12 '$file' 21 ## run
13 #end for 22 bax2bam
14 -o output 23 #for $file in $files
15 $readtype 24 '$file'
16 #if $pulsefeatures 25 #end for
17 --pulsefeatures=$pulsefeatures 26 -o 'output'
18 #end if 27 $readtype
19 $losslessframes 28 #if $pulsefeatures
20 $internal 29 --pulsefeatures=$pulsefeatures
30 #end if
31 $losslessframes
32 $internal
21 ]]></command> 33 ]]></command>
22 <inputs> 34 <inputs>
23 <param name="files" type="data" format="h5" multiple="true" label="Files" help="Should be from the same movie."/> 35 <param name="files" type="data" format="h5" multiple="true" label="Select files" help="Should be from the same movie."/>
24 <param name="readtype" type="select" label="Output read type" help=""> 36 <param name="readtype" type="select" label="Select output read type">
25 <option value="--subread">subread</option> 37 <option value="--hqregion">Hqregion</option>
26 <option value="--hqregion">hqregion</option> 38 <option value="--polymeraseread">Polymeraseread</option>
27 <option value="--polymeraseread">polymeraseread</option> 39 <option value="--subread">Subread</option>
28 </param> 40 </param>
29 <param argument="--pulsefeatures" type="select" multiple="true" label="Select pulse features in the output BAM." help=""> 41 <param argument="--pulsefeatures" type="select" multiple="true" label="Select pulse features in output BAM">
30 <option value="DeletionQV" selected="true">dq - DeletionQV</option> 42 <option value="DeletionQV" selected="true">dq - DeletionQV</option>
31 <option value="DeletionTag" selected="true">dt - DeletionTag</option> 43 <option value="DeletionTag" selected="true">dt - DeletionTag</option>
32 <option value="InsertionQV" selected="true">iq - InsertionQV</option> 44 <option value="InsertionQV" selected="true">iq - InsertionQV</option>
33 <option value="IPD" selected="true">ip - IPD</option> 45 <option value="IPD" selected="true">ip - IPD</option>
46 <option value="MergeQV" selected="true">mq - MergeQV</option>
34 <option value="PulseWidth" selected="true">pw - PulseWidth</option> 47 <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> 48 <option value="SubstitutionQV" selected="true">sq - SubstitutionQV</option>
37 <option value="SubstitutionTag" selected="false">st - SubstitutionTag</option> 49 <option value="SubstitutionTag" selected="false">st - SubstitutionTag</option>
38 </param> 50 </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."/> 51 <param argument="--losslessframes" type="boolean" truevalue="--losslessframes" falsevalue="" label="Store full, 16-bit IPD/PulseWidth data?" help="Instead of 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."/> 52 <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> 53 </inputs>
42
43 <outputs> 54 <outputs>
44 <data name="output_scrap" from_work_dir="output.scraps.bam" format="bam" label="${tool.name} on ${on_string}: scraps"> 55 <data name="output_scrap" from_work_dir="output.scraps.bam" format="bam" label="${tool.name} on ${on_string}: Scraps">
45 <filter>readtype == '--subread'</filter> 56 <filter>readtype == '--subread'</filter>
46 </data> 57 </data>
47 <data name="output_subread" from_work_dir="output.subreads.bam" format="bam" label="${tool.name} on ${on_string}: subreads"> 58 <data name="output_subread" from_work_dir="output.subreads.bam" format="bam" label="${tool.name} on ${on_string}: Subreads">
48 <filter>readtype == '--subread'</filter> 59 <filter>readtype == '--subread'</filter>
49 </data> 60 </data>
50 <data name="output_hqregion" from_work_dir="output.hqregions.bam" format="bam" label="${tool.name} on ${on_string}: hqregions"> 61 <data name="output_hqregion" from_work_dir="output.hqregions.bam" format="bam" label="${tool.name} on ${on_string}: Hqregions">
51 <filter>readtype == '--hqregion'</filter> 62 <filter>readtype == '--hqregion'</filter>
52 </data> 63 </data>
53 <data name="output_lqregion" from_work_dir="output.lqregions.bam" format="bam" label="${tool.name} on ${on_string}: lqregions"> 64 <data name="output_lqregion" from_work_dir="output.lqregions.bam" format="bam" label="${tool.name} on ${on_string}: Lqregions">
54 <filter>readtype == '--hqregion'</filter> 65 <filter>readtype == '--hqregion'</filter>
55 </data> 66 </data>
56 <data name="output_polymeraseread" from_work_dir="output.polymerase.bam" format="bam" label="${tool.name} on ${on_string}: polymerase"> 67 <data name="output_polymeraseread" from_work_dir="output.polymerase.bam" format="bam" label="${tool.name} on ${on_string}: Polymerase">
57 <filter>readtype == '--polymeraseread'</filter> 68 <filter>readtype == '--polymeraseread'</filter>
58 </data> 69 </data>
59 </outputs> 70 </outputs>
60
61 <tests> 71 <tests>
62 <!-- source of test data: https://github.com/PacificBiosciences/PacBioTestData/tree/master/data/HdfSubreadSet/Analysis_Results/ --> 72 <!-- test data source https://github.com/PacificBiosciences/PacBioTestData/tree/master/data/HdfSubreadSet/Analysis_Results/ -->
63 <!-- #1: read type: subread --> 73
64 <test> 74 <!-- #1 subread, default -->
75 <test expect_num_outputs="2">
65 <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/> 76 <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/>
66 <param name="readtype" value="--subread"/> 77 <param name="readtype" value="--subread"/>
67 <output name="output_scrap" file="scraps.bam" compare="sim_size" delta="100"/> 78 <output name="output_scrap">
68 <output name="output_subread" file="subreads.bam" compare="sim_size" delta="100"/> 79 <assert_contents>
80 <has_size value="113578" delta="100"/>
81 </assert_contents>
82 </output>
83 <output name="output_subread">
84 <assert_contents>
85 <has_size value="242552" delta="100"/>
86 </assert_contents>
87 </output>
69 </test> 88 </test>
70 <!-- #2: read type: hqregion --> 89 <!-- #2 hqregion, default -->
71 <test> 90 <test expect_num_outputs="2">
72 <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/> 91 <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/>
73 <param name="readtype" value="--hqregion"/> 92 <param name="readtype" value="--hqregion"/>
74 <output name="output_hqregion" file="hqregions.bam" compare="sim_size" delta="100"/> 93 <output name="output_hqregion">
75 <output name="output_hqregion" file="lqregions.bam" compare="sim_size" delta="100"/> 94 <assert_contents>
95 <has_size value="232342" delta="100"/>
96 </assert_contents>
97 </output>
98 <output name="output_hqregion">
99 <assert_contents>
100 <has_size value="232342" delta="100"/>
101 </assert_contents>
102 </output>
76 </test> 103 </test>
77 <!-- #3: read type: polymeraseread --> 104 <!-- #3 polymeraseread, default -->
78 <test> 105 <test expect_num_outputs="1">
79 <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/> 106 <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/>
80 <param name="readtype" value="--polymeraseread"/> 107 <param name="readtype" value="--polymeraseread"/>
81 <output name="output_polymeraseread" file="polymerase.bam" compare="sim_size" delta="100"/> 108 <output name="output_polymeraseread">
109 <assert_contents>
110 <has_size value="333195" delta="100"/>
111 </assert_contents>
112 </output>
82 </test> 113 </test>
83 <!-- #4: read type: subread, custom parameters --> 114 <!-- #4 subread, custom -->
84 <test> 115 <test expect_num_outputs="2">
85 <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/> 116 <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/>
86 <param name="readtype" value="--subread"/> 117 <param name="readtype" value="--subread"/>
87 <param name="pulsefeatures" value="SubstitutionTag"/> 118 <param name="pulsefeatures" value="SubstitutionTag"/>
88 <param name="losslessframes" value="true"/> 119 <param name="losslessframes" value="true"/>
89 <param name="internal" value="true"/> 120 <param name="internal" value="true"/>
90 <output name="output_scrap" file="scraps_custom.bam" compare="sim_size" delta="100"/> 121 <output name="output_scrap">
91 <output name="output_subread" file="subreads_custom.bam" compare="sim_size" delta="100"/> 122 <assert_contents>
123 <has_size value="23497" delta="100"/>
124 </assert_contents>
125 </output>
126 <output name="output_subread">
127 <assert_contents>
128 <has_size value="45147" delta="100"/>
129 </assert_contents>
130 </output>
92 </test> 131 </test>
93 </tests> 132 </tests>
94 <help><![CDATA[ 133 <help><![CDATA[
95 134
96 .. class:: infomark 135 .. class:: infomark
99 138
100 bax2bam converts the legacy PacBio basecall format (bax.h5) into the BAM basecall format. 139 bax2bam converts the legacy PacBio basecall format (bax.h5) into the BAM basecall format.
101 140
102 **Input** 141 **Input**
103 142
104 bax.h5 files that should be from the same movie. 143 - Sample files that should be from the same movie (bax.h5)
105 144
106 **Output** 145 **Output**
107 146
108 A single BAM file. 147 - Converted sample (BAM)
109 148
110 .. class:: infomark 149 .. class:: infomark
111 150
112 **References** 151 **References**
113 152
114 More information can be found on the github repositories `bax2bam <https://github.com/pacificbiosciences/bax2bam/>`_ and `PacBio Bioconda <https://github.com/PacificBiosciences/pbbioconda>`_. 153 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> 154 ]]></help>
116 <citations> 155 <citations>
117 <citation type="bibtex"> 156 <citation type="bibtex">
118 @misc{PacificBiosciences2018, 157 @misc{PacificBiosciences2018,
119 author = {Pacific Biosciences}, 158 author = {Pacific Biosciences},