Mercurial > repos > iuc > bax2bam
comparison bax2bam.xml @ 2:5bd67e012d54 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 958bbd9e30ae4d320f872f1ab5e1bacfb28b1a00"
author | iuc |
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date | Sat, 17 Apr 2021 10:41:00 +0000 |
parents | ee356d7a5518 |
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1:ee356d7a5518 | 2:5bd67e012d54 |
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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}, |