Mercurial > repos > iuc > bax2bam

annotate bax2bam.xml @ 1:ee356d7a5518 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
author iuc
date Thu, 28 Nov 2019 15:49:50 -0500
parents 4445939cacc9
children 5bd67e012d54
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4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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1 <?xml version="1.0"?>
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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2 <tool id="bax2bam" name="bax2bam" version="@TOOL_VERSION@+@WRAPPER_VERSION@">
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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3 <description>converts PacBio basecall format (bax.h5) into BAM</description>
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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4 <macros>
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5 <import>macros.xml</import>
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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6 </macros>
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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7 <expand macro="requirements"/>
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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8 <stdio></stdio>
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9 <command detect_errors="exit_code"><![CDATA[
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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10 bax2bam
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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11 #for $file in $files
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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12 '$file'
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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13 #end for
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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14 -o output
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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15 $readtype
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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16 #if $pulsefeatures
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17 --pulsefeatures=$pulsefeatures
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18 #end if
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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19 $losslessframes
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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20 $internal
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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21 ]]></command>
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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22 <inputs>
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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23 <param name="files" type="data" format="h5" multiple="true" label="Files" help="Should be from the same movie."/>
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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24 <param name="readtype" type="select" label="Output read type" help="">
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25 <option value="--subread">subread</option>
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26 <option value="--hqregion">hqregion</option>
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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27 <option value="--polymeraseread">polymeraseread</option>
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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28 </param>
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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29 <param argument="--pulsefeatures" type="select" multiple="true" label="Select pulse features in the output BAM." help="">
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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30 <option value="DeletionQV" selected="true">dq - DeletionQV</option>
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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31 <option value="DeletionTag" selected="true">dt - DeletionTag</option>
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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32 <option value="InsertionQV" selected="true">iq - InsertionQV</option>
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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33 <option value="IPD" selected="true">ip - IPD</option>
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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34 <option value="PulseWidth" selected="true">pw - PulseWidth</option>
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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35 <option value="MergeQV" selected="true">mq - MergeQV</option>
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36 <option value="SubstitutionQV" selected="true">sq - SubstitutionQV</option>
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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37 <option value="SubstitutionTag" selected="false">st - SubstitutionTag</option>
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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38 </param>
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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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."/>
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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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."/>
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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41 </inputs>
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42
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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43 <outputs>
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44 <data name="output_scrap" from_work_dir="output.scraps.bam" format="bam" label="${tool.name} on ${on_string}: scraps">
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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45 <filter>readtype == '--subread'</filter>
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46 </data>
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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47 <data name="output_subread" from_work_dir="output.subreads.bam" format="bam" label="${tool.name} on ${on_string}: subreads">
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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48 <filter>readtype == '--subread'</filter>
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49 </data>
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50 <data name="output_hqregion" from_work_dir="output.hqregions.bam" format="bam" label="${tool.name} on ${on_string}: hqregions">
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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51 <filter>readtype == '--hqregion'</filter>
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52 </data>
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53 <data name="output_lqregion" from_work_dir="output.lqregions.bam" format="bam" label="${tool.name} on ${on_string}: lqregions">
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54 <filter>readtype == '--hqregion'</filter>
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55 </data>
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56 <data name="output_polymeraseread" from_work_dir="output.polymerase.bam" format="bam" label="${tool.name} on ${on_string}: polymerase">
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57 <filter>readtype == '--polymeraseread'</filter>
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58 </data>
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59 </outputs>
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60
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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61 <tests>
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62 <!-- source of test data: https://github.com/PacificBiosciences/PacBioTestData/tree/master/data/HdfSubreadSet/Analysis_Results/ -->
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63 <!-- #1: read type: subread -->
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64 <test>
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65 <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/>
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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66 <param name="readtype" value="--subread"/>
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67 <output name="output_scrap" file="scraps.bam" compare="sim_size" delta="100"/>
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68 <output name="output_subread" file="subreads.bam" compare="sim_size" delta="100"/>
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69 </test>
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70 <!-- #2: read type: hqregion -->
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71 <test>
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72 <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/>
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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73 <param name="readtype" value="--hqregion"/>
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74 <output name="output_hqregion" file="hqregions.bam" compare="sim_size" delta="100"/>
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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75 <output name="output_hqregion" file="lqregions.bam" compare="sim_size" delta="100"/>
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76 </test>
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77 <!-- #3: read type: polymeraseread -->
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78 <test>
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79 <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/>
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80 <param name="readtype" value="--polymeraseread"/>
0
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81 <output name="output_polymeraseread" file="polymerase.bam" compare="sim_size" delta="100"/>
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82 </test>
4445939cacc9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
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83 <!-- #4: read type: subread, custom parameters -->
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84 <test>
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85 <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/>
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86 <param name="readtype" value="--subread"/>
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87 <param name="pulsefeatures" value="SubstitutionTag"/>
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88 <param name="losslessframes" value="true"/>
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89 <param name="internal" value="true"/>
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90 <output name="output_scrap" file="scraps_custom.bam" compare="sim_size" delta="100"/>
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91 <output name="output_subread" file="subreads_custom.bam" compare="sim_size" delta="100"/>
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92 </test>
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93 </tests>
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94 <help><![CDATA[
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95
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96 .. class:: infomark
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97
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98 **What it does**
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99
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100 bax2bam converts the legacy PacBio basecall format (bax.h5) into the BAM basecall format.
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101
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102 **Input**
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103
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104 bax.h5 files that should be from the same movie.
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105
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106 **Output**
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107
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108 A single BAM file.
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109
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110 .. class:: infomark
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111
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112 **References**
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113
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114 More information can be found on the github repositories `bax2bam <https://github.com/pacificbiosciences/bax2bam/>`_ and `PacBio Bioconda <https://github.com/PacificBiosciences/pbbioconda>`_.
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115 ]]></help>
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116 <citations>
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117 <citation type="bibtex">
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118 @misc{PacificBiosciences2018,
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119 author = {Pacific Biosciences},
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120 year = {2018},
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121 title = {bax2bam},
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122 publisher = {GitHub},
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123 journal = {GitHub repository},
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124 url = {https://github.com/pacificbiosciences/bax2bam/},
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125 }
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126 </citation>
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127 </citations>
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128 </tool>