Mercurial > repos > jdv > albacore

annotate albacore_denoise.xml @ 2:b658298e65d8 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
author jdv
date Fri, 08 Sep 2017 10:14:40 -0400
parents 0a4f83207e53
children
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0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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1 <tool id="albacore_denoise" name="Albacore de-noise" version="0.001">
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3 <description>Filter noise from barcode bins</description>
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5 <!-- ***************************************************************** -->
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7 <!--
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8 <requirements>
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9 <requirement type="package" version="1.2.6">albacore</requirement>
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10 </requirements>
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11 -->
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13 <!-- ***************************************************************** -->
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15 <version_command>echo "0.001"</version_command>
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17 <!-- ***************************************************************** -->
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19 <command detect_errors="aggressive">
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20 <![CDATA[
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22 perl $__tool_directory__/denoise.pl
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24 --table $table
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26 #if $filter.type == 'topN'
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27 --n_keep ${filter.n_keep}
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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28 #else
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29 --min_score ${filter.min_score}
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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30 --min_frac ${filter.min_frac}
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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31 #end if
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33 $remove_unclassified
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35 #for $input in $inputs
0a4f83207e53 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
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36 --input ${input}
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37 --name ${input.name}
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38 #end for
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40 --summary $summary
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42 ]]>
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43 </command>
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45 <!-- ***************************************************************** -->
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47 <inputs>
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49 <param name="inputs" type="data_collection" collection_type="list" format="fast5.tar" label="Input reads" multiple="true" />
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50 <param name="table" type="data" format="tabular" label="Read table" />
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51 <conditional name="filter">
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52 <param name="type" type="select" label="Filtering type">
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53 <option value="cutoffs" selected="true">By cutoff</option>
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54 <option value="topN">Top N bins</option>
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55 </param>
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56 <when value="cutoffs">
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57 <param name="min_score" value="70" type="float" min="0" max="100" label="Minimum average score (0-100)" />
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58 <param name="min_frac" value="0.05" type="float" min="0" label="Minimum fraction of average count" />
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59 </when>
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60 <when value="topN">
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61 <param name="n_keep" value="1" type="integer" min="1" label="Number of top bins to keep" />
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62 </when>
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63 </conditional>
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64 <param name="remove_unclassified" type="boolean" checked="true" truevalue="--remove_unclassified" falsevalue="" label="Remove unclassified reads" />
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66 </inputs>
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68 <!-- ***************************************************************** -->
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70 <outputs>
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72 <collection type="list" name="outputs" label="${tool.name} on ${on_string} (reads)">
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73 <discover_datasets pattern="(?P&lt;name&gt;.*)\.fast5\.tar\.gz$" directory="outputs" format="fast5.tar.gz" />
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74 </collection>
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76 <data name="summary" format="tabular" label="${tool.name} on ${on_string} (summary)" />
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78 </outputs>
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80 <!-- ***************************************************************** -->
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82 <tests>
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83 </tests>
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85 <!-- ***************************************************************** -->
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86
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87 <help>
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88 <![CDATA[
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89
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90 **Description**
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91
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92 This script will filter "noise" bins from the barcoded output of Albacore
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93 based on read counts and mean quality scores for each barcode bin. It can
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94 either filter the top N bins (if you know the number of barcodes in your
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95 sample) or filter based on minimum read count (as ratio to average value over
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96 all bin) and minimum average score.
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97
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98 ]]>
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99 </help>
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100
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101 <!-- ***************************************************************** -->
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102
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103 <citations>
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104 </citations>
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105
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106 </tool>