annotate presto_buildconsensus.xml @ 0:7c7df98db5a9 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
author iuc
date Wed, 30 May 2018 15:37:30 -0400
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7c7df98db5a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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1 <tool id="presto_buildconsensus" name="pRESTO BuildConsensus" version="@PRESTO_VERSION@">
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2 <description>Builds a consensus sequence for each set of input sequences</description>
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3
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4 <macros>
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5 <import>presto_macros.xml</import>
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6 </macros>
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7
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8 <expand macro="requirements"/>
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9
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10 <version_command>BuildConsensus.py --version</version_command>
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11 <command detect_errors="exit_code"><![CDATA[
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12 ln -s '$fastq_in' in.fastq &&
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13 BuildConsensus.py
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14 --nproc "\${GALAXY_SLOTS:-1}"
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15 -s in.fastq
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16 -n '$n'
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17 --bf '$bf'
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18 -q '$q'
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19 --freq '$freq'
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20 #if $maxgap
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21 --maxgap '$maxgap'
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22 #end if
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23 #if $pf
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24 --pf '$pf'
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25 #end if
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26 #if $prcons
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27 --prcons '$prcons'
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28 #end if
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29 #if $cf
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30 --cf $cf
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31 #end if
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32 #if $act
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33 --act $act
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34 #end if
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35 $dep
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36
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37 #if $filtering.filter == "diversity"
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38 --maxdiv '$filtering.maxdiv'
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39 #end if
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40 #if $filtering.filter == "error"
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41 --maxerror '$filtering.maxerror'
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42 #end if
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43
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44 --outname=tmp
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45 #if $capture_log
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46 --log '$log_out'
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47 #end if
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48 ]]></command>
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49
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50 <inputs>
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51 <param argument="-s" name="fastq_in" type="data" format="fastq" label="Input FASTQ file" help="FASTQ file of sequences with barcodes/UMIs in an annotation."/>
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52 <param argument="-n" type="integer" value="1" label="Min Count" help="Minimum number of squences to form a valid consensus."/>
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53 <param argument="--bf" type="text" value="BARCODE" label="Barcode Field" help="Name of the annotation field which contains the barcode/UMI sequence."/>
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54 <param argument="-q" type="integer" value="0" label="Min Quality" help="Minimum quality under which an ambiguous character is assigned to a consensus base."/>
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55 <param argument="--freq" type="float" value="0.6" label="Min Frequency" help="At a given position the fraction of basecalls required to agree to output an unambiguous base."/>
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56 <param argument="--maxgap" type="float" value="" optional="true" label="Max Gap Fraction" help="Positions with greater than this fraction of gaps are deleted from the consensus."/>
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57 <param argument="--pf" type="text" value="" optional="true" label="Primer Field" help="Name of the annotation field which contains the primer sequence (often PRIMER)."/>
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58 <param argument="--prcons" type="float" value="" optional="true" label="Primer Consensus Frequency" help="Specify to define a minimum primer frequency required to assign a consensus primer, and filter out sequences with minority primers from the consensus building step."/>
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59 <param argument="--cf" type="text" value="" optional="true" label="Copy Fields" help="Zero or more space-separated annotations to copy from input sequences to consensus sequences.">
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60 <expand macro="text-regex-validator"/>
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61 </param>
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62 <param argument="--act" type="text" value="" optional="true" label="Copy Actions" help="Space-separated list of actions to take on copied annotations. Must be of same length as Copy Fields. Options are: min,max,sum,set,majority.">
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63 <expand macro="text-regex-validator"/>
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64 </param>
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65 <param argument="--dep" type="boolean" value="false" truevalue="--dep" falsevalue="" label="Dependent Model" help="Specify to calculate consensus quality with a non-independence assumption."/>
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66 <expand macro="presto-log-param"/>
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67
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68 <conditional name="filtering">
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69 <param name="filter" type="select" label="Filtering Strategy">
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70 <option value="none">No filtering of consensus reads.</option>
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71 <option value="diversity">Filter by diversity (average pairwise error rate of input reads).</option>
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72 <option value="error">Filters by error rate of input reads vs. consensus.</option>
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73 </param>
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74 <when value="diversity">
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75 <param argument="--maxdiv" type="float" value="" label="Max Diversity" help="Remove consensus reads with average pairwise error between input reads above this cutoff [0-1]."/>
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76 </when>
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77 <when value="error">
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78 <param argument="--maxerror" type="float" value="" label="Max Error" help="Remove consensus reads with average error vs. input reads above this cutoff [0-1]."/>
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79 </when>
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80 <when value="none"/>
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81 </conditional>
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82 </inputs>
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83
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84 <outputs>
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85 <data name="fastq_out" format="fastq" from_work_dir="tmp_consensus-pass.fastq"/>
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86 <expand macro="presto-log-output"/>
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87 </outputs>
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88
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89 <tests>
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90 <test>
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91 <param name="fastq_in" value="presto_buildconsensus_test_input.fastq"/>
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92 <param name="n" value="2"/>
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93 <param name="pf" value="PRIMER"/>
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94 <param name="maxgap" value="0.5"/>
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95 <param name="prcons" value="0.6"/>
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96 <param name="filter" value="error"/>
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97 <param name="maxerror" value="0.1"/>
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98 <output name="fastq_out" file="presto_buildconsensus_test_maxerror_output.fastq" sort="true"/>
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99 </test>
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100 <test>
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101 <param name="fastq_in" value="presto_buildconsensus_test_input.fastq"/>
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102 <param name="n" value="2"/>
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103 <param name="pf" value="PRIMER"/>
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104 <param name="maxgap" value="0.5"/>
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105 <param name="prcons" value="0.6"/>
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106 <param name="filter" value="diversity"/>
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107 <param name="maxdiv" value="0.05"/>
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108 <output name="fastq_out" file="presto_buildconsensus_test_maxdiv_output.fastq" sort="true"/>
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109 </test>
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110 </tests>
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111
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112 <help><![CDATA[
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113 Builds a consensus sequence for each set of input sequences.
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114
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115 See the `pRESTO online help <@PRESTO_URL_BASE@/BuildConsensus.html>`_ for more information.
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116
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117 @HELP_NOTE@
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118 ]]></help>
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119 <expand macro="citations" />
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120 </tool>