Mercurial > repos > iuc > split_libraries_fastq

annotate split_libraries_fastq.xml @ 1:4ed38a03aac6 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Fri, 19 May 2017 03:19:56 -0400
parents cdd2c0176c38
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cdd2c0176c38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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1 <tool id="split_libraries_fastq" name="Split fastq libraries" version="@WRAPPER_VERSION@.0">
cdd2c0176c38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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2 <description>to performs demultiplexing of Fastq sequence data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <version_command>split_libraries_fastq.py --version</version_command>
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8 <command detect_errors="aggressive"><![CDATA[
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9 split_libraries_fastq.py
cdd2c0176c38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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10 #set $seq_files = ''
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11 #set $sep = ''
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12 #for $file in $sequence_read_fps
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13 #set $seq_files += $sep + str($file)
cdd2c0176c38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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14 #set $sep = ','
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15 #end for
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16 --sequence_read_fps '$seq_files'
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17
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18 -o split_libraries
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20 #set $mapping_files = ''
cdd2c0176c38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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21 #set $sep = ''
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22 #for $file in $mapping_fps
cdd2c0176c38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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23 #set $mapping_files += $sep + str($file)
cdd2c0176c38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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24 #set $sep = ','
cdd2c0176c38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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25 #end for
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26 --mapping_fps '$mapping_files'
cdd2c0176c38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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27
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28 #set $barcode_files = ''
cdd2c0176c38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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29 #set $sep = ''
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30 #for $file in $barcode_read_fps
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31 #set $barcode_files += $sep + str($file)
cdd2c0176c38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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32 #set $sep = ','
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33 #end for
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34 --barcode_read_fps '$barcode_files'
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35
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36 $store_qual_scores
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37 #if str($sample_ids):
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38 --sample_ids '$sample_ids'
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39 #end if
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40 $store_demultiplexed_fastq
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41 $retain_unassigned_reads
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42
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43 --max_bad_run_length '$max_bad_run_length'
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44 --min_per_read_length_fraction '$min_per_read_length_fraction'
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45 --sequence_max_n '$sequence_max_n'
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46 --start_seq_id '$start_seq_id'
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47 $rev_comp_barcode
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48 $rev_comp_mapping_barcodes
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49 $rev_comp
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50 --phred_quality_threshold '$phred_quality_threshold'
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51 #if str( $barcode.barcode_type ) != "custom_length"
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52 --barcode_type '$barcode.barcode_type'
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53 #else
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54 --barcode_type '$barcode.barcode_length'
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55 #end if
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56 --max_barcode_errors '$max_barcode_errors'
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57 $phred_offset
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58 ]]></command>
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59 <inputs>
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60 <param argument="--sequence_read_fps" type="data" format="fastq,fastqsanger,fastqsolexa" label="Input fastq files" multiple="True"/>
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61 <param argument="--mapping_fps" type="data" format="txt,tabular,tsv,csv" label="Metadata mapping files (optional)" multiple="True" optional="True"/>
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62 <param argument="--barcode_read_fps" type="data" format="fastq,fastqsanger,fastqsolexa" label="Barcode read files (optional)" multiple="True" optional="True"/>
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63 <param argument="--store_qual_scores" type="boolean" label="Store quality strings in files?" truevalue="--store_qual_scores" falsevalue="" checked="False"/>
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64 <param argument="--sample_ids" type="text" label="Comma-separated list of samples ids to be applied to all sequences (optional)" optional="True" help="It must be one per input file path (used when data is not multiplexed)"/>
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65 <param argument="--store_demultiplexed_fastq" type="boolean" label="Write demultiplexed fastq files?" truevalue="--store_demultiplexed_fastq" falsevalue="" checked="False"/>
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66 <param argument="--retain_unassigned_reads" type="boolean" label="Retain sequences which don’t map to a barcode in the mapping file?" truevalue="--retain_unassigned_reads" falsevalue="" checked="False" help="Sample ID will be 'Unassigned'"/>
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67 <param argument="--max_bad_run_length" type="integer" value="3" label="Maximum number of consecutive low quality base calls allowed before truncating a read"/>
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68 <param argument="--min_per_read_length_fraction" type="float" value="0.75" label="Minimum number of consecutive high quality base calls to include a read (per single end read) as a fraction of the input read length"/>
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69 <param argument="--sequence_max_n" type="integer" value="0" label="Maximum number of N characters allowed in a sequence to retain it" help="This is applied after quality trimming, and is total over combined paired end reads if applicable"/>
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70 <param argument="--start_seq_id" type="integer" value="0" label="Start seq_ids as ascending integers beginning with start_seq_id"/>
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71 <param argument="--rev_comp_barcode" type="boolean" label="Reverse complement barcode reads before lookup?" truevalue="--rev_comp_barcode" falsevalue="" checked="False"/>
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72 <param argument="--rev_comp_mapping_barcodes" type="boolean" label="Reverse complement barcode in mapping before lookup?" truevalue="--rev_comp_mapping_barcodes" falsevalue="" checked="False" help="It is useful if barcodes in mapping file are reverse complements of golay codes"/>
cdd2c0176c38 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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73 <param argument="--rev_comp" type="boolean" label="Reverse omplement sequence before writing to output file?" truevalue="--rev_comp" falsevalue="" checked="False"/>
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74 <param argument="--phred_quality_threshold" type="integer" value="3" label="Maximum unacceptable Phred quality score" help="E.g., for Q20 and better, 19 must be specified"/>
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75 <conditional name="barcode">
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76 <param argument="--barcode_type" type="select" label="Type of barcode">
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77 <option value="hamming_8">hamming_8</option>
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78 <option value="golay_12" selected="true">golay_12</option>
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79 <option value="variable_length">variable_length (disable any barcode correction)</option>
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80 <option value="custom_length">Custom length</option>
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81 <option value="not-barcoded">Data not barcoded</option>
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82 </param>
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83 <when value="hamming_8"/>
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84 <when value="golay_12"/>
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85 <when value="variable_length"/>
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86 <when value="custom_length">
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87 <param name="barcode_length" type="integer" value="4" label="Barcode length"/>
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88 </when>
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89 <when value="not-barcoded"/>
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90 </conditional>
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91 <param argument="--max_barcode_errors" type="float" value="1.5" label="Maximum number of errors in barcode"/>
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92 <param argument="--phred_offset" type="select" label="Ascii offset to use when decoding phred scores">
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93 <option value="--phred_offset 33">33</option>
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94 <option value="--phred_offset 64">64</option>
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95 <option value="" selected="true">Automatically determined</option>
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96 </param>
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97 </inputs>
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98 <outputs>
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99 <data name="log" format="txt" from_work_dir="split_libraries/split_library_log.txt" label="${tool.name} on ${on_string}: log"/>
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100 <data name="histograms" format="tabular" from_work_dir="split_libraries/histograms.txt" label="${tool.name} on ${on_string}: histograms"/>
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101 <data name="seqs" format="fasta" from_work_dir="split_libraries/seqs.fna" label="${tool.name} on ${on_string}: sequences"/>
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102 <data name="seqs_qual" format="qual" from_work_dir="split_libraries/seqs.qual" label="${tool.name} on ${on_string}: sequence qualities">
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103 <filter>store_qual_scores is True</filter>
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104 </data>
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105 <data name="seqs_fastq" format="fastq" from_work_dir="split_libraries/seqs.fastq" label="${tool.name} on ${on_string}: demultiplexed sequences (fastq)">
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106 <filter>store_demultiplexed_fastq is True</filter>
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107 </data>
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108 </outputs>
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109 <tests>
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110 <test>
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111 <param name="sequence_read_fps" value="split_libraries_fastq/forward_reads.fastq"/>
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112 <param name="mapping_fps" value="split_libraries_fastq/map.tsv"/>
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113 <param name="barcode_read_fps" value="split_libraries_fastq/barcodes.fastq"/>
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114 <param name="store_qual_scores" value="--store_qual_scores"/>
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115 <param name="store_demultiplexed_fastq" value="--store_demultiplexed_fastq"/>
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116 <param name="retain_unassigned_reads" value=""/>
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117 <param name="max_bad_run_length" value="3"/>
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118 <param name="min_per_read_length_fraction" value="0.75"/>
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119 <param name="sequence_max_n" value="0"/>
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120 <param name="start_seq_id" value="0"/>
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121 <param name="rev_comp_barcode" value=""/>
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122 <param name="rev_comp_mapping_barcodes" value=""/>
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123 <param name="rev_comp" value=""/>
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124 <param name="barcode_selector" value="golay_12"/>
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125 <param name="max_barcode_errors" value="1.5"/>
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126 <param name="phred_offset" value=""/>
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127 <output name="log">
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128 <assert_contents>
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129 <has_line line="Median sequence length: 132.50"></has_line>
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130 <has_text text="L1S76"></has_text>
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131 <has_text text="L1S281"></has_text>
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132 <has_text text="L1S8"></has_text>
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133 </assert_contents>
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134 </output>
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135 <output name="seqs" file="split_libraries_fastq/sequences.fasta"/>
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136 <output name="histograms" file="split_libraries_fastq/histograms.tabular"/>
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137 <output name="seqs_qual" file="split_libraries_fastq/sequence_qualities.qual"/>
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138 <output name="seqs_fastq" file="split_libraries_fastq/demultiplexed_sequences.fastq"/>
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139 </test>
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140 </tests>
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141 <help><![CDATA[
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142 **What it does**
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143
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144 This tool performs demultiplexing of Fastq sequence data where barcodes and sequences are contained in two separate fastq files (common on Illumina runs).
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145
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146 More information about this tool is available on
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147 `QIIME documentation <http://qiime.org/scripts/split_libraries_fastq.html>`_.
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148 ]]></help>
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149 <citations>
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150 <expand macro="citations"/>
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151 </citations>
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152 </tool>