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comparison split_libraries_fastq.xml @ 0:cdd2c0176c38 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
author iuc
date Thu, 18 May 2017 09:20:51 -0400
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-1:000000000000 0:cdd2c0176c38
1 <tool id="split_libraries_fastq" name="Split fastq libraries" version="@WRAPPER_VERSION@.0">
2 <description>to performs demultiplexing of Fastq sequence data</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <version_command>split_libraries_fastq.py --version</version_command>
8 <command detect_errors="aggressive"><![CDATA[
9 split_libraries_fastq.py
10 #set $seq_files = ''
11 #set $sep = ''
12 #for $file in $sequence_read_fps
13 #set $seq_files += $sep + str($file)
14 #set $sep = ','
15 #end for
16 --sequence_read_fps '$seq_files'
17
18 -o split_libraries
19
20 #set $mapping_files = ''
21 #set $sep = ''
22 #for $file in $mapping_fps
23 #set $mapping_files += $sep + str($file)
24 #set $sep = ','
25 #end for
26 --mapping_fps '$mapping_files'
27
28 #set $barcode_files = ''
29 #set $sep = ''
30 #for $file in $barcode_read_fps
31 #set $barcode_files += $sep + str($file)
32 #set $sep = ','
33 #end for
34 --barcode_read_fps '$barcode_files'
35
36 $store_qual_scores
37 #if str($sample_ids):
38 --sample_ids '$sample_ids'
39 #end if
40 $store_demultiplexed_fastq
41 $retain_unassigned_reads
42
43 --max_bad_run_length '$max_bad_run_length'
44 --min_per_read_length_fraction '$min_per_read_length_fraction'
45 --sequence_max_n '$sequence_max_n'
46 --start_seq_id '$start_seq_id'
47 $rev_comp_barcode
48 $rev_comp_mapping_barcodes
49 $rev_comp
50 --phred_quality_threshold '$phred_quality_threshold'
51 #if str( $barcode.barcode_type ) != "custom_length"
52 --barcode_type '$barcode.barcode_type'
53 #else
54 --barcode_type '$barcode.barcode_length'
55 #end if
56 --max_barcode_errors '$max_barcode_errors'
57 $phred_offset
58 ]]></command>
59 <inputs>
60 <param argument="--sequence_read_fps" type="data" format="fastq,fastqsanger,fastqsolexa" label="Input fastq files" multiple="True"/>
61 <param argument="--mapping_fps" type="data" format="txt,tabular,tsv,csv" label="Metadata mapping files (optional)" multiple="True" optional="True"/>
62 <param argument="--barcode_read_fps" type="data" format="fastq,fastqsanger,fastqsolexa" label="Barcode read files (optional)" multiple="True" optional="True"/>
63 <param argument="--store_qual_scores" type="boolean" label="Store quality strings in files?" truevalue="--store_qual_scores" falsevalue="" checked="False"/>
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)"/>
65 <param argument="--store_demultiplexed_fastq" type="boolean" label="Write demultiplexed fastq files?" truevalue="--store_demultiplexed_fastq" falsevalue="" checked="False"/>
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'"/>
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"/>
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"/>
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"/>
70 <param argument="--start_seq_id" type="integer" value="0" label="Start seq_ids as ascending integers beginning with start_seq_id"/>
71 <param argument="--rev_comp_barcode" type="boolean" label="Reverse complement barcode reads before lookup?" truevalue="--rev_comp_barcode" falsevalue="" checked="False"/>
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"/>
73 <param argument="--rev_comp" type="boolean" label="Reverse omplement sequence before writing to output file?" truevalue="--rev_comp" falsevalue="" checked="False"/>
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"/>
75 <conditional name="barcode">
76 <param argument="--barcode_type" type="select" label="Type of barcode">
77 <option value="hamming_8">hamming_8</option>
78 <option value="golay_12" selected="true">golay_12</option>
79 <option value="variable_length">variable_length (disable any barcode correction)</option>
80 <option value="custom_length">Custom length</option>
81 <option value="not-barcoded">Data not barcoded</option>
82 </param>
83 <when value="hamming_8"/>
84 <when value="golay_12"/>
85 <when value="variable_length"/>
86 <when value="custom_length">
87 <param name="barcode_length" type="integer" value="4" label="Barcode length"/>
88 </when>
89 <when value="not-barcoded"/>
90 </conditional>
91 <param argument="--max_barcode_errors" type="float" value="1.5" label="Maximum number of errors in barcode"/>
92 <param argument="--phred_offset" type="select" label="Ascii offset to use when decoding phred scores">
93 <option value="--phred_offset 33">33</option>
94 <option value="--phred_offset 64">64</option>
95 <option value="" selected="true">Automatically determined</option>
96 </param>
97 </inputs>
98 <outputs>
99 <data name="log" format="txt" from_work_dir="split_libraries/split_library_log.txt" label="${tool.name} on ${on_string}: log"/>
100 <data name="histograms" format="tabular" from_work_dir="split_libraries/histograms.txt" label="${tool.name} on ${on_string}: histograms"/>
101 <data name="seqs" format="fasta" from_work_dir="split_libraries/seqs.fna" label="${tool.name} on ${on_string}: sequences"/>
102 <data name="seqs_qual" format="qual" from_work_dir="split_libraries/seqs.qual" label="${tool.name} on ${on_string}: sequence qualities">
103 <filter>store_qual_scores is True</filter>
104 </data>
105 <data name="seqs_fastq" format="fastq" from_work_dir="split_libraries/seqs.fastq" label="${tool.name} on ${on_string}: demultiplexed sequences (fastq)">
106 <filter>store_demultiplexed_fastq is True</filter>
107 </data>
108 </outputs>
109 <tests>
110 <test>
111 <param name="sequence_read_fps" value="split_libraries_fastq/forward_reads.fastq"/>
112 <param name="mapping_fps" value="split_libraries_fastq/map.tsv"/>
113 <param name="barcode_read_fps" value="split_libraries_fastq/barcodes.fastq"/>
114 <param name="store_qual_scores" value="--store_qual_scores"/>
115 <param name="store_demultiplexed_fastq" value="--store_demultiplexed_fastq"/>
116 <param name="retain_unassigned_reads" value=""/>
117 <param name="max_bad_run_length" value="3"/>
118 <param name="min_per_read_length_fraction" value="0.75"/>
119 <param name="sequence_max_n" value="0"/>
120 <param name="start_seq_id" value="0"/>
121 <param name="rev_comp_barcode" value=""/>
122 <param name="rev_comp_mapping_barcodes" value=""/>
123 <param name="rev_comp" value=""/>
124 <param name="barcode_selector" value="golay_12"/>
125 <param name="max_barcode_errors" value="1.5"/>
126 <param name="phred_offset" value=""/>
127 <output name="log">
128 <assert_contents>
129 <has_line line="Median sequence length: 132.50"></has_line>
130 <has_text text="L1S76"></has_text>
131 <has_text text="L1S281"></has_text>
132 <has_text text="L1S8"></has_text>
133 </assert_contents>
134 </output>
135 <output name="seqs" file="split_libraries_fastq/sequences.fasta"/>
136 <output name="histograms" file="split_libraries_fastq/histograms.tabular"/>
137 <output name="seqs_qual" file="split_libraries_fastq/sequence_qualities.qual"/>
138 <output name="seqs_fastq" file="split_libraries_fastq/demultiplexed_sequences.fastq"/>
139 </test>
140 </tests>
141 <help><![CDATA[
142 **What it does**
143
144 This tool performs demultiplexing of Fastq sequence data where barcodes and sequences are contained in two separate fastq files (common on Illumina runs).
145
146 More information about this tool is available on
147 `QIIME documentation <http://qiime.org/scripts/split_libraries_fastq.html>`_.
148 ]]></help>
149 <citations>
150 <expand macro="citations"/>
151 </citations>
152 </tool>