Mercurial > repos > iuc > split_libraries_fastq
diff split_libraries_fastq.xml @ 0:6f55444df744 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
| author | iuc |
|---|---|
| date | Thu, 18 May 2017 09:37:08 -0400 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/split_libraries_fastq.xml Thu May 18 09:37:08 2017 -0400 @@ -0,0 +1,152 @@ +<tool id="split_libraries_fastq" name="Split fastq libraries" version="@WRAPPER_VERSION@.0"> + <description>to performs demultiplexing of Fastq sequence data</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <version_command>split_libraries_fastq.py --version</version_command> + <command detect_errors="aggressive"><![CDATA[ + split_libraries_fastq.py + #set $seq_files = '' + #set $sep = '' + #for $file in $sequence_read_fps + #set $seq_files += $sep + str($file) + #set $sep = ',' + #end for + --sequence_read_fps '$seq_files' + + -o split_libraries + + #set $mapping_files = '' + #set $sep = '' + #for $file in $mapping_fps + #set $mapping_files += $sep + str($file) + #set $sep = ',' + #end for + --mapping_fps '$mapping_files' + + #set $barcode_files = '' + #set $sep = '' + #for $file in $barcode_read_fps + #set $barcode_files += $sep + str($file) + #set $sep = ',' + #end for + --barcode_read_fps '$barcode_files' + + $store_qual_scores + #if str($sample_ids): + --sample_ids '$sample_ids' + #end if + $store_demultiplexed_fastq + $retain_unassigned_reads + + --max_bad_run_length '$max_bad_run_length' + --min_per_read_length_fraction '$min_per_read_length_fraction' + --sequence_max_n '$sequence_max_n' + --start_seq_id '$start_seq_id' + $rev_comp_barcode + $rev_comp_mapping_barcodes + $rev_comp + --phred_quality_threshold '$phred_quality_threshold' + #if str( $barcode.barcode_type ) != "custom_length" + --barcode_type '$barcode.barcode_type' + #else + --barcode_type '$barcode.barcode_length' + #end if + --max_barcode_errors '$max_barcode_errors' + $phred_offset + ]]></command> + <inputs> + <param argument="--sequence_read_fps" type="data" format="fastq,fastqsanger,fastqsolexa" label="Input fastq files" multiple="True"/> + <param argument="--mapping_fps" type="data" format="txt,tabular,tsv,csv" label="Metadata mapping files (optional)" multiple="True" optional="True"/> + <param argument="--barcode_read_fps" type="data" format="fastq,fastqsanger,fastqsolexa" label="Barcode read files (optional)" multiple="True" optional="True"/> + <param argument="--store_qual_scores" type="boolean" label="Store quality strings in files?" truevalue="--store_qual_scores" falsevalue="" checked="False"/> + <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)"/> + <param argument="--store_demultiplexed_fastq" type="boolean" label="Write demultiplexed fastq files?" truevalue="--store_demultiplexed_fastq" falsevalue="" checked="False"/> + <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'"/> + <param argument="--max_bad_run_length" type="integer" value="3" label="Maximum number of consecutive low quality base calls allowed before truncating a read"/> + <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"/> + <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"/> + <param argument="--start_seq_id" type="integer" value="0" label="Start seq_ids as ascending integers beginning with start_seq_id"/> + <param argument="--rev_comp_barcode" type="boolean" label="Reverse complement barcode reads before lookup?" truevalue="--rev_comp_barcode" falsevalue="" checked="False"/> + <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"/> + <param argument="--rev_comp" type="boolean" label="Reverse omplement sequence before writing to output file?" truevalue="--rev_comp" falsevalue="" checked="False"/> + <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"/> + <conditional name="barcode"> + <param argument="--barcode_type" type="select" label="Type of barcode"> + <option value="hamming_8">hamming_8</option> + <option value="golay_12" selected="true">golay_12</option> + <option value="variable_length">variable_length (disable any barcode correction)</option> + <option value="custom_length">Custom length</option> + <option value="not-barcoded">Data not barcoded</option> + </param> + <when value="hamming_8"/> + <when value="golay_12"/> + <when value="variable_length"/> + <when value="custom_length"> + <param name="barcode_length" type="integer" value="4" label="Barcode length"/> + </when> + <when value="not-barcoded"/> + </conditional> + <param argument="--max_barcode_errors" type="float" value="1.5" label="Maximum number of errors in barcode"/> + <param argument="--phred_offset" type="select" label="Ascii offset to use when decoding phred scores"> + <option value="--phred_offset 33">33</option> + <option value="--phred_offset 64">64</option> + <option value="" selected="true">Automatically determined</option> + </param> + </inputs> + <outputs> + <data name="log" format="txt" from_work_dir="split_libraries/split_library_log.txt" label="${tool.name} on ${on_string}: log"/> + <data name="histograms" format="tabular" from_work_dir="split_libraries/histograms.txt" label="${tool.name} on ${on_string}: histograms"/> + <data name="seqs" format="fasta" from_work_dir="split_libraries/seqs.fna" label="${tool.name} on ${on_string}: sequences"/> + <data name="seqs_qual" format="qual" from_work_dir="split_libraries/seqs.qual" label="${tool.name} on ${on_string}: sequence qualities"> + <filter>store_qual_scores is True</filter> + </data> + <data name="seqs_fastq" format="fastq" from_work_dir="split_libraries/seqs.fastq" label="${tool.name} on ${on_string}: demultiplexed sequences (fastq)"> + <filter>store_demultiplexed_fastq is True</filter> + </data> + </outputs> + <tests> + <test> + <param name="sequence_read_fps" value="split_libraries_fastq/forward_reads.fastq"/> + <param name="mapping_fps" value="split_libraries_fastq/map.tsv"/> + <param name="barcode_read_fps" value="split_libraries_fastq/barcodes.fastq"/> + <param name="store_qual_scores" value="--store_qual_scores"/> + <param name="store_demultiplexed_fastq" value="--store_demultiplexed_fastq"/> + <param name="retain_unassigned_reads" value=""/> + <param name="max_bad_run_length" value="3"/> + <param name="min_per_read_length_fraction" value="0.75"/> + <param name="sequence_max_n" value="0"/> + <param name="start_seq_id" value="0"/> + <param name="rev_comp_barcode" value=""/> + <param name="rev_comp_mapping_barcodes" value=""/> + <param name="rev_comp" value=""/> + <param name="barcode_selector" value="golay_12"/> + <param name="max_barcode_errors" value="1.5"/> + <param name="phred_offset" value=""/> + <output name="log"> + <assert_contents> + <has_line line="Median sequence length: 132.50"></has_line> + <has_text text="L1S76"></has_text> + <has_text text="L1S281"></has_text> + <has_text text="L1S8"></has_text> + </assert_contents> + </output> + <output name="seqs" file="split_libraries_fastq/sequences.fasta"/> + <output name="histograms" file="split_libraries_fastq/histograms.tabular"/> + <output name="seqs_qual" file="split_libraries_fastq/sequence_qualities.qual"/> + <output name="seqs_fastq" file="split_libraries_fastq/demultiplexed_sequences.fastq"/> + </test> + </tests> + <help><![CDATA[ +**What it does** + +This tool performs demultiplexing of Fastq sequence data where barcodes and sequences are contained in two separate fastq files (common on Illumina runs). + +More information about this tool is available on +`QIIME documentation <http://qiime.org/scripts/split_libraries_fastq.html>`_. + ]]></help> + <citations> + <expand macro="citations"/> + </citations> +</tool>