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Updated split_libraries_fastq
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@lparsons
lparsons committed Oct 5, 2015
1 parent 84add23 commit 28e4feb
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Showing 4 changed files with 2,075 additions and 17 deletions.
2 changes: 1 addition & 1 deletion tools/qiime1.9.0/macros.xml
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Expand Up @@ -2,7 +2,7 @@
<macros>
<xml name="requirements">
<requirements>
<requirement type="package">qiime</requirement>
<requirement type="package" version="1.9.1">qiime</requirement>
</requirements>
</xml>
<xml name="citations">
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90 changes: 74 additions & 16 deletions tools/qiime1.9.0/split_libraries_fastq.xml
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@@ -1,10 +1,17 @@
<?xml version="1.0" ?>
<tool id="split_libraries_fastq" name="split libraries fastq" version="1.9.1">
<description>This script performs demultiplexing of Fastq sequence data where barcodes and sequences are contained in two separate fastq files (common on Illumina runs).</description>
<requirements>
<requirement type="package">qiime</requirement>
</requirements>
<command>split_libraries_fastq.py
<tool id="split_libraries_fastq" name="split libraries fastq" version="1.9.1galaxy1">
<description>This script performs demultiplexing of Fastq sequence data where barcodes and sequences are contained in two separate fastq files (common on Illumina runs).</description>

<macros>
<import>macros.xml</import>
</macros>

<expand macro="requirements" />

<version_command>split_libraries_fastq.py --version</version_command>

<command><![CDATA[
split_libraries_fastq.py
#def list_dict_to_string(list_dict):
#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
#for d in list_dict[1:]:
Expand Down Expand Up @@ -81,17 +88,32 @@
--phred_offset=$phred_offset
#end if
;
compress_path.py -i split_libraries_fastq_output -o $output_dir
</command>
cp split_libraries_fastq_output/histograms.txt "$histograms"
&&
cp split_libraries_fastq_output/split_library_log.txt "$log"
&&
cp split_libraries_fastq_output/seqs.fna "$seqs"
#if $store_qual_scores:
&&
cp split_libraries_fastq_output/seqs.qual "$seqs_qual"
#end if
#if $store_demultiplexed_fastq:
&&
cp split_libraries_fastq_output/seqs.fastq "$seqs_fastq"
#end if
]]>
</command>

<inputs>
<repeat name="input_files_sequence_read_fps" optional="False" title="sequence_read_fps">
<param label="-i/--sequence_read_fps: the sequence read fastq files (comma-separated if more than one)" name="additional_input" type="data"/>
<param label="-i/--sequence_read_fps: the sequence read fastq files (comma-separated if more than one)" name="additional_input" type="data" format="fastq,fastqsanger,fastqsolexa"/>
</repeat>
<repeat name="input_files_mapping_fps" optional="True" title="mapping_fps">
<param label="-m/--mapping_fps: metadata mapping files (comma-separated if more than one) [default: None]" name="additional_input" type="data"/>
<param label="-m/--mapping_fps: metadata mapping files (comma-separated if more than one) [default: None]" name="additional_input" type="data" format="data"/>
</repeat>
<repeat name="input_files_barcode_read_fps" optional="True" title="barcode_read_fps">
<param label="-b/--barcode_read_fps: the barcode read fastq files (comma-separated if more than one) [default: None]" name="additional_input" type="data"/>
<param label="-b/--barcode_read_fps: the barcode read fastq files (comma-separated if more than one) [default: None]" name="additional_input" type="data" format="data"/>
</repeat>
<param label="--store_qual_scores: store qual strings in .qual files [default: False]" name="store_qual_scores" selected="False" type="boolean"/>
<param default="None" label="--sample_ids: comma-separated list of samples ids to be applied to all sequences, must be one per input file path (used when data is not multiplexed) [default: None]" name="sample_ids" optional="True" type="text"/>
Expand All @@ -112,10 +134,46 @@ compress_path.py -i split_libraries_fastq_output -o $output_dir
<option value="33">33</option>
<option value="64">64</option>
</param>
</inputs>
</inputs>

<outputs>
<data format="tgz" name="output_dir"/>
</outputs>
<help>
</help>
<data name="log" format="txt" label="${tool.name} on ${on_string}: log"/>
<data name="histograms" format="tabular" label="${tool.name} on ${on_string}: histograms"/>
<data name="seqs" format="fasta" label="${tool.name} on ${on_string}: sequences"/>
<data name="seqs_qual" format="qualillumina" label="${tool.name} on ${on_string}: sequence qualities">
<filter>store_qual_scores == True</filter>
</data>
<data name="seqs_fastq" format="fastqsanger" label="${tool.name} on ${on_string}: sequences (fastq)">
<filter>store_demultiplexed_fastq == True</filter>
</data>
</outputs>

<tests>
<test>
<param name="input_files_sequence_read_fps_0|additional_input" value="forward_reads.fastq"/>
<param name="input_files_mapping_fps_0|additional_input" value="map.tsv"/>
<param name="input_files_barcode_read_fps_0|additional_input" value="barcodes.fastq"/>
<param name="store_qual_scores" value="True"/>
<param name="store_demultiplexed_fastq" value="True"/>
<output name="log">
<assert_contents>
<has_line_matching expression="Total number of input sequences: 250"/>
</assert_contents>
</output>
<output name="histograms" file="split_libraries_fastq_histograms.txt"/>
<output name="seqs" file="split_libraries_fastq_seqs.fna"/>
<output name="seqs_qual" file="split_libraries_fastq_seqs.qual"/>
<output name="seqs_fastq" file="split_libraries_fastq_seqs.fastq"/>
</test>
</tests>



<help><![CDATA[
This tool performs demultiplexing of Fastq sequence data where barcodes and sequences are contained in two separate fastq files (common on Illumina runs).
]]>
</help>

<expand macro="citations" />

</tool>

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