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view fastq_paired_end_interlacer.xml @ 4:49b7bc41c7b0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
author | iuc |
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date | Wed, 19 Feb 2020 16:57:03 +0000 |
parents | a59c6f7b14c3 |
children | 15fab8bda4e3 |
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<tool id="fastq_paired_end_interlacer" name="FASTQ interlacer" version="1.2.0.1+galaxy0"> <description>on paired end reads</description> <edam_topics> <edam_topic>topic_0622</edam_topic> </edam_topics> <edam_operations> <edam_operation>operation_3436</edam_operation> </edam_operations> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command><![CDATA[ gx-fastq-paired-end-interlacer #if $reads.reads_selector == 'paired' '${reads.input1_file}' ${reads.input1_file.extension[len('fastq'):]} '${reads.input2_file}' ${reads.input2_file.extension[len('fastq'):]} '$outfile_pairs' '$outfile_singles' #else '${reads.reads_coll.forward}' ${reads.reads_coll.forward.extension[len('fastq'):]} '${reads.reads_coll.reverse}' ${reads.reads_coll.reverse.extension[len('fastq'):]} '$outfile_pairs_from_coll' '$outfile_singles_from_coll' #end if ]]></command> <inputs> <conditional name="reads"> <param name="reads_selector" type="select" label="Type of paired-end datasets"> <option value="paired">2 separate datasets</option> <option value="paired_collection">1 paired dataset collection</option> </param> <when value="paired"> <param name="input1_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="Left-hand mates" /> <param name="input2_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="Right-hand mates" /> </when> <when value="paired_collection"> <param name="reads_coll" type="data_collection" collection_type="paired" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="Paired-end reads collection" /> </when> </conditional> </inputs> <outputs> <!-- $input1_file.name = filename , e.g. paired_end_2_errors.fastqsanger --> <!-- $input1_file.id = ID , e.g. 10 --> <!-- $input1_file.hid = history ID, e.g. 5 --> <data name="outfile_pairs" format_source="input1_file" label="FASTQ interlacer pairs from ${on_string}"> <filter>reads['reads_selector'] == 'paired'</filter> </data> <data name="outfile_singles" format_source="input1_file" label="FASTQ interlacer singles from ${on_string}"> <filter>reads['reads_selector'] == 'paired'</filter> </data> <data name="outfile_pairs_from_coll" format_source="reads_coll['forward']" label="FASTQ interlacer pairs from ${on_string}"> <filter>reads['reads_selector'] == 'paired_collection'</filter> </data> <data name="outfile_singles_from_coll" format_source="reads_coll['forward']" label="FASTQ interlacer singles from ${on_string}"> <filter>reads['reads_selector'] == 'paired_collection'</filter> </data> </outputs> <tests> <test> <param name="reads_selector" value="paired" /> <param name="input1_file" value="paired_end_1.fastqsanger" ftype="fastqsanger" /> <param name="input2_file" value="paired_end_2.fastqsanger" ftype="fastqsanger" /> <output name="outfile_pairs" file="paired_end_merged.fastqsanger" ftype="fastqsanger" /> <output name="outfile_singles" file="paired_end_merged_singles.fastqsanger" ftype="fastqsanger" /> </test> <test> <param name="reads_selector" value="paired" /> <param name="input1_file" value="paired_end_1_errors.fastqsanger" ftype="fastqsanger" /> <param name="input2_file" value="paired_end_2_errors.fastqsanger" ftype="fastqsanger" /> <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger" /> <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger" /> </test> <test> <param name="reads_selector" value="paired" /> <param name="input1_file" value="paired_end_1_errors.fastqsanger.gz" ftype="fastqsanger.gz" /> <param name="input2_file" value="paired_end_2_errors.fastqsanger.gz" ftype="fastqsanger.gz" /> <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger.gz" decompress="true" /> <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger.gz" decompress="true" /> </test> <test> <param name="reads_selector" value="paired" /> <param name="input1_file" value="paired_end_1_errors.fastqsanger.bz2" ftype="fastqsanger.bz2" /> <param name="input2_file" value="paired_end_2_errors.fastqsanger.bz2" ftype="fastqsanger.bz2" /> <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger.bz2" decompress="true" /> <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger.bz2" decompress="true" /> </test> <test> <param name="reads_selector" value="paired_collection" /> <param name="reads_coll"> <collection type="paired"> <element name="forward" value="paired_end_1.fastqsanger" ftype="fastqsanger" /> <element name="reverse" value="paired_end_2.fastqsanger" ftype="fastqsanger" /> </collection> </param> <output name="outfile_pairs_from_coll" file="paired_end_merged.fastqsanger" ftype="fastqsanger" /> <output name="outfile_singles_from_coll" file="paired_end_merged_singles.fastqsanger" ftype="fastqsanger" /> </test> </tests> <help><![CDATA[ **What it does** This tool joins paired end FASTQ reads from two separate files, one with the left mates and one with the right mates, into a single files where left mates alternate with their right mates. The join is performed using sequence identifiers, allowing the two files to contain differing ordering. If a sequence identifier does not appear in both files, it is included in a separate file. Sequence identifiers with /1 and /2 appended override the left-hand and right-hand designation; i.e. if the reads end with /1 and /2, the read containing /1 will be used as the left-hand read and the read containing /2 will be used as the right-hand read. Sequences without this designation will follow the left-hand and right-hand settings set by the user. ----- **Input** Left-hand mates, for example:: @1539:931/1 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG +1539:931/1 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB Right-hand mates, for example:: @1539:931/2 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT +1539:931/2 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB ----- **Output** A multiple-fastq file containing interlaced left and right paired reads:: @1539:931/1 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG +1539:931/1 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB @1539:931/2 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT +1539:931/2 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB A multiple-fastq file containing reads that have no mate is also produced. ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/btq281</citation> </citations> </tool>