| Previous changeset 1:ec6ddf449651 (2016-03-19) Next changeset 3:ef49268ee579 (2017-10-07) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a |
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modified:
fastq_paired_end_interlacer.xml |
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removed:
fastq_paired_end_interlacer.py tool_dependencies.xml |
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| diff -r ec6ddf449651 -r effda79f510c fastq_paired_end_interlacer.py --- a/fastq_paired_end_interlacer.py Sat Mar 19 09:41:17 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,59 +0,0 @@ -#Florent Angly -import sys -from galaxy_utils.sequence.fastq import fastqReader, fastqWriter, fastqNamedReader, fastqJoiner - -def main(): - mate1_filename = sys.argv[1] - mate1_type = sys.argv[2] or 'sanger' - mate2_filename = sys.argv[3] - mate2_type = sys.argv[4] or 'sanger' - outfile_pairs = sys.argv[5] - outfile_singles = sys.argv[6] - - if mate1_type != mate2_type: - print "WARNING: You are trying to interlace files of two different types: %s and %s." % ( mate1_type, mate2_type ) - return - - type = mate1_type - joiner = fastqJoiner( type ) - out_pairs = fastqWriter( open( outfile_pairs, 'wb' ), format = type ) - out_singles = fastqWriter( open( outfile_singles, 'wb' ), format = type ) - - # Pairs + singles present in mate1 - nof_singles = 0 - nof_pairs = 0 - mate2_input = fastqNamedReader( open( mate2_filename, 'rb' ), format = type ) - i = None - for i, mate1 in enumerate( fastqReader( open( mate1_filename, 'rb' ), format = type ) ): - mate2 = mate2_input.get( joiner.get_paired_identifier( mate1 ) ) - if mate2: - out_pairs.write( mate1 ) - out_pairs.write( mate2 ) - nof_pairs += 1 - else: - out_singles.write( mate1 ) - nof_singles += 1 - - # Singles present in mate2 - mate1_input = fastqNamedReader( open( mate1_filename, 'rb' ), format = type ) - j = None - for j, mate2 in enumerate( fastqReader( open( mate2_filename, 'rb' ), format = type ) ): - mate1 = mate1_input.get( joiner.get_paired_identifier( mate2 ) ) - if not mate1: - out_singles.write( mate2 ) - nof_singles += 1 - - if (i is None) and (j is None): - print "Your input files contained no valid FASTQ sequences." - else: - print 'There were %s single reads.' % ( nof_singles ) - print 'Interlaced %s pairs of sequences.' % ( nof_pairs ) - - mate1_input.close() - mate2_input.close() - out_pairs.close() - out_singles.close() - - -if __name__ == "__main__": - main() |
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| diff -r ec6ddf449651 -r effda79f510c fastq_paired_end_interlacer.xml --- a/fastq_paired_end_interlacer.xml Sat Mar 19 09:41:17 2016 -0400 +++ b/fastq_paired_end_interlacer.xml Sat Sep 30 14:59:00 2017 -0400 |
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| b'@@ -1,67 +1,78 @@\n-<tool id="fastq_paired_end_interlacer" name="FASTQ interlacer" version="1.2">\n- <description>on paired end reads</description>\n- <requirements>\n- <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>\n- </requirements>\n- <command>\n-python $__tool_directory__/fastq_paired_end_interlacer.py\n+<tool id="fastq_paired_end_interlacer" name="FASTQ interlacer" version="1.2.0">\n+ <description>on paired end reads</description>\n+ <requirements>\n+ <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement>\n+ </requirements>\n+ <command><![CDATA[\n+gx-fastq-paired-end-interlacer\n #if $reads.reads_selector == \'paired\'\n \'${reads.input1_file}\' ${reads.input1_file.extension[len(\'fastq\'):]} \'${reads.input2_file}\' ${reads.input2_file.extension[len(\'fastq\'):]}\n+ \'$outfile_pairs\' \'$outfile_singles\'\n #else\n \'${reads.reads_coll.forward}\' ${reads.reads_coll.forward.extension[len(\'fastq\'):]} \'${reads.reads_coll.reverse}\' ${reads.reads_coll.reverse.extension[len(\'fastq\'):]}\n+ \'$outfile_pairs_from_coll\' \'$outfile_singles_from_coll\'\n #end if\n-\'$outfile_pairs\' \'$outfile_singles\'\n- </command>\n- <inputs>\n- <conditional name="reads">\n- <param name="reads_selector" type="select" label="Type of paired-end datasets">\n- <option value="paired">2 separate datasets</option>\n- <option value="paired_collection">1 paired dataset collection</option>\n- </param>\n- <when value="paired">\n- <param name="input1_file" type="data" format="fastqsanger,fastqcssanger" label="Left-hand mates" />\n- <param name="input2_file" type="data" format="fastqsanger,fastqcssanger" label="Right-hand mates" />\n- </when>\n- <when value="paired_collection">\n- <param name="reads_coll" type="data_collection" collection_type="paired" format="fastqsanger,fastqcssanger" label="Paired-end reads collection" />\n- </when>\n- </conditional>\n- </inputs>\n- <outputs>\n- <!-- $input1_file.name = filename , e.g. paired_end_2_errors.fastqsanger -->\n- <!-- $input1_file.id = ID , e.g. 10 -->\n- <!-- $input1_file.hid = history ID, e.g. 5 -->\n- <data name="outfile_pairs" format="input" label="FASTQ interlacer pairs from ${on_string}"/>\n- <data name="outfile_singles" format="input" label="FASTQ interlacer singles from ${on_string}"/>\n- </outputs>\n- <tests>\n- <test>\n- <param name="reads_selector" value="paired" />\n- <param name="input1_file" value="paired_end_1.fastqsanger" ftype="fastqsanger" />\n- <param name="input2_file" value="paired_end_2.fastqsanger" ftype="fastqsanger" />\n- <output name="outfile_pairs" file="paired_end_merged.fastqsanger" ftype="fastqsanger" />\n- <output name="outfile_singles" file="paired_end_merged_singles.fastqsanger" ftype="fastqsanger" />\n- </test>\n- <test>\n- <param name="reads_selector" value="paired" />\n- <param name="input1_file" value="paired_end_1_errors.fastqsanger" ftype="fastqsanger" />\n- <param name="input2_file" value="paired_end_2_errors.fastqsanger" ftype="fastqsanger" />\n- <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger" />\n- <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger" />\n- </test>\n- <test>\n- <param name="reads_selector" value="paired_collection" />\n- <param name="reads_coll">\n- <collection type="paired">\n- <element name="forward" value="paired_end_1.fastqsanger" ftype="fastqsanger" />\n- <element name="reverse" value="paired_end_2.fastqsanger" ftype="fastqsanger" />\n- </collection>\n- </param>\n- <output name="outfile_pairs" file="paired_end_merged.fastqsanger" ftype="fastqsanger" />\n- <output name="outfile_singles" file="paired_end_merged_singles.fastqsanger" ftype="fastqsanger" />\n- </test>\n- </tests>\n- <help>\n+ ]]></command>\n+ <inputs>\n+ '..b'hand mates" />\n+ </when>\n+ <when value="paired_collection">\n+ <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" />\n+ </when>\n+ </conditional>\n+ </inputs>\n+ <outputs>\n+ <!-- $input1_file.name = filename , e.g. paired_end_2_errors.fastqsanger -->\n+ <!-- $input1_file.id = ID , e.g. 10 -->\n+ <!-- $input1_file.hid = history ID, e.g. 5 -->\n+ <data name="outfile_pairs" format_source="input1_file" label="FASTQ interlacer pairs from ${on_string}">\n+ <filter>reads[\'reads_selector\'] == \'paired\'</filter>\n+ </data>\n+ <data name="outfile_singles" format_source="input1_file" label="FASTQ interlacer singles from ${on_string}">\n+ <filter>reads[\'reads_selector\'] == \'paired\'</filter>\n+ </data>\n+ <data name="outfile_pairs_from_coll" format_source="reads_coll[\'forward\']" label="FASTQ interlacer pairs from ${on_string}">\n+ <filter>reads[\'reads_selector\'] == \'paired_collection\'</filter>\n+ </data>\n+ <data name="outfile_singles_from_coll" format_source="reads_coll[\'forward\']" label="FASTQ interlacer singles from ${on_string}">\n+ <filter>reads[\'reads_selector\'] == \'paired_collection\'</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="reads_selector" value="paired" />\n+ <param name="input1_file" value="paired_end_1.fastqsanger" ftype="fastqsanger" />\n+ <param name="input2_file" value="paired_end_2.fastqsanger" ftype="fastqsanger" />\n+ <output name="outfile_pairs" file="paired_end_merged.fastqsanger" ftype="fastqsanger" />\n+ <output name="outfile_singles" file="paired_end_merged_singles.fastqsanger" ftype="fastqsanger" />\n+ </test>\n+ <test>\n+ <param name="reads_selector" value="paired" />\n+ <param name="input1_file" value="paired_end_1_errors.fastqsanger" ftype="fastqsanger" />\n+ <param name="input2_file" value="paired_end_2_errors.fastqsanger" ftype="fastqsanger" />\n+ <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger" />\n+ <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger" />\n+ </test>\n+ <test>\n+ <param name="reads_selector" value="paired_collection" />\n+ <param name="reads_coll">\n+ <collection type="paired">\n+ <element name="forward" value="paired_end_1.fastqsanger" ftype="fastqsanger" />\n+ <element name="reverse" value="paired_end_2.fastqsanger" ftype="fastqsanger" />\n+ </collection>\n+ </param>\n+ <output name="outfile_pairs_from_coll" file="paired_end_merged.fastqsanger" ftype="fastqsanger" />\n+ <output name="outfile_singles_from_coll" file="paired_end_merged_singles.fastqsanger" ftype="fastqsanger" />\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n **What it does**\n \n 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.\n@@ -102,8 +113,8 @@\n WNUUZ\\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n \n A multiple-fastq file containing reads that have no mate is also produced.\n- </help>\n- <citations>\n- <citation doi="10.1093/bioinformatics/btq281" />\n- </citations>\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btq281</citation>\n+ </citations>\n </tool>\n' |
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| diff -r ec6ddf449651 -r effda79f510c tool_dependencies.xml --- a/tool_dependencies.xml Sat Mar 19 09:41:17 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="galaxy_sequence_utils" version="1.0.1"> - <repository changeset_revision="c1ab450748ba" name="package_galaxy_sequence_utils_1_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |