| Previous changeset 3:83fbdf93d51e (2021-05-10) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44 |
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modified:
illuminapairedend.xml macros.xml test-data/input_ngsfilter_extrafile.txt |
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| diff -r 83fbdf93d51e -r 8cb6bd511879 illuminapairedend.xml --- a/illuminapairedend.xml Mon May 10 19:36:09 2021 +0000 +++ b/illuminapairedend.xml Wed Mar 20 13:17:09 2024 +0000 |
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| b'@@ -1,95 +1,97 @@\n-<tool id="obi_illumina_pairend" name="Illuminapairedend" version="@TOOL_VERSION@" profile="@PROFILE@">\n- <description>Construct consensus reads from Illumina pair-end reads</description>\n- <macros>\n- <import>macros.xml</import>\n- </macros>\n- <expand macro="requirements"/>\n- <expand macro="stdio"/>\n- <command>\n- <![CDATA[\n- #if $inputfastq3p.ext.endswith(".gz")\n- gunzip -c \'$inputfastq3p\' > fastq3p.fastq &&\n- gunzip -c \'$inputfastq5p\' > fastq5p.fastq &&\n- #else\n- ln -s \'$inputfastq3p\' fastq3p.fastq &&\n- ln -s \'$inputfastq5p\' fastq5p.fastq &&\n- #end if\n-\n- illuminapairedend\n- ##--index-file=\n- #if $inputfastq3p.ext.startswith("fastqsolexa")\n- ##input file is in fastq nucleic format produced by solexa sequencer\n- --solexa\n- #else if $inputfastq3p.ext.startswith("fastqillumina")\n- ##input file is in fastq nucleic format produced by solexa sequencer\n- --illumina\n- #else\n- ## input file is in sanger fastq nucleic format (standard fastq)\n- --sanger\n- #end if\n- --without-progress-bar\n- --score-min=\'$score\'\n- -r fastq3p.fastq \n- fastq5p.fastq\n- #if $inputfastq3p.ext.endswith(".gz")\n- | gzip -c \n- #end if\n- > \'$output\'\n- ]]>\n- </command>\n- <inputs>\n- <param name="inputfastq3p" type="data" format="fastq,fastq.gz" label="Read from file" help="file of 3p (1:) Illumina pair-end reads to assemble in sanger fastq nucleic format (standard fastq)" />\n- <param name="inputfastq5p" type="data" format="fastq,fastq.gz" label="Read from file" help="file of 5p (2:) Illumina pair-end reads to assemble in sanger fastq nucleic format (standard fastq)" />\n- <param name="score" type="float" value="40.0" label="minimum score for keeping aligment"/>\n- </inputs>\n- <outputs>\n- <data name="output" format_source="inputfastq3p" label="${tool.name} on ${on_string}: assembly results" />\n- </outputs>\n-\n- <tests>\n- <test>\n- <param name="inputfastq3p" value="wolf_small.F.fastq" ftype="fastqsanger" />\n- <param name="inputfastq5p" value="wolf_small.R.fastq" ftype="fastqsanger" />\n- <param name="score" value="40.0" />\n- <output name="output" file="illuminapairedend.output.fastq" ftype="fastqsanger" />\n- </test>\n- <test>\n- <param name="inputfastq3p" value="wolf_small.F.fastq.gz" ftype="fastqsanger.gz" />\n- <param name="inputfastq5p" value="wolf_small.R.fastq.gz" ftype="fastqsanger.gz" />\n- <param name="score" value="40.0" />\n- <output name="output" file="illuminapairedend.output.fastq.gz" ftype="fastqsanger.gz" decompress="true"/>\n- </test>\n- </tests>\n-\n- <help><![CDATA[\n-\n-.. class:: warning\n-\n-**Warning:**\n-Sequence records corresponding to the same read pair must be in the same order in the two files\n-\n---------\n-\n-.. class:: infomark\n-\n-**What it does**\n-\n-illuminapairedend aims at aligning the two reads of a pair-end library sequenced using an Illumina platform :\n-\n-\\* If the two reads overlap, it returns the consensus sequence together with its quality\n-\\* Otherwise, it concatenates sequence merging the forward read and the reversed-complemented reverse read.\n-\n-The program uses as input one or two fastq sequences reads files.\n-\n-\\* If two files are used one of them must be specified using the -r option. Sequence records corresponding to the same read pair must be in the same order in the two files.\n-\\* If just one file is provided, sequence records are supposed to be all of the same length. The first half of th e sequence is used as forward read, the second half is used as the reverse read.\n-\n-illuminapairedend align the forward sequence record with the reverse complement of the reverse sequence record. The alignment algorit'..b'_tools"/>\r\n+ <expand macro="requirements"/>\r\n+ <expand macro="stdio"/>\r\n+ <command>\r\n+ <![CDATA[\r\n+ #if $inputfastq3p.ext.endswith(".gz")\r\n+ gunzip -c \'$inputfastq3p\' > fastq3p.fastq &&\r\n+ gunzip -c \'$inputfastq5p\' > fastq5p.fastq &&\r\n+ #else\r\n+ ln -s \'$inputfastq3p\' fastq3p.fastq &&\r\n+ ln -s \'$inputfastq5p\' fastq5p.fastq &&\r\n+ #end if\r\n+\r\n+ illuminapairedend\r\n+ ##--index-file=\r\n+ #if $inputfastq3p.ext.startswith("fastqsolexa")\r\n+ ##input file is in fastq nucleic format produced by solexa sequencer\r\n+ --solexa\r\n+ #else if $inputfastq3p.ext.startswith("fastqillumina")\r\n+ ##input file is in fastq nucleic format produced by solexa sequencer\r\n+ --illumina\r\n+ #else\r\n+ ## input file is in sanger fastq nucleic format (standard fastq)\r\n+ --sanger\r\n+ #end if\r\n+ --without-progress-bar\r\n+ --score-min=\'$score\'\r\n+ -r fastq3p.fastq \r\n+ fastq5p.fastq\r\n+ #if $inputfastq3p.ext.endswith(".gz")\r\n+ | gzip -c \r\n+ #end if\r\n+ > \'$output\'\r\n+ ]]>\r\n+ </command>\r\n+ <inputs>\r\n+ <param name="inputfastq3p" type="data" format="fastq,fastq.gz" label="Read from file" help="file of 3p (1:) Illumina pair-end reads to assemble in sanger fastq nucleic format (standard fastq)" />\r\n+ <param name="inputfastq5p" type="data" format="fastq,fastq.gz" label="Read from file" help="file of 5p (2:) Illumina pair-end reads to assemble in sanger fastq nucleic format (standard fastq)" />\r\n+ <param name="score" type="float" value="40.0" label="minimum score for keeping aligment"/>\r\n+ </inputs>\r\n+ <outputs>\r\n+ <data name="output" format_source="inputfastq3p" label="${tool.name} on ${on_string}: assembly results" />\r\n+ </outputs>\r\n+\r\n+ <tests>\r\n+ <test expect_num_outputs="1">\r\n+ <param name="inputfastq3p" value="wolf_small.F.fastq" ftype="fastqsanger" />\r\n+ <param name="inputfastq5p" value="wolf_small.R.fastq" ftype="fastqsanger" />\r\n+ <param name="score" value="40.0" />\r\n+ <output name="output" file="illuminapairedend.output.fastq" ftype="fastqsanger" />\r\n+ </test>\r\n+ <test expect_num_outputs="1">\r\n+ <param name="inputfastq3p" value="wolf_small.F.fastq.gz" ftype="fastqsanger.gz" />\r\n+ <param name="inputfastq5p" value="wolf_small.R.fastq.gz" ftype="fastqsanger.gz" />\r\n+ <param name="score" value="40.0" />\r\n+ <output name="output" file="illuminapairedend.output.fastq.gz" ftype="fastqsanger.gz" decompress="true"/>\r\n+ </test>\r\n+ </tests>\r\n+\r\n+ <help><![CDATA[\r\n+\r\n+.. class:: warning\r\n+\r\n+**Warning:**\r\n+Sequence records corresponding to the same read pair must be in the same order in the two files\r\n+\r\n+--------\r\n+\r\n+.. class:: infomark\r\n+\r\n+**What it does**\r\n+\r\n+illuminapairedend aims at aligning the two reads of a pair-end library sequenced using an Illumina platform :\r\n+\r\n+\\* If the two reads overlap, it returns the consensus sequence together with its quality\r\n+\\* Otherwise, it concatenates sequence merging the forward read and the reversed-complemented reverse read.\r\n+\r\n+The program uses as input one or two fastq sequences reads files.\r\n+\r\n+\\* If two files are used one of them must be specified using the -r option. Sequence records corresponding to the same read pair must be in the same order in the two files.\r\n+\\* If just one file is provided, sequence records are supposed to be all of the same length. The first half of th e sequence is used as forward read, the second half is used as the reverse read.\r\n+\r\n+illuminapairedend align the forward sequence record with the reverse complement of the reverse sequence record. The alignment algorithm takes into account the base qualities.\r\n+\r\n+@OBITOOLS_LINK@\r\n+\r\n+]]>\r\n+ </help>\r\n+ <expand macro="citation" />\r\n+\r\n+</tool>\r\n+\r\n' |
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| diff -r 83fbdf93d51e -r 8cb6bd511879 macros.xml --- a/macros.xml Mon May 10 19:36:09 2021 +0000 +++ b/macros.xml Wed Mar 20 13:17:09 2024 +0000 |
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| @@ -5,7 +5,11 @@ <requirement type="package" version="@TOOL_VERSION@">obitools</requirement> </requirements> </xml> - + <xml name="bio_tools"> + <xrefs> + <xref type="bio.tools">obitools</xref> + </xrefs> + </xml> <token name="@TOOL_VERSION@">1.2.13</token> <token name="@PROFILE@">21.01</token> |
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| diff -r 83fbdf93d51e -r 8cb6bd511879 test-data/input_ngsfilter_extrafile.txt --- a/test-data/input_ngsfilter_extrafile.txt Mon May 10 19:36:09 2021 +0000 +++ b/test-data/input_ngsfilter_extrafile.txt Wed Mar 20 13:17:09 2024 +0000 |
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| @@ -1,4 +1,4 @@ -wolf_diet 13a_F730603 aattaac TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @ -wolf_diet 15a_F730814 gaagtag TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @ -wolf_diet 26a_F040644 gaatatc TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @ -wolf_diet 29a_F260619 gcctcct TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @ +wolf_diet 13a_F730603 aattaac TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @ +wolf_diet 15a_F730814 gaagtag TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @ +wolf_diet 26a_F040644 gaatatc TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @ +wolf_diet 29a_F260619 gcctcct TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @ |