| Previous changeset 13:f4fa77189eb0 (2017-07-18) Next changeset 15:d5fe9aead222 (2017-09-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2 |
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modified:
hisat2.xml hisat2_macros.xml |
| b |
| diff -r f4fa77189eb0 -r 526b91fbde60 hisat2.xml --- a/hisat2.xml Tue Jul 18 14:25:13 2017 -0400 +++ b/hisat2.xml Wed Jul 19 04:57:27 2017 -0400 |
| [ |
| b'@@ -5,13 +5,12 @@\n <import>hisat2_macros.xml</import>\n </macros>\n <requirements>\n- <!-- Conda dependency -->\n <requirement type="package" version="2.0.5">hisat2</requirement>\n <requirement type="package" version="1.4">samtools</requirement>\n </requirements>\n <stdio>\n- <regex match="hisat2-align exited with value 1" source="both" level="fatal"/>\n- <regex match="hisat2: not found" source="both" level="fatal"/>\n+ <regex level="fatal" match="hisat2-align exited with value 1" source="both" />\n+ <regex level="fatal" match="hisat2: not found" source="both" />\n <exit_code range="1:" />\n </stdio>\n <version_command>hisat2 --version</version_command>\n@@ -31,27 +30,27 @@\n #set index_path = $reference_genome.index.fields.path\n #end if\n hisat2 -p \\${GALAXY_SLOTS:-1} -x \'${index_path}\'\n- #if str($input_format.paired.paired_selector) != \'single\':\n+ #if str($input_format.paired.paired_selector) == \'paired\':\n -1 \'${read1}\' -2 \'${read2}\'\n @paired_end_options@\n #else:\n -U \'${read1}\'\n #if str( $input_format.paired.unaligned_file ) == "true":\n #if $compressed == "GZ":\n- --un-gz \'$output_unaligned_reads_l\'\n+ --un-gz \'$output_unaligned_reads\'\n #else if $compressed == "BZ2":\n- --un-bz2 \'$output_unaligned_reads_l\'\n+ --un-bz2 \'$output_unaligned_reads\'\n #else:\n- --un \'$output_unaligned_reads_l\'\n+ --un \'$output_unaligned_reads\'\n #end if\n #end if\n #if str( $input_format.paired.aligned_file ) == "true":\n #if $compressed == "GZ":\n- --al-gz \'$output_aligned_reads_l\'\n+ --al-gz \'$output_aligned_reads\'\n #else if $compressed == "BZ2":\n- --al-bz2 \'$output_aligned_reads_l\'\n+ --al-bz2 \'$output_aligned_reads\'\n #else:\n- --al \'$output_aligned_reads_l\'\n+ --al \'$output_aligned_reads\'\n #end if\n #end if\n #end if\n@@ -113,21 +112,18 @@\n ${paired_options.dovetail} ${paired_options.contain} ${paired_options.overlap}\n #end if\n | samtools sort - -@ \\${GALAXY_SLOTS:-1} -l 6 -o \'${output_alignments}\'\n-\n ## Rename any output fastq files\n- #if str($input_format.paired.paired_selector) == \'paired\' or str($input_format.paired.paired_selector) == \'paired_collection\':\n- #if $output_unaligned_reads_l and $output_unaligned_reads_r:\n- #set left = str($output_unaligned_reads_l).replace(".dat", ".1.dat")\n- #set right = str($output_unaligned_reads_l).replace(".dat", ".2.dat")\n- && mv \'${left}\' \'${output_unaligned_reads_l}\'\n- && mv \'${right}\' \'${output_unaligned_reads_r}\'\n- #end if\n- #if $output_aligned_reads_l and $output_aligned_reads_r:\n- #set left = str($output_aligned_reads_l).replace(".dat", ".1.dat")\n- #set right = str($output_aligned_reads_l).replace(".dat", ".2.dat")\n- && mv \'${left}\' \'${output_aligned_reads_l}\'\n- && mv \'${right}\' \'${output_aligned_reads_r}\'\n- #end if\n+ #if $output_unaligned_reads_l and $output_unaligned_reads_r:\n+ #set left = str($output_unaligned_reads_l).replace(".dat", ".1.dat")\n+ #set right = str($output_unaligned_reads_l).replace(".dat", ".2.dat")\n+ && mv \'${left}\' \'${output_unaligned_reads_l}\'\n+ && mv \'${right}\' \'${output_unaligned_reads_r}\'\n+ #end if\n+ #if $output_aligned_reads_l and $output_aligned_reads_r:\n+ #set left = str($output_aligned_reads_l).replace(".dat", ".1.dat")\n+ #set right = st'..b'e" />\n <param name="reference_genome_source" value="history" />\n- <param name="history_item" value="phiX.fa" ftype="fasta" />\n- <param name="reads_f" value="test_unaligned_reads.fasta" ftype="fasta" />\n- <param name="reads_r" value="test_unaligned_reads.fasta" ftype="fasta" />\n+ <param name="history_item" ftype="fasta" value="phiX.fa" />\n+ <param name="forward" ftype="fasta" value="test_unaligned_reads.fasta" />\n+ <param name="reverse" ftype="fasta" value="test_unaligned_reads.fasta" />\n <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" />\n <output name="output_unaligned_reads_r" file="test_unaligned_reads.fasta" />\n </test>\n <test><!-- Ensure fastqsanger.gz works -->\n <param name="input_format_selector" value="fastq" />\n <param name="paired_selector" value="paired" />\n+ <param name="collection_selector" value="files" />\n <param name="reference_genome_source" value="history" />\n- <param name="history_item" value="phiX.fa" ftype="fasta" />\n+ <param name="history_item" ftype="fasta" value="phiX.fa" />\n <param name="input_options_selector" value="advanced" />\n <param name="trim_three" value="15" />\n <param name="trim_five" value="15" />\n- <param name="reads_f" ftype="fastqsanger.gz" value="hisat_input_2_forward.fastq.gz" />\n- <param name="reads_r" ftype="fastqsanger.gz" value="hisat_input_2_reverse.fastq.gz" />\n+ <param name="forward" ftype="fastqsanger.gz" value="hisat_input_2_forward.fastq.gz" />\n+ <param name="reverse" ftype="fastqsanger.gz" value="hisat_input_2_reverse.fastq.gz" />\n <param name="paired_end_options_selector" value="advanced" />\n <param name="no_mixed" value="True" />\n <param name="no_discordant" value="True" />\n- <output name="output_alignments" ftype="bam" file="hisat_output_3.bam" lines_diff="2" />\n+ <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" />\n </test>\n <test><!-- Ensure fastqsanger.bz2 works -->\n <param name="input_format_selector" value="fastq" />\n <param name="paired_selector" value="paired" />\n+ <param name="collection_selector" value="files" />\n <param name="reference_genome_source" value="history" />\n- <param name="history_item" value="phiX.fa" ftype="fasta" />\n+ <param name="history_item" ftype="fasta" value="phiX.fa" />\n <param name="input_options_selector" value="advanced" />\n <param name="trim_three" value="15" />\n <param name="trim_five" value="15" />\n- <param name="reads_f" ftype="fastqsanger.bz2" value="hisat_input_2_forward.fastq.bz2" />\n- <param name="reads_r" ftype="fastqsanger.bz2" value="hisat_input_2_reverse.fastq.bz2" />\n+ <param name="forward" ftype="fastqsanger.bz2" value="hisat_input_2_forward.fastq.bz2" />\n+ <param name="reverse" ftype="fastqsanger.bz2" value="hisat_input_2_reverse.fastq.bz2" />\n <param name="paired_end_options_selector" value="advanced" />\n <param name="no_mixed" value="True" />\n <param name="no_discordant" value="True" />\n- <output name="output_alignments" ftype="bam" file="hisat_output_3.bam" lines_diff="2" />\n+ <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" />\n </test>\n </tests>\n- <help>\n- <![CDATA[\n+ <help><![CDATA[\n Introduction\n ============\n \n@@ -622,8 +631,7 @@\n 96.70% overall alignment rate\n \n The indentation indicates how subtotals relate to totals.\n- ]]>\n- </help>\n+ ]]></help>\n <citations>\n <citation type="doi">10.1038/nmeth.3317</citation>\n </citations>\n' |
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| diff -r f4fa77189eb0 -r 526b91fbde60 hisat2_macros.xml --- a/hisat2_macros.xml Tue Jul 18 14:25:13 2017 -0400 +++ b/hisat2_macros.xml Wed Jul 19 04:57:27 2017 -0400 |
| b |
| b'@@ -1,52 +1,55 @@\n <?xml version="1.0"?>\n <macros>\n <xml name="single_paired_selector">\n- <param label="Single end or paired reads?" name="paired_selector" type="select">\n- <option value="paired_collection">Collection of paired reads</option>\n- <option value="paired">Individual paired reads</option>\n- <option value="single">Individual unpaired reads</option>\n+ <param name="paired_selector" type="select" label="Single end or paired reads?">\n+ <option value="paired">Paired reads</option>\n+ <option value="single">Unpaired reads</option>\n </param>\n </xml>\n <xml name="paired_input_conditional" tokens="ftype">\n <conditional name="paired">\n <expand macro="single_paired_selector" />\n- <when value="paired_collection">\n- <param collection_type="paired" format="@FTYPE@" label="Paired reads" name="reads" type="data_collection" />\n- <expand macro="paired_end_conditional" />\n- <expand macro="paired_end_output" />\n- </when>\n <when value="paired">\n- <param format="@FTYPE@" label="Forward reads" name="reads_f" type="data" />\n- <param format="@FTYPE@" label="Reverse reads" name="reads_r" type="data" />\n+ <conditional name="collection" label="Data structure">\n+ <param name="collection_selector" type="select" label="Input is structured as" help="If a list of pairs is selected, HISAT2 will run in batch mode over each pair in the list, producing a list of output bam files">\n+ <option value="files">Individual files</option>\n+ <option value="collection">Pair collection or list of pairs</option>\n+ </param>\n+ <when value="collection">\n+ <param name="reads" type="data_collection" collection_type="paired" format="@FTYPE@" label="Paired reads" />\n+ </when>\n+ <when value="files">\n+ <param name="forward" type="data" format="@FTYPE@" label="Forward reads" />\n+ <param name="reverse" type="data" format="@FTYPE@" label="Reverse reads" />\n+ </when>\n+ </conditional>\n <expand macro="paired_end_conditional" />\n <expand macro="paired_end_output" />\n </when>\n <when value="single">\n- <param format="@FTYPE@" label="Reads" name="reads" type="data" />\n- <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" argument="--un / --un-gz" />\n- <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" argument="--al / --al-gz" />\n+ <param name="reads" type="data" format="@FTYPE@" label="Reads" />\n+ <param name="unaligned_file" argument="--un-gz" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" />\n+ <param name="aligned_file" argument="--al-gz" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" />\n </when>\n </conditional>\n </xml>\n <xml name="paired_end_conditional">\n <conditional name="paired_end_options">\n- <param label="Paired-end options" name="paired_end_options_selector" type="select">\n+ <param name="paired_end_options_selector" type="select" label="Paired-end options">\n <option value="defaults">Use default values</option>\n <option value="advanced">Specify paired-end parameters</option>\n </'..b'2"\n+ #set compressed = "BZ2"\n+ #else:\n+ #set read1 = "input_f.fastq"\n+ #end if\n+ ln -f -s \'${input_format.paired.collection.reads.forward}\' ${read1} &&\n+\n+ #if $input_format.paired.collection.reads.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):\n+ #set read2 = "input_r.fastq.gz"\n+ #set compressed = "GZ"\n+ #else if $input_format.paired.collection.reads.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n+ #set read2 = "input_r.fastq.bz2"\n+ #set compressed = "BZ2"\n+ #else:\n+ #set read2 = "input_r.fastq"\n+ #end if\n+ ln -f -s \'${input_format.paired.collection.reads.reverse}\' ${read2} &&\n #else:\n- #set read1 = "input_f.fastq"\n- #end if\n- ln -f -s \'${input_format.paired.reads_f}\' ${read1} &&\n+ #if $input_format.paired.collection.forward.is_of_type("fastq.gz", "fastqsanger.gz"):\n+ #set read1 = "input_f.fastq.gz"\n+ #set compressed = "GZ"\n+ #else if $input_format.paired.collection.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n+ #set read1 = "input_f.fastq.bz2"\n+ #set compressed = "BZ2"\n+ #else:\n+ #set read1 = "input_f.fastq"\n+ #end if\n+ ln -f -s \'${input_format.paired.collection.forward}\' ${read1} &&\n \n- #if $input_format.paired.reads_r.is_of_type("fastq.gz", "fastqsanger.gz"):\n- #set read2 = "input_r.fastq.gz"\n- #set compressed = "GZ"\n- #else if $input_format.paired.reads_r.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n- #set read2 = "input_r.fastq.bz2"\n- #set compressed = "BZ2"\n- #else:\n- #set read2 = "input_r.fastq"\n+ #if $input_format.paired.collection.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):\n+ #set read2 = "input_r.fastq.gz"\n+ #set compressed = "GZ"\n+ #else if $input_format.paired.collection.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n+ #set read2 = "input_r.fastq.bz2"\n+ #set compressed = "BZ2"\n+ #else:\n+ #set read2 = "input_r.fastq"\n+ #end if\n+ ln -f -s \'${input_format.paired.collection.reverse}\' ${read2} &&\n #end if\n- ln -f -s \'${input_format.paired.reads_r}\' ${read2} &&\n- #else if str($input_format.paired.paired_selector) == \'paired_collection\':\n- #if $input_format.paired.reads.forward.is_of_type("fastq.gz", "fastqsanger.gz"):\n- #set read1 = "input_f.fastq.gz"\n- #set compressed = "GZ"\n- #else if $input_format.paired.reads.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n- #set read1 = "input_f.fastq.bz2"\n- #set compressed = "BZ2"\n- #else:\n- #set read1 = "input_f.fastq"\n- #end if\n- ln -s \'${input_format.paired.reads.forward}\' ${read1} &&\n-\n- #if $input_format.paired.reads.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):\n- #set read2 = "input_r.fastq.gz"\n- #set compressed = "GZ"\n- #else if $input_format.paired.reads.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n- #set read2 = "input_r.fastq.bz2"\n- #set compressed = "BZ2"\n- #else:\n- #set read2 = "input_r.fastq"\n- #end if\n- ln -s \'${input_format.paired.reads.reverse}\' ${read2} &&\n #else:\n #if $input_format.paired.reads.is_of_type("fastq.gz", "fastqsanger.gz"):\n #set read1 = "input_f.fastq.gz"\n' |