| Previous changeset 28:d4b55e2beb12 (2020-11-26) Next changeset 30:6c19daec423d (2021-07-18) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit f18e8826ecb395a40fc321b5f3b66ab6d7f51625" |
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modified:
hisat2.xml |
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added:
test-data/hisat_output_5.bam |
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| diff -r d4b55e2beb12 -r 26371a1df031 hisat2.xml --- a/hisat2.xml Thu Nov 26 10:10:04 2020 +0000 +++ b/hisat2.xml Mon Jan 25 17:29:15 2021 +0000 |
| [ |
| b'@@ -1,11 +1,11 @@\n-<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy6" profile="17.01">\n+<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy7" profile="17.01">\n <description>A fast and sensitive alignment program</description>\n <macros>\n <import>hisat2_macros.xml</import>\n </macros>\n <requirements>\n <requirement type="package" version="2.1.0">hisat2</requirement>\n- <requirement type="package" version="1.9">samtools</requirement>\n+ <requirement type="package" version="1.11">samtools</requirement>\n <requirement type="package" version="1.3">seqtk</requirement>\n </requirements>\n <stdio>\n@@ -300,6 +300,26 @@\n #end if\n \n \n+## SAM options\n+\n+#if str($adv.sam_options.sam_options_selector) == "advanced":\n+ #if $adv.sam_options.no_unal:\n+ --no-unal\n+ #end if\n+ #if str($adv.sam_options.read_groups.rg_labels) == "Yes":\n+ --rg-id \'$adv.sam_options.read_groups.rg_id\'\n+ #if len(\'$adv.sam_options.read_groups.read_groups\'):\n+ #for $i, $id in enumerate($adv.sam_options.read_groups.read_groups):\n+ --rg \'$id.rg\'\n+ #end for\n+ #end if\n+ #end if\n+ $adv.sam_options.chr_text\n+ #if $adv.sam_options.omit_sec_seq:\n+ --omit-sec-seq\n+ #end if\n+#end if\n+\n ## Other options\n \n #if str( $adv.other_options.other_options_selector ) == "advanced":\n@@ -406,8 +426,8 @@\n \n <!-- Summary Options -->\n <section name="sum" title="Summary Options" expanded="False">\n- <param name="new_summary" argument="--new-summary" type="boolean" checked="False" label="Output alignment summary in a more machine-friendly style." help="Select this option for compatibility with MultiQC" />\n- <param name="summary_file" argument="--summary-file" type="boolean" checked="False" label="Print alignment summary to a file." help="Output alignment summary to a file in addition to stderr." />\n+ <param name="new_summary" argument="--new-summary" type="boolean" checked="false" label="Output alignment summary in a more machine-friendly style." help="Select this option for compatibility with MultiQC" />\n+ <param name="summary_file" argument="--summary-file" type="boolean" checked="false" label="Print alignment summary to a file." help="Output alignment summary to a file in addition to stderr." />\n </section>\n \n <!-- Advanced Options -->\n@@ -427,8 +447,8 @@\n <option value="--phred33" selected="True">Input qualities are ASCII chars equal to the Phred quality plus 33. This is also called the "Phred+33" encoding, which is used by the very latest Illumina pipelines (--phred33)</option>\n <option value="--phred64">Input qualities are ASCII chars equal to the Phred quality plus 64. This is also called the "Phred+64" encoding (--phred64)</option>\n </param>\n- <param name="solexa_quals" argument="--solexa-quals" type="boolean" truevalue="--solexa-quals" falsevalue="" checked="False" label="Convert input qualities from Solexa (which can be negative) to Phred (which can\'t). This scheme was used in older Illumina GA Pipeline versions (prior to 1.3)" help="--solexa-quals; default: False"/>\n- <param name="int_quals" argument="--int-quals" type="boolean" truevalue="--int-quals" falsevalue="" checked="False" label="Are quality values provided as space separated integers?" help="Quality values are represented in the read input file as space-separated ASCII integers, e.g., 40 40 30 40..., rather than ASCII characters, e.g., II?I.... Integers are treated as being on the Phred quality scale unless --solexa-quals is also specified [default: False]"/>\n+ <param name="solexa_quals" argument="--solexa-quals" type="boolean" truevalue="--solexa-quals" falsevalue="" checked="false" label="Convert input qualities from Solexa (which can be negative) to Phred (which can\'t). Th'..b' <param name="chr_text" type="select" label="Add/remove \'chr\' from reference names in alignment files">\n+ <option value="" selected="true">Use default values</option>\n+ <option value="--remove-chrname">Remove \xe2\x80\x98chr\xe2\x80\x99 from reference names in alignment (e.g., chr18 to 18)</option>\n+ <option value="--add-chrname">Add \xe2\x80\x98chr\xe2\x80\x99 to reference names in alignment (e.g., 18 to chr18)</option>\n+ </param>\n+ <param name="omit_sec_seq" argument="--omit-sec-seq" type="boolean" truevalue="true" falsevalue="false" checked="false" label="When printing secondary alignments, HISAT2 by default will write out the SEQ and QUAL strings. Specifying this option causes HISAT2 to print an asterisk in those fields instead." help="Default: false"/>\n+ </when> \n+ </conditional>\n+\n <conditional name="other_options">\n <param name="other_options_selector" type="select" label="Other options">\n <option value="defaults">Use default values</option>\n@@ -877,6 +927,25 @@\n <output name="output_alignments" file="hisat_output_spliced_1.bam" ftype="bam" lines_diff="2" />\n <output name="novel_splicesite_output" file="novel_splicesite_out.tab" ftype="tabular" />\n </test>\n+ <!-- Ensure SAM output settings work -->\n+ <test expect_num_outputs="1" >\n+ <param name="type" value="paired_interleaved" />\n+ <param name="source" value="history" />\n+ <param name="history_item" ftype="fasta" value="phiX.fa" />\n+ <param name="input_1" ftype="fastqsanger.bz2" value="hisat_input_1_interleaved.fastq.bz2" />\n+ <param name="adv|sam_options|sam_options_selector" value="advanced"/>\n+ <param name="adv|sam_options|no_unal" value="true"/>\n+ <param name="adv|sam_options|read_groups|rg_labels" value="Yes"/>\n+ <repeat name="adv|sam_options|read_groups|read_groups">\n+ <param name="rg" value="BC:test1"/> \n+ </repeat> \n+ <repeat name="adv|sam_options|read_groups|read_groups">\n+ <param name="rg" value="CN:test2"/> \n+ </repeat> \n+ <param name="adv|sam_options|chr_text" value="--add-chrname"/>\n+ <param name="adv|sam_options|omit_sec_seq" value="True"/> \n+ <output name="output_alignments" file="hisat_output_5.bam" ftype="bam" lines_diff="2" />\n+ </test>\n </tests>\n \n <help><![CDATA[\n@@ -1218,6 +1287,28 @@\n align uniquely, but that does not satisfy the paired-end constraints\n (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior.\n \n+-----\n+\n+** SAM options\n+\n+ --no-unal\n+ Suppress SAM records for reads that failed to align.\n+ --rg-id <text>\n+\n+ Set the read group ID to <text>. This causes the SAM @RG header line to be printed, with <text> as the value associated with the ID: tag. It also causes the RG:Z: extra field to be attached to each SAM output record, with value set to <text>.\n+ --rg <text>\n+ Add <text> (usually of the form TAG:VAL, e.g. SM:Pool1) as a field on the @RG header line. Note: in order for the @RG line to appear, --rg-id must also be specified. This is because the ID tag is required by the SAM Spec. Specify --rg multiple times to set multiple fields. See the SAM Spec for details about what fields are legal.\n+ \n+ --remove-chrname\n+ Remove \xe2\x80\x98chr\xe2\x80\x99 from reference names in alignment (e.g., chr18 to 18)\n+ \n+ --add-chrname\n+ Add \xe2\x80\x98chr\xe2\x80\x99 to reference names in alignment (e.g., 18 to chr18)\n+ \n+ --omit-sec-seq\n+ When printing secondary alignments, HISAT2 by default will write out the SEQ and QUAL strings. Specifying this option causes HISAT2 to print an asterisk in those fields instead.\n+\n+-----\n \n **Output options**::\n \n' |
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| diff -r d4b55e2beb12 -r 26371a1df031 test-data/hisat_output_5.bam |
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| Binary file test-data/hisat_output_5.bam has changed |