Mercurial > repos > iuc > hisat2
changeset 29:26371a1df031 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit f18e8826ecb395a40fc321b5f3b66ab6d7f51625"
| author | iuc |
|---|---|
| date | Mon, 25 Jan 2021 17:29:15 +0000 |
| parents | d4b55e2beb12 |
| children | 6c19daec423d |
| files | hisat2.xml test-data/hisat_output_5.bam |
| diffstat | 2 files changed, 99 insertions(+), 8 deletions(-) [+] |
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--- a/hisat2.xml Thu Nov 26 10:10:04 2020 +0000 +++ b/hisat2.xml Mon Jan 25 17:29:15 2021 +0000 @@ -1,11 +1,11 @@ -<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy6" profile="17.01"> +<tool id="hisat2" name="HISAT2" version="2.1.0+galaxy7" profile="17.01"> <description>A fast and sensitive alignment program</description> <macros> <import>hisat2_macros.xml</import> </macros> <requirements> <requirement type="package" version="2.1.0">hisat2</requirement> - <requirement type="package" version="1.9">samtools</requirement> + <requirement type="package" version="1.11">samtools</requirement> <requirement type="package" version="1.3">seqtk</requirement> </requirements> <stdio> @@ -300,6 +300,26 @@ #end if +## SAM options + +#if str($adv.sam_options.sam_options_selector) == "advanced": + #if $adv.sam_options.no_unal: + --no-unal + #end if + #if str($adv.sam_options.read_groups.rg_labels) == "Yes": + --rg-id '$adv.sam_options.read_groups.rg_id' + #if len('$adv.sam_options.read_groups.read_groups'): + #for $i, $id in enumerate($adv.sam_options.read_groups.read_groups): + --rg '$id.rg' + #end for + #end if + #end if + $adv.sam_options.chr_text + #if $adv.sam_options.omit_sec_seq: + --omit-sec-seq + #end if +#end if + ## Other options #if str( $adv.other_options.other_options_selector ) == "advanced": @@ -406,8 +426,8 @@ <!-- Summary Options --> <section name="sum" title="Summary Options" expanded="False"> - <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" /> - <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." /> + <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" /> + <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." /> </section> <!-- Advanced Options --> @@ -427,8 +447,8 @@ <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> <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> </param> - <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"/> - <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]"/> + <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"/> + <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]"/> </when> </conditional> @@ -529,11 +549,41 @@ </param> <when value="defaults" /> <when value="advanced"> - <param name="unaligned_file" argument="--un/--un-conc" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="This triggers --un parameter for single reads and --un-conc for paired reads" /> - <param name="aligned_file" argument="--al/--al-conc" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" help="This triggers --al parameter for single reads and --al-conc for paired reads" /> + <param name="unaligned_file" argument="--un/--un-conc" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write unaligned reads (in fastq format) to separate file(s)" help="This triggers --un parameter for single reads and --un-conc for paired reads" /> + <param name="aligned_file" argument="--al/--al-conc" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write aligned reads (in fastq format) to separate file(s)" help="This triggers --al parameter for single reads and --al-conc for paired reads" /> </when> </conditional> + <conditional name="sam_options"> + <param name="sam_options_selector" type="select" label="SAM options"> + <option value="defaults">Use default values</option> + <option value="advanced">Specify output options</option> + </param> + <when value="defaults" /> + <when value="advanced"> + <param name="no_unal" argument="--no-unal" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress SAM records for reads that failed to align." help="Default: false"/> + <conditional name="read_groups"> + <param name="rg_labels" type="select" label="Edit Read Group IDs"> + <option value="No" /> + <option value="Yes" /> + </param> + <when value="No"/> + <when value="Yes"> + <param name="rg_id" argument="--rg-id" type="text" value="read_group" label="Read Group ID" help="Set the read group ID to the value set here. This causes the SAM @RG header line to be printed, with this input value 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 the value set here." /> + <repeat name="read_groups" title="Read Groups text"> + <param name="rg" argument="--rg" type="text" optional="true" label="Read Group text" help="Add specified 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, Read Group 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." /> + </repeat> + </when> + </conditional> + <param name="chr_text" type="select" label="Add/remove 'chr' from reference names in alignment files"> + <option value="" selected="true">Use default values</option> + <option value="--remove-chrname">Remove ‘chr’ from reference names in alignment (e.g., chr18 to 18)</option> + <option value="--add-chrname">Add ‘chr’ to reference names in alignment (e.g., 18 to chr18)</option> + </param> + <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"/> + </when> + </conditional> + <conditional name="other_options"> <param name="other_options_selector" type="select" label="Other options"> <option value="defaults">Use default values</option> @@ -877,6 +927,25 @@ <output name="output_alignments" file="hisat_output_spliced_1.bam" ftype="bam" lines_diff="2" /> <output name="novel_splicesite_output" file="novel_splicesite_out.tab" ftype="tabular" /> </test> + <!-- Ensure SAM output settings work --> + <test expect_num_outputs="1" > + <param name="type" value="paired_interleaved" /> + <param name="source" value="history" /> + <param name="history_item" ftype="fasta" value="phiX.fa" /> + <param name="input_1" ftype="fastqsanger.bz2" value="hisat_input_1_interleaved.fastq.bz2" /> + <param name="adv|sam_options|sam_options_selector" value="advanced"/> + <param name="adv|sam_options|no_unal" value="true"/> + <param name="adv|sam_options|read_groups|rg_labels" value="Yes"/> + <repeat name="adv|sam_options|read_groups|read_groups"> + <param name="rg" value="BC:test1"/> + </repeat> + <repeat name="adv|sam_options|read_groups|read_groups"> + <param name="rg" value="CN:test2"/> + </repeat> + <param name="adv|sam_options|chr_text" value="--add-chrname"/> + <param name="adv|sam_options|omit_sec_seq" value="True"/> + <output name="output_alignments" file="hisat_output_5.bam" ftype="bam" lines_diff="2" /> + </test> </tests> <help><![CDATA[ @@ -1218,6 +1287,28 @@ align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior. +----- + +** SAM options + + --no-unal + Suppress SAM records for reads that failed to align. + --rg-id <text> + + 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>. + --rg <text> + 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. + + --remove-chrname + Remove ‘chr’ from reference names in alignment (e.g., chr18 to 18) + + --add-chrname + Add ‘chr’ to reference names in alignment (e.g., 18 to chr18) + + --omit-sec-seq + 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. + +----- **Output options**::