Mercurial > repos > iuc > pear
changeset 4:037f0acc7830 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit c142110046b4ed562e8240a65f5603640752dc2e
| author | iuc |
|---|---|
| date | Mon, 12 Aug 2024 07:15:00 +0000 |
| parents | b4c6f054210a |
| children | |
| files | pear.xml |
| diffstat | 1 files changed, 42 insertions(+), 74 deletions(-) [+] |
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--- a/pear.xml Mon Apr 04 08:31:45 2022 +0000 +++ b/pear.xml Mon Aug 12 07:15:00 2024 +0000 @@ -1,19 +1,19 @@ -<tool id="iuc_pear" name="Pear" version="@TOOL_VERSION@.@VERSION_SUFFIX@" profile="20.09"> +<tool id="iuc_pear" name="Pear" version="@TOOL_VERSION@.@VERSION_SUFFIX@" profile="23.0"> <description>Paired-End read merger</description> <macros> <token name="@TOOL_VERSION@">0.9.6</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@VERSION_SUFFIX@">3</token> <xml name="format_action"> <actions> <conditional name="library.type"> <when value="paired"> <action type="format"> - <option type="from_param" name="library.forward" param_attribute="ext" /> + <option type="from_param" name="library.forward" param_attribute="ext"/> </action> </when> <when value="paired_collection"> <action type="format"> - <option type="from_param" name="library.input_collection" param_attribute="forward.ext" /> + <option type="from_param" name="library.input_collection" param_attribute="forward.ext"/> </action> </when> </conditional> @@ -26,18 +26,12 @@ <requirements> <requirement type="package" version="@TOOL_VERSION@">pear</requirement> </requirements> - <stdio> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> - <command> + <command detect_errors="aggressive"> <![CDATA[ pear #if str( $library.type ) == "paired": - -f "$library.forward" - -r "$library.reverse" + -f '$library.forward' + -r '$library.reverse' #if $library.forward.is_of_type( 'fastqillumina' ): --phred-base 64 #else: @@ -45,8 +39,8 @@ #end if #else ## prepare collection - -f "$library.input_collection.forward" - -r "$library.input_collection.reverse" + -f '$library.input_collection.forward' + -r '$library.input_collection.reverse' #if $library.input_collection.forward.is_of_type( 'fastqillumina' ): --phred-base 64 #else: @@ -57,7 +51,7 @@ --output pear --p-value $pvalue --min-overlap $min_overlap - #if int($max_assembly_length) > 0: + #if $max_assembly_length and int($max_assembly_length) > 0: --max-asm-length $max_assembly_length #end if --min-asm-length $min_assembly_length @@ -66,7 +60,7 @@ --max-uncalled-base $max_uncalled_base --test-method $test_method --empirical-freqs $empirical_freqs - -j "\${GALAXY_SLOTS:-8}" + --threads "\${GALAXY_SLOTS:-8}" --score-method $score_method --cap $cap $nbase @@ -75,64 +69,38 @@ <inputs> <conditional name="library"> <param name="type" type="select" label="Dataset type"> - <option value="paired">Paired-end</option> - <option value="paired_collection">Paired-end Dataset Collection</option> + <option value="paired">Paired-end</option> + <option value="paired_collection">Paired-end Dataset Collection</option> </param> <when value="paired"> - <param name="forward" type="data" format="fastqillumina,fastqsanger" - label="Name of file that contains the forward paired-end reads" help="-f" /> - <param name="reverse" type="data" format="fastqillumina,fastqsanger" - label="Name of file that contains the reverse paired-end reads" help="-r" /> + <param name="forward" type="data" format="fastqillumina,fastqsanger" label="Name of file that contains the forward paired-end reads" help="-f"/> + <param name="reverse" type="data" format="fastqillumina,fastqsanger" label="Name of file that contains the reverse paired-end reads" help="-r"/> </when> <when value="paired_collection"> - <param name="input_collection" format="fastqillumina,fastqsanger" - type="data_collection" collection_type="paired" - label="FASTQ Paired Dataset" help="Nucleotide-space: Must have PHRED-scaled quality values. (-f and -r)" /> + <param name="input_collection" type="data_collection" format="fastqillumina,fastqsanger" label="FASTQ Paired Dataset" help="Nucleotide-space: Must have PHRED-scaled quality values. (-f and -r)" collection_type="paired"/> </when> </conditional> - <!-- optional --> - <param name="pvalue" type="float" value="0.01" min="0" optional="true" max="1" label="Specify a p-value for the statistical test" - help="If the computed p-value of a possible assembly exceeds the specified p-value then the paired-end read will not be assembled. Setting 1.0 disables the test. (--p-value)" /> - - <param name="min_overlap" type="integer" value="10" optional="true" label="Minimum overlap size" - help="The minimum overlap may be set to 1 when the statistical test is used. However, further restricting the minimum overlap size to a proper value may reduce false-positive assembles. (--min-overlap)" /> - - <param name="max_assembly_length" type="integer" value="0" optional="true" label="Maximum possible length of the assembled sequences" - help="Setting this value to 0 disables the restriction and assembled sequences may be arbitrary long. (--max-assembly-length)" /> - - <param name="min_assembly_length" type="integer" value="50" optional="true" label="Minimum possible length of the assembled sequences" - help="Setting this value to 0 disables the restriction and assembled sequences may be arbitrary short. (--min-assembly-length)" /> - - <param name="min_trim_length" type="integer" value="1" optional="true" label="Minimum length of reads after trimming the low quality part" - help="See option -q. (--min-trim-length)" /> - - <param name="quality_threshold" type="integer" value="0" optional="true" label="Quality score threshold for trimming the low quality part of a read" - help="If the quality scores of two consecutive bases are strictly less than the specified threshold, the rest of the read will be trimmed. (--quality-threshold)" /> - - <param name="max_uncalled_base" type="float" value="1.0" min="0" optional="true" max="1" label="Maximal proportion of uncalled bases in a read" - help="Setting this value to 0 will cause PEAR to discard all reads containing uncalled bases. The other extreme setting is 1 which causes PEAR to process all reads independent on the number of uncalled bases. (--max-uncalled-base)" /> - - <param name="cap" type="integer" value="40" optional="true" label="Specify the upper bound for the resulting quality score" - help="If set to zero, capping is disabled. (--cap)" /> - + <param name="pvalue" argument="--p-value" type="float" min="0" max="1" value="0.01" label="Specify a p-value for the statistical test" help="If the computed p-value of a possible assembly exceeds the specified p-value then the paired-end read will not be assembled. Setting 1.0 disables the test. (--p-value)"/> + <param argument="--min-overlap" type="integer" value="10" min="0" label="Minimum overlap size" help="The minimum overlap may be set to 1 when the statistical test is used. However, further restricting the minimum overlap size to a proper value may reduce false-positive assembles. (--min-overlap)"/> + <param argument="--max-assembly-length" min="0" type="integer" value="0" label="Maximum possible length of the assembled sequences" help="Setting this value to 0 disables the restriction and assembled sequences may be arbitrary long. (--max-assembly-length)"/> + <param argument="--min-assembly-length" min="0" type="integer" value="50" label="Minimum possible length of the assembled sequences" help="Setting this value to 0 disables the restriction and assembled sequences may be arbitrary short."/> + <param argument="--min-trim-length" min="0" type="integer" value="1" label="Minimum length of reads after trimming the low quality part" help="See option --quality-threshold."/> + <param argument="--quality-threshold" type="integer" value="0" label="Quality score threshold for trimming the low quality part of a read" help="If the quality scores of two consecutive bases are strictly less than the specified threshold, the rest of the read will be trimmed."/> + <param argument="--max-uncalled-base" type="float" min="0" max="1" value="1.0" label="Maximal proportion of uncalled bases in a read" help="Setting this value to 0 will cause PEAR to discard all reads containing uncalled bases. The other extreme setting is 1 which causes PEAR to process all reads independent on the number of uncalled bases."/> + <param argument="--cap" type="integer" value="40" min="0" label="Specify the upper bound for the resulting quality score" help="If set to zero, capping is disabled."/> <param name="test_method" type="select" label="Type of statistical test" help="(--test-method)"> <option value="1" selected="true">Given the minimum allowed overlap, test using the highest OES (1)</option> <option value="2">Use the acceptance probability (2)</option> </param> - - <param name="empirical_freqs" type="boolean" truevalue="-e" falsevalue="" checked="false" - label="Disable empirical base frequencies" help="(--empirical-freqs)" /> - <param name="nbase" type="boolean" truevalue="--nbase" falsevalue="" checked="false" - label="Use N base if uncertain" help="When merging a base-pair that consists of two non-equal bases out of which none is degenerate, set the merged base to N and use the highest quality score of the two bases. (--nbase)" /> - + <param name="empirical_freqs" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Disable empirical base frequencies" help="(--empirical-freqs)"/> + <param name="nbase" type="boolean" truevalue="--nbase" falsevalue="" checked="false" label="Use N base if uncertain" help="When merging a base-pair that consists of two non-equal bases out of which none is degenerate, set the merged base to N and use the highest quality score of the two bases. (--nbase)"/> <param name="score_method" type="select" label="Scoring method" help="(--score-method)"> <option value="1">OES with +1 for match and -1 for mismatch</option> <option value="2" selected="true">Assembly score (AS) use +1 for match and -1 for mismatch multiplied by base quality scores</option> <option value="3">Ignore quality scores and use +1 for a match and -1 for a mismatch</option> </param> - - <param name="outputs" type="select" optional="false" multiple="true" label="Output files"> + <param name="outputs" type="select" optional="false" label="Output files" multiple="true"> <option value="assembled" selected="true">Assembled reads</option> <option value="unassembled_forward">Forward unassembled reads</option> <option value="unassembled_reverse">Reverse unassembled reads</option> @@ -161,13 +129,13 @@ <test expect_num_outputs="2"> <conditional name="library"> <param name="type" value="paired"/> - <param name="forward" value="forward.fastq" ftype="fastqsanger" /> - <param name="reverse" value="reverse.fastq" ftype="fastqsanger" /> + <param name="forward" value="forward.fastq" ftype="fastqsanger"/> + <param name="reverse" value="reverse.fastq" ftype="fastqsanger"/> </conditional> - <param name="min_overlap" value="10" /> - <param name="min_assembly_length" value="50" /> - <param name="cap" value="0" /> - <param name="outputs" value="assembled,unassembled_forward" /> + <param name="min_overlap" value="10"/> + <param name="min_assembly_length" value="50"/> + <param name="cap" value="0"/> + <param name="outputs" value="assembled,unassembled_forward"/> <output name="assembled_reads" file="pear_assembled_results1.fastq" ftype="fastqsanger"/> <output name="unassembled_forward_reads" file="pear_unassembled_forward_results1.fastq" ftype="fastqsanger"/> </test> @@ -178,15 +146,15 @@ <param name="type" value="paired_collection"/> <param name="input_collection"> <collection type="paired"> - <element name="forward" value="forward.fastq" ftype="fastqillumina" /> - <element name="reverse" value="reverse.fastq" ftype="fastqillumina" /> + <element name="forward" value="forward.fastq" ftype="fastqillumina"/> + <element name="reverse" value="reverse.fastq" ftype="fastqillumina"/> </collection> </param> </conditional> - <param name="min_overlap" value="10" /> - <param name="min_assembly_length" value="50" /> - <param name="cap" value="0" /> - <param name="outputs" value="assembled,unassembled_forward" /> + <param name="min_overlap" value="10"/> + <param name="min_assembly_length" value="50"/> + <param name="cap" value="0"/> + <param name="outputs" value="assembled,unassembled_forward"/> <output name="assembled_reads" ftype="fastqillumina"> <assert_contents> <has_line_matching expression="@.*"/> @@ -222,7 +190,7 @@ ]]> </help> - <citations> - <citation type="doi">10.1093/bioinformatics/btt593</citation> - </citations> + <citations> + <citation type="doi">10.1093/bioinformatics/btt593</citation> + </citations> </tool>