| Previous changeset 3:b4c6f054210a (2022-04-04) Next changeset 5:f69501361cec (2024-09-02) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit c142110046b4ed562e8240a65f5603640752dc2e |
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modified:
pear.xml |
| b |
| diff -r b4c6f054210a -r 037f0acc7830 pear.xml --- a/pear.xml Mon Apr 04 08:31:45 2022 +0000 +++ b/pear.xml Mon Aug 12 07:15:00 2024 +0000 |
| [ |
| b'@@ -1,19 +1,19 @@\n-<tool id="iuc_pear" name="Pear" version="@TOOL_VERSION@.@VERSION_SUFFIX@" profile="20.09">\n+<tool id="iuc_pear" name="Pear" version="@TOOL_VERSION@.@VERSION_SUFFIX@" profile="23.0">\n <description>Paired-End read merger</description>\n <macros>\n <token name="@TOOL_VERSION@">0.9.6</token>\n- <token name="@VERSION_SUFFIX@">2</token>\n+ <token name="@VERSION_SUFFIX@">3</token>\n <xml name="format_action">\n <actions>\n <conditional name="library.type">\n <when value="paired">\n <action type="format">\n- <option type="from_param" name="library.forward" param_attribute="ext" />\n+ <option type="from_param" name="library.forward" param_attribute="ext"/>\n </action>\n </when>\n <when value="paired_collection">\n <action type="format">\n- <option type="from_param" name="library.input_collection" param_attribute="forward.ext" />\n+ <option type="from_param" name="library.input_collection" param_attribute="forward.ext"/>\n </action>\n </when>\n </conditional>\n@@ -26,18 +26,12 @@\n <requirements>\n <requirement type="package" version="@TOOL_VERSION@">pear</requirement>\n </requirements>\n- <stdio>\n- <exit_code range="1:" />\n- <exit_code range=":-1" />\n- <regex match="Error:" />\n- <regex match="Exception:" />\n- </stdio>\n- <command>\n+ <command detect_errors="aggressive">\n <![CDATA[\n pear\n #if str( $library.type ) == "paired":\n- -f "$library.forward"\n- -r "$library.reverse"\n+ -f \'$library.forward\'\n+ -r \'$library.reverse\'\n #if $library.forward.is_of_type( \'fastqillumina\' ):\n --phred-base 64\n #else:\n@@ -45,8 +39,8 @@\n #end if\n #else\n ## prepare collection\n- -f "$library.input_collection.forward"\n- -r "$library.input_collection.reverse"\n+ -f \'$library.input_collection.forward\'\n+ -r \'$library.input_collection.reverse\'\n #if $library.input_collection.forward.is_of_type( \'fastqillumina\' ):\n --phred-base 64\n #else:\n@@ -57,7 +51,7 @@\n --output pear\n --p-value $pvalue\n --min-overlap $min_overlap\n- #if int($max_assembly_length) > 0:\n+ #if $max_assembly_length and int($max_assembly_length) > 0:\n --max-asm-length $max_assembly_length\n #end if\n --min-asm-length $min_assembly_length\n@@ -66,7 +60,7 @@\n --max-uncalled-base $max_uncalled_base\n --test-method $test_method\n --empirical-freqs $empirical_freqs\n- -j "\\${GALAXY_SLOTS:-8}"\n+ --threads "\\${GALAXY_SLOTS:-8}"\n --score-method $score_method\n --cap $cap\n $nbase\n@@ -75,64 +69,38 @@\n <inputs>\n <conditional name="library">\n <param name="type" type="select" label="Dataset type">\n- <option value="paired">Paired-end</option>\n- <option value="paired_collection">Paired-end Dataset Collection</option>\n+ <option value="paired">Paired-end</option>\n+ <option value="paired_collection">Paired-end Dataset Collection</option>\n </param>\n <when value="paired">\n- <param name="forward" type="data" format="fastqillumina,fastqsanger"\n- label="Name of file that contains the forward paired-end reads" help="-f" />\n- <param name="reverse" type="data" format="fastqillumina,fastqsanger"\n- label="Name of file that contains the reverse paired-end reads" help="-r" />\n+ <param name="forward" type="data" format'..b'--empirical-freqs)"/>\n+ <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)"/>\n <param name="score_method" type="select" label="Scoring method" help="(--score-method)">\n <option value="1">OES with +1 for match and -1 for mismatch</option>\n <option value="2" selected="true">Assembly score (AS) use +1 for match and -1 for mismatch multiplied by base quality scores</option>\n <option value="3">Ignore quality scores and use +1 for a match and -1 for a mismatch</option>\n </param>\n-\n- <param name="outputs" type="select" optional="false" multiple="true" label="Output files">\n+ <param name="outputs" type="select" optional="false" label="Output files" multiple="true">\n <option value="assembled" selected="true">Assembled reads</option>\n <option value="unassembled_forward">Forward unassembled reads</option>\n <option value="unassembled_reverse">Reverse unassembled reads</option>\n@@ -161,13 +129,13 @@\n <test expect_num_outputs="2">\n <conditional name="library">\n <param name="type" value="paired"/>\n- <param name="forward" value="forward.fastq" ftype="fastqsanger" />\n- <param name="reverse" value="reverse.fastq" ftype="fastqsanger" />\n+ <param name="forward" value="forward.fastq" ftype="fastqsanger"/>\n+ <param name="reverse" value="reverse.fastq" ftype="fastqsanger"/>\n </conditional>\n- <param name="min_overlap" value="10" />\n- <param name="min_assembly_length" value="50" />\n- <param name="cap" value="0" />\n- <param name="outputs" value="assembled,unassembled_forward" />\n+ <param name="min_overlap" value="10"/>\n+ <param name="min_assembly_length" value="50"/>\n+ <param name="cap" value="0"/>\n+ <param name="outputs" value="assembled,unassembled_forward"/>\n <output name="assembled_reads" file="pear_assembled_results1.fastq" ftype="fastqsanger"/>\n <output name="unassembled_forward_reads" file="pear_unassembled_forward_results1.fastq" ftype="fastqsanger"/>\n </test>\n@@ -178,15 +146,15 @@\n <param name="type" value="paired_collection"/>\n <param name="input_collection">\n <collection type="paired">\n- <element name="forward" value="forward.fastq" ftype="fastqillumina" />\n- <element name="reverse" value="reverse.fastq" ftype="fastqillumina" />\n+ <element name="forward" value="forward.fastq" ftype="fastqillumina"/>\n+ <element name="reverse" value="reverse.fastq" ftype="fastqillumina"/>\n </collection>\n </param>\n </conditional>\n- <param name="min_overlap" value="10" />\n- <param name="min_assembly_length" value="50" />\n- <param name="cap" value="0" />\n- <param name="outputs" value="assembled,unassembled_forward" />\n+ <param name="min_overlap" value="10"/>\n+ <param name="min_assembly_length" value="50"/>\n+ <param name="cap" value="0"/>\n+ <param name="outputs" value="assembled,unassembled_forward"/>\n <output name="assembled_reads" ftype="fastqillumina">\n <assert_contents>\n <has_line_matching expression="@.*"/>\n@@ -222,7 +190,7 @@\n \n ]]>\n </help>\n- <citations>\n- <citation type="doi">10.1093/bioinformatics/btt593</citation>\n- </citations>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btt593</citation>\n+ </citations>\n </tool>\n' |