| Previous changeset 2:2f804526f5fd (2017-11-09) Next changeset 4:037f0acc7830 (2024-08-12) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit 6e869b3e13ed7b012b270f14fce812613642e5f2" |
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modified:
pear.xml |
| b |
| diff -r 2f804526f5fd -r b4c6f054210a pear.xml --- a/pear.xml Thu Nov 09 07:28:37 2017 -0500 +++ b/pear.xml Mon Apr 04 08:31:45 2022 +0000 |
| [ |
| b'@@ -1,7 +1,30 @@\n-<tool id="iuc_pear" name="Pear" version="0.9.6.1">\n+<tool id="iuc_pear" name="Pear" version="@TOOL_VERSION@.@VERSION_SUFFIX@" profile="20.09">\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+ <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+ </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+ </action>\n+ </when>\n+ </conditional>\n+ </actions>\n+ </xml>\n+ </macros>\n+ <xrefs>\n+ <xref type="bio.tools">pear</xref>\n+ </xrefs>\n <requirements>\n- <requirement type="package" version="0.9.6">pear</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">pear</requirement>\n </requirements>\n <stdio>\n <exit_code range="1:" />\n@@ -69,32 +92,32 @@\n </conditional>\n \n <!-- optional -->\n- <param name="pvalue" type="float" value="0.01" min="0" optional="True" max="1" label="Specify a p-value for the statistical test"\n+ <param name="pvalue" type="float" value="0.01" min="0" optional="true" max="1" label="Specify a p-value for the statistical test"\n 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)" />\n \n- <param name="min_overlap" type="integer" value="10" optional="True" label="Minimum overlap size"\n+ <param name="min_overlap" type="integer" value="10" optional="true" label="Minimum overlap size"\n 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)" />\n \n- <param name="max_assembly_length" type="integer" value="0" optional="True" label="Maximum possible length of the assembled sequences"\n+ <param name="max_assembly_length" type="integer" value="0" optional="true" label="Maximum possible length of the assembled sequences"\n help="Setting this value to 0 disables the restriction and assembled sequences may be arbitrary long. (--max-assembly-length)" />\n \n- <param name="min_assembly_length" type="integer" value="50" optional="True" label="Minimum possible length of the assembled sequences"\n+ <param name="min_assembly_length" type="integer" value="50" optional="true" label="Minimum possible length of the assembled sequences"\n help="Setting this value to 0 disables the restriction and assembled sequences may be arbitrary short. (--min-assembly-length)" />\n \n- <param name="min_trim_length" type="integer" value="1" optional="True" label="Minimum length of reads after trimming the low quality part"\n+ <param name="min_trim_length" type="integer" value="1" optional="true" label="Minimum length of reads after trimming the low quality part"\n help="See option -q. (--min-trim-length)" />\n \n- <param name="quality_threshold" type="integer" value="0" optional="True" label="Quality score threshold for trimming the low quality part of a read"\n+ <param name="quality_threshold" type="integer" value="0" optional="true" label="Quality score threshold for trimming the low quality part of a read"\n help="If the quality scores of two consecutive bases are strictly less than the spe'..b'mbled.forward.fastq" label="${tool.name} on ${on_string}: Unassembled forward reads">\n+ <expand macro="format_action"/>\n+ <filter>\'unassembled_forward\' in outputs</filter>\n </data>\n- <data format="input" name="unassembled_reverse_reads" from_work_dir="pear.unassembled.reverse.fastq" label="${tool.name} on ${on_string}: Unassembled reverse reads">\n- <filter>\'reverse\' in outputs</filter>\n+ <data format="auto" name="unassembled_reverse_reads" from_work_dir="pear.unassembled.reverse.fastq" label="${tool.name} on ${on_string}: Unassembled reverse reads">\n+ <expand macro="format_action"/>\n+ <filter>\'unassembled_reverse\' in outputs</filter>\n </data>\n- <data format="input" name="discarded_reads" from_work_dir="pear.discarded.fastq" label="${tool.name} on ${on_string}: Discarded reads">\n+ <data format="auto" name="discarded_reads" from_work_dir="pear.discarded.fastq" label="${tool.name} on ${on_string}: Discarded reads">\n+ <expand macro="format_action"/>\n <filter>\'discarded\' in outputs</filter>\n </data>\n </outputs>\n <tests>\n- <test>\n- <param name="forward" value="forward.fastq" ftype="fastqsanger" />\n- <param name="reverse" value="reverse.fastq" ftype="fastqsanger" />\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+ </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,forward" />\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+ <!-- same test as before using collection input and fastqillumina \n+ (even if it isn\'t) .. therefore only loose check of outputs -->\n+ <test expect_num_outputs="2">\n+ <conditional name="library">\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+ </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+ <output name="assembled_reads" ftype="fastqillumina">\n+ <assert_contents>\n+ <has_line_matching expression="@.*"/>\n+ </assert_contents>\n+ </output>\n+ <output name="unassembled_forward_reads" ftype="fastqillumina">\n+ <assert_contents>\n+ <has_line_matching expression="@.*"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n </tests>\n <help>\n < license\n' |