Mercurial > repos > iuc > pear
changeset 3:b4c6f054210a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit 6e869b3e13ed7b012b270f14fce812613642e5f2"
| author | iuc |
|---|---|
| date | Mon, 04 Apr 2022 08:31:45 +0000 |
| parents | 2f804526f5fd |
| children | 037f0acc7830 |
| files | pear.xml |
| diffstat | 1 files changed, 84 insertions(+), 26 deletions(-) [+] |
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--- a/pear.xml Thu Nov 09 07:28:37 2017 -0500 +++ b/pear.xml Mon Apr 04 08:31:45 2022 +0000 @@ -1,7 +1,30 @@ -<tool id="iuc_pear" name="Pear" version="0.9.6.1"> +<tool id="iuc_pear" name="Pear" version="@TOOL_VERSION@.@VERSION_SUFFIX@" profile="20.09"> <description>Paired-End read merger</description> + <macros> + <token name="@TOOL_VERSION@">0.9.6</token> + <token name="@VERSION_SUFFIX@">2</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" /> + </action> + </when> + <when value="paired_collection"> + <action type="format"> + <option type="from_param" name="library.input_collection" param_attribute="forward.ext" /> + </action> + </when> + </conditional> + </actions> + </xml> + </macros> + <xrefs> + <xref type="bio.tools">pear</xref> + </xrefs> <requirements> - <requirement type="package" version="0.9.6">pear</requirement> + <requirement type="package" version="@TOOL_VERSION@">pear</requirement> </requirements> <stdio> <exit_code range="1:" /> @@ -69,32 +92,32 @@ </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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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="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="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> @@ -105,42 +128,76 @@ <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="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" display="checkboxes" optional="False" multiple="True" label="Output files"> - <option value="assembled" selected="True">Assembled reads</option> - <option value="forward">Forward unassembled reads</option> - <option value="reverse">Reverse unassembled reads</option> + <param name="outputs" type="select" optional="false" multiple="true" label="Output files"> + <option value="assembled" selected="true">Assembled reads</option> + <option value="unassembled_forward">Forward unassembled reads</option> + <option value="unassembled_reverse">Reverse unassembled reads</option> <option value="discarded">Discarded reads</option> </param> </inputs> <outputs> - <data format="input" name="assembled_reads" from_work_dir="pear.assembled.fastq" label="${tool.name} on ${on_string}: Assembled reads"> + <data name="assembled_reads" from_work_dir="pear.assembled.fastq" label="${tool.name} on ${on_string}: Assembled reads"> + <expand macro="format_action"/> <filter>'assembled' in outputs</filter> </data> - <data format="input" name="unassembled_forward_reads" from_work_dir="pear.unassembled.forward.fastq" label="${tool.name} on ${on_string}: Unassembled forward reads"> - <filter>'forward' in outputs</filter> + <data format="auto" name="unassembled_forward_reads" from_work_dir="pear.unassembled.forward.fastq" label="${tool.name} on ${on_string}: Unassembled forward reads"> + <expand macro="format_action"/> + <filter>'unassembled_forward' in outputs</filter> </data> - <data format="input" name="unassembled_reverse_reads" from_work_dir="pear.unassembled.reverse.fastq" label="${tool.name} on ${on_string}: Unassembled reverse reads"> - <filter>'reverse' in outputs</filter> + <data format="auto" name="unassembled_reverse_reads" from_work_dir="pear.unassembled.reverse.fastq" label="${tool.name} on ${on_string}: Unassembled reverse reads"> + <expand macro="format_action"/> + <filter>'unassembled_reverse' in outputs</filter> </data> - <data format="input" name="discarded_reads" from_work_dir="pear.discarded.fastq" label="${tool.name} on ${on_string}: Discarded reads"> + <data format="auto" name="discarded_reads" from_work_dir="pear.discarded.fastq" label="${tool.name} on ${on_string}: Discarded reads"> + <expand macro="format_action"/> <filter>'discarded' in outputs</filter> </data> </outputs> <tests> - <test> - <param name="forward" value="forward.fastq" ftype="fastqsanger" /> - <param name="reverse" value="reverse.fastq" ftype="fastqsanger" /> + <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" /> + </conditional> <param name="min_overlap" value="10" /> <param name="min_assembly_length" value="50" /> <param name="cap" value="0" /> - <param name="outputs" value="assembled,forward" /> + <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> + <!-- same test as before using collection input and fastqillumina + (even if it isn't) .. therefore only loose check of outputs --> + <test expect_num_outputs="2"> + <conditional name="library"> + <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" /> + </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" /> + <output name="assembled_reads" ftype="fastqillumina"> + <assert_contents> + <has_line_matching expression="@.*"/> + </assert_contents> + </output> + <output name="unassembled_forward_reads" ftype="fastqillumina"> + <assert_contents> + <has_line_matching expression="@.*"/> + </assert_contents> + </output> + </test> </tests> <help> < license