Mercurial > repos > iuc > pear
comparison pear.xml @ 3:b4c6f054210a draft default tip
"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 |
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| 2:2f804526f5fd | 3:b4c6f054210a |
|---|---|
| 1 <tool id="iuc_pear" name="Pear" version="0.9.6.1"> | 1 <tool id="iuc_pear" name="Pear" version="@TOOL_VERSION@.@VERSION_SUFFIX@" profile="20.09"> |
| 2 <description>Paired-End read merger</description> | 2 <description>Paired-End read merger</description> |
| 3 <macros> | |
| 4 <token name="@TOOL_VERSION@">0.9.6</token> | |
| 5 <token name="@VERSION_SUFFIX@">2</token> | |
| 6 <xml name="format_action"> | |
| 7 <actions> | |
| 8 <conditional name="library.type"> | |
| 9 <when value="paired"> | |
| 10 <action type="format"> | |
| 11 <option type="from_param" name="library.forward" param_attribute="ext" /> | |
| 12 </action> | |
| 13 </when> | |
| 14 <when value="paired_collection"> | |
| 15 <action type="format"> | |
| 16 <option type="from_param" name="library.input_collection" param_attribute="forward.ext" /> | |
| 17 </action> | |
| 18 </when> | |
| 19 </conditional> | |
| 20 </actions> | |
| 21 </xml> | |
| 22 </macros> | |
| 23 <xrefs> | |
| 24 <xref type="bio.tools">pear</xref> | |
| 25 </xrefs> | |
| 3 <requirements> | 26 <requirements> |
| 4 <requirement type="package" version="0.9.6">pear</requirement> | 27 <requirement type="package" version="@TOOL_VERSION@">pear</requirement> |
| 5 </requirements> | 28 </requirements> |
| 6 <stdio> | 29 <stdio> |
| 7 <exit_code range="1:" /> | 30 <exit_code range="1:" /> |
| 8 <exit_code range=":-1" /> | 31 <exit_code range=":-1" /> |
| 9 <regex match="Error:" /> | 32 <regex match="Error:" /> |
| 67 label="FASTQ Paired Dataset" help="Nucleotide-space: Must have PHRED-scaled quality values. (-f and -r)" /> | 90 label="FASTQ Paired Dataset" help="Nucleotide-space: Must have PHRED-scaled quality values. (-f and -r)" /> |
| 68 </when> | 91 </when> |
| 69 </conditional> | 92 </conditional> |
| 70 | 93 |
| 71 <!-- optional --> | 94 <!-- optional --> |
| 72 <param name="pvalue" type="float" value="0.01" min="0" optional="True" max="1" label="Specify a p-value for the statistical test" | 95 <param name="pvalue" type="float" value="0.01" min="0" optional="true" max="1" label="Specify a p-value for the statistical test" |
| 73 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)" /> | 96 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)" /> |
| 74 | 97 |
| 75 <param name="min_overlap" type="integer" value="10" optional="True" label="Minimum overlap size" | 98 <param name="min_overlap" type="integer" value="10" optional="true" label="Minimum overlap size" |
| 76 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)" /> | 99 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)" /> |
| 77 | 100 |
| 78 <param name="max_assembly_length" type="integer" value="0" optional="True" label="Maximum possible length of the assembled sequences" | 101 <param name="max_assembly_length" type="integer" value="0" optional="true" label="Maximum possible length of the assembled sequences" |
| 79 help="Setting this value to 0 disables the restriction and assembled sequences may be arbitrary long. (--max-assembly-length)" /> | 102 help="Setting this value to 0 disables the restriction and assembled sequences may be arbitrary long. (--max-assembly-length)" /> |
| 80 | 103 |
| 81 <param name="min_assembly_length" type="integer" value="50" optional="True" label="Minimum possible length of the assembled sequences" | 104 <param name="min_assembly_length" type="integer" value="50" optional="true" label="Minimum possible length of the assembled sequences" |
| 82 help="Setting this value to 0 disables the restriction and assembled sequences may be arbitrary short. (--min-assembly-length)" /> | 105 help="Setting this value to 0 disables the restriction and assembled sequences may be arbitrary short. (--min-assembly-length)" /> |
| 83 | 106 |
| 84 <param name="min_trim_length" type="integer" value="1" optional="True" label="Minimum length of reads after trimming the low quality part" | 107 <param name="min_trim_length" type="integer" value="1" optional="true" label="Minimum length of reads after trimming the low quality part" |
| 85 help="See option -q. (--min-trim-length)" /> | 108 help="See option -q. (--min-trim-length)" /> |
| 86 | 109 |
| 87 <param name="quality_threshold" type="integer" value="0" optional="True" label="Quality score threshold for trimming the low quality part of a read" | 110 <param name="quality_threshold" type="integer" value="0" optional="true" label="Quality score threshold for trimming the low quality part of a read" |
| 88 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)" /> | 111 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)" /> |
| 89 | 112 |
| 90 <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" | 113 <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" |
| 91 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)" /> | 114 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)" /> |
| 92 | 115 |
| 93 <param name="cap" type="integer" value="40" optional="True" label="Specify the upper bound for the resulting quality score" | 116 <param name="cap" type="integer" value="40" optional="true" label="Specify the upper bound for the resulting quality score" |
| 94 help="If set to zero, capping is disabled. (--cap)" /> | 117 help="If set to zero, capping is disabled. (--cap)" /> |
| 95 | 118 |
| 96 <param name="test_method" type="select" label="Type of statistical test" help="(--test-method)"> | 119 <param name="test_method" type="select" label="Type of statistical test" help="(--test-method)"> |
| 97 <option value="1" selected="True">Given the minimum allowed overlap, test using the highest OES (1)</option> | 120 <option value="1" selected="true">Given the minimum allowed overlap, test using the highest OES (1)</option> |
| 98 <option value="2">Use the acceptance probability (2)</option> | 121 <option value="2">Use the acceptance probability (2)</option> |
| 99 </param> | 122 </param> |
| 100 | 123 |
| 101 <param name="empirical_freqs" type="boolean" truevalue="-e" falsevalue="" checked="false" | 124 <param name="empirical_freqs" type="boolean" truevalue="-e" falsevalue="" checked="false" |
| 102 label="Disable empirical base frequencies" help="(--empirical-freqs)" /> | 125 label="Disable empirical base frequencies" help="(--empirical-freqs)" /> |
| 103 <param name="nbase" type="boolean" truevalue="--nbase" falsevalue="" checked="false" | 126 <param name="nbase" type="boolean" truevalue="--nbase" falsevalue="" checked="false" |
| 104 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)" /> | 127 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)" /> |
| 105 | 128 |
| 106 <param name="score_method" type="select" label="Scoring method" help="(--score-method)"> | 129 <param name="score_method" type="select" label="Scoring method" help="(--score-method)"> |
| 107 <option value="1">OES with +1 for match and -1 for mismatch</option> | 130 <option value="1">OES with +1 for match and -1 for mismatch</option> |
| 108 <option value="2" selected="True">Assembly score (AS) use +1 for match and -1 for mismatch multiplied by base quality scores</option> | 131 <option value="2" selected="true">Assembly score (AS) use +1 for match and -1 for mismatch multiplied by base quality scores</option> |
| 109 <option value="3">Ignore quality scores and use +1 for a match and -1 for a mismatch</option> | 132 <option value="3">Ignore quality scores and use +1 for a match and -1 for a mismatch</option> |
| 110 </param> | 133 </param> |
| 111 | 134 |
| 112 <param name="outputs" type="select" display="checkboxes" optional="False" multiple="True" label="Output files"> | 135 <param name="outputs" type="select" optional="false" multiple="true" label="Output files"> |
| 113 <option value="assembled" selected="True">Assembled reads</option> | 136 <option value="assembled" selected="true">Assembled reads</option> |
| 114 <option value="forward">Forward unassembled reads</option> | 137 <option value="unassembled_forward">Forward unassembled reads</option> |
| 115 <option value="reverse">Reverse unassembled reads</option> | 138 <option value="unassembled_reverse">Reverse unassembled reads</option> |
| 116 <option value="discarded">Discarded reads</option> | 139 <option value="discarded">Discarded reads</option> |
| 117 </param> | 140 </param> |
| 118 </inputs> | 141 </inputs> |
| 119 <outputs> | 142 <outputs> |
| 120 <data format="input" name="assembled_reads" from_work_dir="pear.assembled.fastq" label="${tool.name} on ${on_string}: Assembled reads"> | 143 <data name="assembled_reads" from_work_dir="pear.assembled.fastq" label="${tool.name} on ${on_string}: Assembled reads"> |
| 144 <expand macro="format_action"/> | |
| 121 <filter>'assembled' in outputs</filter> | 145 <filter>'assembled' in outputs</filter> |
| 122 </data> | 146 </data> |
| 123 <data format="input" name="unassembled_forward_reads" from_work_dir="pear.unassembled.forward.fastq" label="${tool.name} on ${on_string}: Unassembled forward reads"> | 147 <data format="auto" name="unassembled_forward_reads" from_work_dir="pear.unassembled.forward.fastq" label="${tool.name} on ${on_string}: Unassembled forward reads"> |
| 124 <filter>'forward' in outputs</filter> | 148 <expand macro="format_action"/> |
| 125 </data> | 149 <filter>'unassembled_forward' in outputs</filter> |
| 126 <data format="input" name="unassembled_reverse_reads" from_work_dir="pear.unassembled.reverse.fastq" label="${tool.name} on ${on_string}: Unassembled reverse reads"> | 150 </data> |
| 127 <filter>'reverse' in outputs</filter> | 151 <data format="auto" name="unassembled_reverse_reads" from_work_dir="pear.unassembled.reverse.fastq" label="${tool.name} on ${on_string}: Unassembled reverse reads"> |
| 128 </data> | 152 <expand macro="format_action"/> |
| 129 <data format="input" name="discarded_reads" from_work_dir="pear.discarded.fastq" label="${tool.name} on ${on_string}: Discarded reads"> | 153 <filter>'unassembled_reverse' in outputs</filter> |
| 154 </data> | |
| 155 <data format="auto" name="discarded_reads" from_work_dir="pear.discarded.fastq" label="${tool.name} on ${on_string}: Discarded reads"> | |
| 156 <expand macro="format_action"/> | |
| 130 <filter>'discarded' in outputs</filter> | 157 <filter>'discarded' in outputs</filter> |
| 131 </data> | 158 </data> |
| 132 </outputs> | 159 </outputs> |
| 133 <tests> | 160 <tests> |
| 134 <test> | 161 <test expect_num_outputs="2"> |
| 135 <param name="forward" value="forward.fastq" ftype="fastqsanger" /> | 162 <conditional name="library"> |
| 136 <param name="reverse" value="reverse.fastq" ftype="fastqsanger" /> | 163 <param name="type" value="paired"/> |
| 164 <param name="forward" value="forward.fastq" ftype="fastqsanger" /> | |
| 165 <param name="reverse" value="reverse.fastq" ftype="fastqsanger" /> | |
| 166 </conditional> | |
| 137 <param name="min_overlap" value="10" /> | 167 <param name="min_overlap" value="10" /> |
| 138 <param name="min_assembly_length" value="50" /> | 168 <param name="min_assembly_length" value="50" /> |
| 139 <param name="cap" value="0" /> | 169 <param name="cap" value="0" /> |
| 140 <param name="outputs" value="assembled,forward" /> | 170 <param name="outputs" value="assembled,unassembled_forward" /> |
| 141 <output name="assembled_reads" file="pear_assembled_results1.fastq" ftype="fastqsanger"/> | 171 <output name="assembled_reads" file="pear_assembled_results1.fastq" ftype="fastqsanger"/> |
| 142 <output name="unassembled_forward_reads" file="pear_unassembled_forward_results1.fastq" ftype="fastqsanger"/> | 172 <output name="unassembled_forward_reads" file="pear_unassembled_forward_results1.fastq" ftype="fastqsanger"/> |
| 173 </test> | |
| 174 <!-- same test as before using collection input and fastqillumina | |
| 175 (even if it isn't) .. therefore only loose check of outputs --> | |
| 176 <test expect_num_outputs="2"> | |
| 177 <conditional name="library"> | |
| 178 <param name="type" value="paired_collection"/> | |
| 179 <param name="input_collection"> | |
| 180 <collection type="paired"> | |
| 181 <element name="forward" value="forward.fastq" ftype="fastqillumina" /> | |
| 182 <element name="reverse" value="reverse.fastq" ftype="fastqillumina" /> | |
| 183 </collection> | |
| 184 </param> | |
| 185 </conditional> | |
| 186 <param name="min_overlap" value="10" /> | |
| 187 <param name="min_assembly_length" value="50" /> | |
| 188 <param name="cap" value="0" /> | |
| 189 <param name="outputs" value="assembled,unassembled_forward" /> | |
| 190 <output name="assembled_reads" ftype="fastqillumina"> | |
| 191 <assert_contents> | |
| 192 <has_line_matching expression="@.*"/> | |
| 193 </assert_contents> | |
| 194 </output> | |
| 195 <output name="unassembled_forward_reads" ftype="fastqillumina"> | |
| 196 <assert_contents> | |
| 197 <has_line_matching expression="@.*"/> | |
| 198 </assert_contents> | |
| 199 </output> | |
| 143 </test> | 200 </test> |
| 144 </tests> | 201 </tests> |
| 145 <help> | 202 <help> |
| 146 < license | 220 [CC Attribution-NonCommercial-ShareAlike](https://creativecommons.org/licenses/by-nc-sa/3.0/) license |
| 163 and that commercial partners should obtain a license. | 221 and that commercial partners should obtain a license. |
| 164 | 222 |