Mercurial > repos > iuc > pear
comparison pear.xml @ 4:037f0acc7830 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit c142110046b4ed562e8240a65f5603640752dc2e
author | iuc |
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date | Mon, 12 Aug 2024 07:15:00 +0000 |
parents | b4c6f054210a |
children | f69501361cec |
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3:b4c6f054210a | 4:037f0acc7830 |
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1 <tool id="iuc_pear" name="Pear" version="@TOOL_VERSION@.@VERSION_SUFFIX@" profile="20.09"> | 1 <tool id="iuc_pear" name="Pear" version="@TOOL_VERSION@.@VERSION_SUFFIX@" profile="23.0"> |
2 <description>Paired-End read merger</description> | 2 <description>Paired-End read merger</description> |
3 <macros> | 3 <macros> |
4 <token name="@TOOL_VERSION@">0.9.6</token> | 4 <token name="@TOOL_VERSION@">0.9.6</token> |
5 <token name="@VERSION_SUFFIX@">2</token> | 5 <token name="@VERSION_SUFFIX@">3</token> |
6 <xml name="format_action"> | 6 <xml name="format_action"> |
7 <actions> | 7 <actions> |
8 <conditional name="library.type"> | 8 <conditional name="library.type"> |
9 <when value="paired"> | 9 <when value="paired"> |
10 <action type="format"> | 10 <action type="format"> |
11 <option type="from_param" name="library.forward" param_attribute="ext" /> | 11 <option type="from_param" name="library.forward" param_attribute="ext"/> |
12 </action> | 12 </action> |
13 </when> | 13 </when> |
14 <when value="paired_collection"> | 14 <when value="paired_collection"> |
15 <action type="format"> | 15 <action type="format"> |
16 <option type="from_param" name="library.input_collection" param_attribute="forward.ext" /> | 16 <option type="from_param" name="library.input_collection" param_attribute="forward.ext"/> |
17 </action> | 17 </action> |
18 </when> | 18 </when> |
19 </conditional> | 19 </conditional> |
20 </actions> | 20 </actions> |
21 </xml> | 21 </xml> |
24 <xref type="bio.tools">pear</xref> | 24 <xref type="bio.tools">pear</xref> |
25 </xrefs> | 25 </xrefs> |
26 <requirements> | 26 <requirements> |
27 <requirement type="package" version="@TOOL_VERSION@">pear</requirement> | 27 <requirement type="package" version="@TOOL_VERSION@">pear</requirement> |
28 </requirements> | 28 </requirements> |
29 <stdio> | 29 <command detect_errors="aggressive"> |
30 <exit_code range="1:" /> | |
31 <exit_code range=":-1" /> | |
32 <regex match="Error:" /> | |
33 <regex match="Exception:" /> | |
34 </stdio> | |
35 <command> | |
36 <![CDATA[ | 30 <![CDATA[ |
37 pear | 31 pear |
38 #if str( $library.type ) == "paired": | 32 #if str( $library.type ) == "paired": |
39 -f "$library.forward" | 33 -f '$library.forward' |
40 -r "$library.reverse" | 34 -r '$library.reverse' |
41 #if $library.forward.is_of_type( 'fastqillumina' ): | 35 #if $library.forward.is_of_type( 'fastqillumina' ): |
42 --phred-base 64 | 36 --phred-base 64 |
43 #else: | 37 #else: |
44 --phred-base 33 | 38 --phred-base 33 |
45 #end if | 39 #end if |
46 #else | 40 #else |
47 ## prepare collection | 41 ## prepare collection |
48 -f "$library.input_collection.forward" | 42 -f '$library.input_collection.forward' |
49 -r "$library.input_collection.reverse" | 43 -r '$library.input_collection.reverse' |
50 #if $library.input_collection.forward.is_of_type( 'fastqillumina' ): | 44 #if $library.input_collection.forward.is_of_type( 'fastqillumina' ): |
51 --phred-base 64 | 45 --phred-base 64 |
52 #else: | 46 #else: |
53 --phred-base 33 | 47 --phred-base 33 |
54 #end if | 48 #end if |
55 #end if | 49 #end if |
56 | 50 |
57 --output pear | 51 --output pear |
58 --p-value $pvalue | 52 --p-value $pvalue |
59 --min-overlap $min_overlap | 53 --min-overlap $min_overlap |
60 #if int($max_assembly_length) > 0: | 54 #if $max_assembly_length and int($max_assembly_length) > 0: |
61 --max-asm-length $max_assembly_length | 55 --max-asm-length $max_assembly_length |
62 #end if | 56 #end if |
63 --min-asm-length $min_assembly_length | 57 --min-asm-length $min_assembly_length |
64 --min-trim-length $min_trim_length | 58 --min-trim-length $min_trim_length |
65 --quality-theshold $quality_threshold | 59 --quality-theshold $quality_threshold |
66 --max-uncalled-base $max_uncalled_base | 60 --max-uncalled-base $max_uncalled_base |
67 --test-method $test_method | 61 --test-method $test_method |
68 --empirical-freqs $empirical_freqs | 62 --empirical-freqs $empirical_freqs |
69 -j "\${GALAXY_SLOTS:-8}" | 63 --threads "\${GALAXY_SLOTS:-8}" |
70 --score-method $score_method | 64 --score-method $score_method |
71 --cap $cap | 65 --cap $cap |
72 $nbase | 66 $nbase |
73 ]]> | 67 ]]> |
74 </command> | 68 </command> |
75 <inputs> | 69 <inputs> |
76 <conditional name="library"> | 70 <conditional name="library"> |
77 <param name="type" type="select" label="Dataset type"> | 71 <param name="type" type="select" label="Dataset type"> |
78 <option value="paired">Paired-end</option> | 72 <option value="paired">Paired-end</option> |
79 <option value="paired_collection">Paired-end Dataset Collection</option> | 73 <option value="paired_collection">Paired-end Dataset Collection</option> |
80 </param> | 74 </param> |
81 <when value="paired"> | 75 <when value="paired"> |
82 <param name="forward" type="data" format="fastqillumina,fastqsanger" | 76 <param name="forward" type="data" format="fastqillumina,fastqsanger" label="Name of file that contains the forward paired-end reads" help="-f"/> |
83 label="Name of file that contains the forward paired-end reads" help="-f" /> | 77 <param name="reverse" type="data" format="fastqillumina,fastqsanger" label="Name of file that contains the reverse paired-end reads" help="-r"/> |
84 <param name="reverse" type="data" format="fastqillumina,fastqsanger" | |
85 label="Name of file that contains the reverse paired-end reads" help="-r" /> | |
86 </when> | 78 </when> |
87 <when value="paired_collection"> | 79 <when value="paired_collection"> |
88 <param name="input_collection" format="fastqillumina,fastqsanger" | 80 <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"/> |
89 type="data_collection" collection_type="paired" | |
90 label="FASTQ Paired Dataset" help="Nucleotide-space: Must have PHRED-scaled quality values. (-f and -r)" /> | |
91 </when> | 81 </when> |
92 </conditional> | 82 </conditional> |
93 | |
94 <!-- optional --> | 83 <!-- optional --> |
95 <param name="pvalue" type="float" value="0.01" min="0" optional="true" max="1" label="Specify a p-value for the statistical test" | 84 <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)"/> |
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)" /> | 85 <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)"/> |
97 | 86 <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)"/> |
98 <param name="min_overlap" type="integer" value="10" optional="true" label="Minimum overlap size" | 87 <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."/> |
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)" /> | 88 <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."/> |
100 | 89 <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."/> |
101 <param name="max_assembly_length" type="integer" value="0" optional="true" label="Maximum possible length of the assembled sequences" | 90 <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."/> |
102 help="Setting this value to 0 disables the restriction and assembled sequences may be arbitrary long. (--max-assembly-length)" /> | 91 <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."/> |
103 | |
104 <param name="min_assembly_length" type="integer" value="50" optional="true" label="Minimum possible length of the assembled sequences" | |
105 help="Setting this value to 0 disables the restriction and assembled sequences may be arbitrary short. (--min-assembly-length)" /> | |
106 | |
107 <param name="min_trim_length" type="integer" value="1" optional="true" label="Minimum length of reads after trimming the low quality part" | |
108 help="See option -q. (--min-trim-length)" /> | |
109 | |
110 <param name="quality_threshold" type="integer" value="0" optional="true" label="Quality score threshold for trimming the low quality part of a read" | |
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)" /> | |
112 | |
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" | |
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)" /> | |
115 | |
116 <param name="cap" type="integer" value="40" optional="true" label="Specify the upper bound for the resulting quality score" | |
117 help="If set to zero, capping is disabled. (--cap)" /> | |
118 | |
119 <param name="test_method" type="select" label="Type of statistical test" help="(--test-method)"> | 92 <param name="test_method" type="select" label="Type of statistical test" help="(--test-method)"> |
120 <option value="1" selected="true">Given the minimum allowed overlap, test using the highest OES (1)</option> | 93 <option value="1" selected="true">Given the minimum allowed overlap, test using the highest OES (1)</option> |
121 <option value="2">Use the acceptance probability (2)</option> | 94 <option value="2">Use the acceptance probability (2)</option> |
122 </param> | 95 </param> |
123 | 96 <param name="empirical_freqs" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Disable empirical base frequencies" help="(--empirical-freqs)"/> |
124 <param name="empirical_freqs" type="boolean" truevalue="-e" falsevalue="" checked="false" | 97 <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)"/> |
125 label="Disable empirical base frequencies" help="(--empirical-freqs)" /> | |
126 <param name="nbase" type="boolean" truevalue="--nbase" falsevalue="" checked="false" | |
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)" /> | |
128 | |
129 <param name="score_method" type="select" label="Scoring method" help="(--score-method)"> | 98 <param name="score_method" type="select" label="Scoring method" help="(--score-method)"> |
130 <option value="1">OES with +1 for match and -1 for mismatch</option> | 99 <option value="1">OES with +1 for match and -1 for mismatch</option> |
131 <option value="2" selected="true">Assembly score (AS) use +1 for match and -1 for mismatch multiplied by base quality scores</option> | 100 <option value="2" selected="true">Assembly score (AS) use +1 for match and -1 for mismatch multiplied by base quality scores</option> |
132 <option value="3">Ignore quality scores and use +1 for a match and -1 for a mismatch</option> | 101 <option value="3">Ignore quality scores and use +1 for a match and -1 for a mismatch</option> |
133 </param> | 102 </param> |
134 | 103 <param name="outputs" type="select" optional="false" label="Output files" multiple="true"> |
135 <param name="outputs" type="select" optional="false" multiple="true" label="Output files"> | |
136 <option value="assembled" selected="true">Assembled reads</option> | 104 <option value="assembled" selected="true">Assembled reads</option> |
137 <option value="unassembled_forward">Forward unassembled reads</option> | 105 <option value="unassembled_forward">Forward unassembled reads</option> |
138 <option value="unassembled_reverse">Reverse unassembled reads</option> | 106 <option value="unassembled_reverse">Reverse unassembled reads</option> |
139 <option value="discarded">Discarded reads</option> | 107 <option value="discarded">Discarded reads</option> |
140 </param> | 108 </param> |
159 </outputs> | 127 </outputs> |
160 <tests> | 128 <tests> |
161 <test expect_num_outputs="2"> | 129 <test expect_num_outputs="2"> |
162 <conditional name="library"> | 130 <conditional name="library"> |
163 <param name="type" value="paired"/> | 131 <param name="type" value="paired"/> |
164 <param name="forward" value="forward.fastq" ftype="fastqsanger" /> | 132 <param name="forward" value="forward.fastq" ftype="fastqsanger"/> |
165 <param name="reverse" value="reverse.fastq" ftype="fastqsanger" /> | 133 <param name="reverse" value="reverse.fastq" ftype="fastqsanger"/> |
166 </conditional> | 134 </conditional> |
167 <param name="min_overlap" value="10" /> | 135 <param name="min_overlap" value="10"/> |
168 <param name="min_assembly_length" value="50" /> | 136 <param name="min_assembly_length" value="50"/> |
169 <param name="cap" value="0" /> | 137 <param name="cap" value="0"/> |
170 <param name="outputs" value="assembled,unassembled_forward" /> | 138 <param name="outputs" value="assembled,unassembled_forward"/> |
171 <output name="assembled_reads" file="pear_assembled_results1.fastq" ftype="fastqsanger"/> | 139 <output name="assembled_reads" file="pear_assembled_results1.fastq" ftype="fastqsanger"/> |
172 <output name="unassembled_forward_reads" file="pear_unassembled_forward_results1.fastq" ftype="fastqsanger"/> | 140 <output name="unassembled_forward_reads" file="pear_unassembled_forward_results1.fastq" ftype="fastqsanger"/> |
173 </test> | 141 </test> |
174 <!-- same test as before using collection input and fastqillumina | 142 <!-- same test as before using collection input and fastqillumina |
175 (even if it isn't) .. therefore only loose check of outputs --> | 143 (even if it isn't) .. therefore only loose check of outputs --> |
176 <test expect_num_outputs="2"> | 144 <test expect_num_outputs="2"> |
177 <conditional name="library"> | 145 <conditional name="library"> |
178 <param name="type" value="paired_collection"/> | 146 <param name="type" value="paired_collection"/> |
179 <param name="input_collection"> | 147 <param name="input_collection"> |
180 <collection type="paired"> | 148 <collection type="paired"> |
181 <element name="forward" value="forward.fastq" ftype="fastqillumina" /> | 149 <element name="forward" value="forward.fastq" ftype="fastqillumina"/> |
182 <element name="reverse" value="reverse.fastq" ftype="fastqillumina" /> | 150 <element name="reverse" value="reverse.fastq" ftype="fastqillumina"/> |
183 </collection> | 151 </collection> |
184 </param> | 152 </param> |
185 </conditional> | 153 </conditional> |
186 <param name="min_overlap" value="10" /> | 154 <param name="min_overlap" value="10"/> |
187 <param name="min_assembly_length" value="50" /> | 155 <param name="min_assembly_length" value="50"/> |
188 <param name="cap" value="0" /> | 156 <param name="cap" value="0"/> |
189 <param name="outputs" value="assembled,unassembled_forward" /> | 157 <param name="outputs" value="assembled,unassembled_forward"/> |
190 <output name="assembled_reads" ftype="fastqillumina"> | 158 <output name="assembled_reads" ftype="fastqillumina"> |
191 <assert_contents> | 159 <assert_contents> |
192 <has_line_matching expression="@.*"/> | 160 <has_line_matching expression="@.*"/> |
193 </assert_contents> | 161 </assert_contents> |
194 </output> | 162 </output> |
220 [CC Attribution-NonCommercial-ShareAlike](https://creativecommons.org/licenses/by-nc-sa/3.0/) license | 188 [CC Attribution-NonCommercial-ShareAlike](https://creativecommons.org/licenses/by-nc-sa/3.0/) license |
221 and that commercial partners should obtain a license. | 189 and that commercial partners should obtain a license. |
222 | 190 |
223 ]]> | 191 ]]> |
224 </help> | 192 </help> |
225 <citations> | 193 <citations> |
226 <citation type="doi">10.1093/bioinformatics/btt593</citation> | 194 <citation type="doi">10.1093/bioinformatics/btt593</citation> |
227 </citations> | 195 </citations> |
228 </tool> | 196 </tool> |