Mercurial > repos > iuc > necat
comparison macros.xml @ 0:6ee7eb5821f0 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat commit 6946d81de9419c90e9bc4ea2f7bd5e4168dd6dd6
author | iuc |
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date | Fri, 25 Nov 2022 14:24:27 +0000 |
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-1:000000000000 | 0:6ee7eb5821f0 |
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1 <?xml version="1.0"?> | |
2 | |
3 <macros> | |
4 <token name="@TOOL_VERSION@">0.0.1_update20200803</token> | |
5 <token name="@VERSION_SUFFIX@">0</token> | |
6 <xml name="job_conf"> | |
7 <configfile name="job_configfile"> | |
8 <![CDATA[ | |
9 PROJECT=project | |
10 ONT_READ_LIST=read_list.txt | |
11 GENOME_SIZE=${genome_size} | |
12 THREADS=\${GALAXY_SLOTS:-4} | |
13 | |
14 MIN_READ_LENGTH=${min_read_length} | |
15 PREP_OUTPUT_COVERAGE=${correction_coverage} | |
16 | |
17 OVLP_FAST_OPTIONS=-k ${adv.ovf.k} -z ${adv.ovf.z} -q ${adv.ovf.q} -b ${adv.ovf.b} -n ${adv.ovf.n} -a ${adv.ovf.a} -d ${adv.ovf.d} -e ${adv.ovf.e} -m ${adv.ovf.m} -j 0 -u 1 | |
18 | |
19 OVLP_SENSITIVE_OPTIONS=-k ${adv.ovs.k} -z ${adv.ovs.z} -q ${adv.ovs.q} -b ${adv.ovs.b} -n ${adv.ovs.n} -a ${adv.ovs.a} -d ${adv.ovs.d} -e ${adv.ovs.e} -m ${adv.ovs.m} -j 0 -u 1 | |
20 | |
21 CNS_FAST_OPTIONS=-a ${adv.cnf.a} -x ${adv.cnf.x} -y ${adv.cnf.y} -l ${adv.cnf.l} -e ${adv.cnf.e} -p ${adv.cnf.p} -r ${adv.cnf.r} -u ${adv.cnf.u} | |
22 | |
23 CNS_SENSITIVE_OPTIONS=-a ${adv.cns.a} -x ${adv.cns.x} -y ${adv.cns.y} -l ${adv.cns.l} -e ${adv.cns.e} -p ${adv.cns.p} -r ${adv.cns.r} -u ${adv.cns.u} | |
24 | |
25 TRIM_OVLP_OPTIONS=-n ${adv.tov.n} -a ${adv.tov.a} -z ${adv.tov.z} -b ${adv.tov.b} -e ${adv.tov.e} -j 1 -u 1 | |
26 | |
27 ASM_OVLP_OPTIONS=-n ${adv.aov.n} -a ${adv.aov.a} -z ${adv.aov.z} -b ${adv.aov.b} -e ${adv.aov.e} -j 1 -u 0 | |
28 | |
29 NUM_ITER=2 | |
30 | |
31 #if $assembly.should_assemble == "yes": | |
32 CNS_OUTPUT_COVERAGE=$assembly.assembly_coverage | |
33 POLISH_CONTIGS=$assembly.polish_contigs | |
34 #else: | |
35 CNS_OUTPUT_COVERAGE=30 | |
36 POLISH_CONTIGS=false | |
37 #end if | |
38 | |
39 CLEANUP=1 | |
40 USE_GRID=false | |
41 GRID_NODE=0 | |
42 GRID_OPTIONS= | |
43 SMALL_MEMORY=0 | |
44 FSA_OL_FILTER_OPTIONS= | |
45 --min_length={adv.fol.min_length} | |
46 --max_length={adv.fol.max_length} | |
47 --min_identity={adv.fol.min_identity} | |
48 --min_aligned_length={adv.fol.min_aligned_length} | |
49 --max_overhang={adv.fol.max_overhang} | |
50 --min_coverage={adv.fol.min_coverage} | |
51 --max_coverage={adv.fol.max_coverage} | |
52 --max_diff_coverage={adv.fol.max_diff_coverage} | |
53 --coverage_discard={adv.fol.coverage_discard} | |
54 --bestn={adv.fol.bestn} | |
55 --genome_size={adv.fol.genome_size} | |
56 --coverage={adv.fol.coverage} | |
57 --thread_size=\${GALAXY_SLOTS:-4} | |
58 --identity_global_deviation1={adv.fol.identity_global_deviation1} | |
59 --identity_global_deviation2={adv.fol.identity_global_deviation2} | |
60 --overhang_global_deviation1={adv.fol.overhang_global_deviation1} | |
61 --overhang_global_deviation2={adv.fol.overhang_global_deviation2} | |
62 --identity_local_deviation1={adv.fol.identity_local_deviation1} | |
63 --identity_local_deviation2={adv.fol.identity_local_deviation2} | |
64 --overhang_local_deviation1={adv.fol.overhang_local_deviation1} | |
65 --overhang_local_deviation2={adv.fol.overhang_local_deviation2} | |
66 --identity_local_condition={adv.fol.identity_local_condition} | |
67 --local_low_coverage={adv.fol.local_low_coverage} | |
68 --overlap_file_type=m4 | |
69 | |
70 FSA_ASSEMBLE_OPTIONS= | |
71 --min_length={adv.fa.min_length} | |
72 --min_identity={adv.fa.min_identity} | |
73 --min_aligned_length={adv.fa.min_aligned_length} | |
74 --min_contig_length={adv.fa.min_contig_length} | |
75 --max_spur_length={adv.fa.max_spur_length} | |
76 --select_branch={adv.fa.select_branch} | |
77 --overlap_file_type=m4 | |
78 --thread_size=\${GALAXY_SLOTS:-4} | |
79 | |
80 FSA_CTG_BRIDGE_OPTIONS= | |
81 --read_min_length={adv.fcb.read_min_length} | |
82 --ctg_min_length={adv.fcb.ctg_min_length} | |
83 --ctg2ctg_min_identity={adv.fcb.ctg2ctg_min_identity} | |
84 --ctg2ctg_max_overhang={adv.fcb.ctg2ctg_max_overhang} | |
85 --ctg2ctg_min_aligned_length={adv.fcb.ctg2ctg_min_aligned_length} | |
86 --read2ctg_min_identity={adv.fcb.read2ctg_min_identity} | |
87 --read2ctg_max_overhang={adv.fcb.read2ctg_max_overhang} | |
88 --read2ctg_min_aligned_length={adv.fcb.read2ctg_min_aligned_length} | |
89 --read2ctg_min_coverage={adv.fcb.read2ctg_min_coverage} | |
90 --min_contig_length={adv.fcb.min_contig_length} | |
91 --select_branch={adv.fcb.select_branch} | |
92 --window_size={adv.fcb.window_size} | |
93 --thread_size=\${GALAXY_SLOTS:-4} | |
94 ]]> | |
95 </configfile> | |
96 </xml> | |
97 | |
98 | |
99 | |
100 <xml name="overlap_sensitive_options"> | |
101 <section name="ovs" title="Overlap sensitive options (for oc2pmov subprogram)" expanded="false" help="OVLP_SENSITIVE_OPTIONS. Passed to oc2pmov in the first round of error correction."> | |
102 <param argument="-n" type="integer" min="1" max="100000" value="500" label="number of candidates" help="" /> | |
103 <param argument="-k" type="integer" min="1" max="100" value="15" label="kmer size" help="" /> | |
104 <param argument="-q" type="integer" min="1" max="100000" value="500" label="max kmer occurances" help="" /> | |
105 <param argument="-z" type="integer" min="1" max="100" value="10" label="scan window size" help="" /> | |
106 <param argument="-b" type="integer" min="1" max="100000" value="2000" label="block size" help="" /> | |
107 <param argument="-a" type="integer" min="1" max="100000" value="1000" label="min align length" help="" /> | |
108 <param argument="-d" type="float" min="0" max="1" value="0.25" label="ddf score cutoff" help="" /> | |
109 <param argument="-e" type="float" min="0" max="1" value="0.50" label="sequencing error" help="" /> | |
110 <param argument="-m" type="integer" min="1" max="100000" value="500" label="number of output" help="" /> | |
111 </section> | |
112 </xml> | |
113 | |
114 | |
115 | |
116 <xml name="consensus_sensitive_options"> | |
117 <section name="cns" title="Consensus sensitive options (for oc2cns subprogram)" expanded="false" help="CNS_SENSITIVE_OPTIONS. Passed to oc2cns in the first round of error correction."> | |
118 <param argument="-a" type="integer" min="1" max="100000" value="2000" label="align length cutoff" help="" /> | |
119 <param argument="-x" type="integer" min="1" max="10000" value="4" label="minimal coverage" help="" /> | |
120 <param argument="-y" type="integer" min="1" max="10000" value="12" label="maximal coverage" help="" /> | |
121 <param argument="-l" type="integer" min="1" max="10000000" value="1000" label="minimal length of corrected reads" help="" /> | |
122 <param argument="-e" type="float" min="0" max="1" value="0.50" label="sequencing error" help="" /> | |
123 <param argument="-p" type="float" min="0" max="1" value="0.80" label="minimal mapping ratio" help="" /> | |
124 <param argument="-r" type="boolean" truevalue="1" falsevalue="0" label="rescue long indels?" help=""/> | |
125 <param argument="-u" type="boolean" truevalue="1" falsevalue="0" label="use fixed ident cutoff?" help="default (no) is dynamic cutoff."/> | |
126 </section> | |
127 </xml> | |
128 | |
129 | |
130 | |
131 <xml name="overlap_fast_options"> | |
132 <section name="ovf" title="Overlap fast options (for oc2pmov subprogram)" expanded="false" help="OVLP_FAST_OPTIONS. Passed to oc2pmov in the second round of error correction."> | |
133 <param argument="-n" type="integer" min="1" max="100000" value="500" label="number of candidates" help="" /> | |
134 <param argument="-k" type="integer" min="1" max="100" value="15" label="kmer size" help="" /> | |
135 <param argument="-q" type="integer" min="1" max="100000" value="500" label="max kmer occurances" help="" /> | |
136 <param argument="-z" type="integer" min="1" max="100" value="20" label="scan window size" help="" /> | |
137 <param argument="-b" type="integer" min="1" max="100000" value="2000" label="block size" help="" /> | |
138 <param argument="-a" type="integer" min="1" max="100000" value="1000" label="min align length" help="" /> | |
139 <param argument="-d" type="float" min="0" max="1" value="0.25" label="ddf score cutoff" help="" /> | |
140 <param argument="-e" type="float" min="0" max="1" value="0.50" label="sequencing error" help="" /> | |
141 <param argument="-m" type="integer" min="1" max="100000" value="500" label="number of outputs" help="" /> | |
142 </section> | |
143 </xml> | |
144 | |
145 | |
146 | |
147 <xml name="consensus_fast_options"> | |
148 <section name="cnf" title="Consensus fast options (for oc2cns subprogram)" expanded="false" help="CNS_FAST_OPTIONS. Passed to oc2cns in the second round of error correction."> | |
149 <param argument="-a" type="integer" min="1" max="100000" value="400" label="align length cutoff" help="" /> | |
150 <param argument="-x" type="integer" min="1" max="10000" value="4" label="minimal coverage" help="" /> | |
151 <param argument="-y" type="integer" min="1" max="10000" value="12" label="maximal coverage" help="" /> | |
152 <param argument="-l" type="integer" min="1" max="10000000" value="500" label="minimal length of corrected reads" help="" /> | |
153 <param argument="-e" type="float" min="0" max="1" value="0.50" label="sequencing error" help="" /> | |
154 <param argument="-p" type="float" min="0" max="1" value="0.80" label="minimal mapping ratio" help="" /> | |
155 <param argument="-r" type="boolean" truevalue="1" falsevalue="0" label="rescue long indels?" help=""/> | |
156 <param argument="-u" type="boolean" truevalue="1" falsevalue="0" label="use fixed ident cutoff?" help="default (no) is dynamic cutoff."/> | |
157 </section> | |
158 </xml> | |
159 | |
160 | |
161 <xml name="trimming_overlap_options"> | |
162 <section name="tov" title="Trimming overlap options (for oc2asmpm subprogram)" expanded="false" help="TRIM_OVLP_OPTIONS. Passed to oc2asmpm. "> | |
163 <param argument="-n" type="integer" min="1" max="100000" value="100" label="number of candidates" help="" /> | |
164 <param argument="-a" type="integer" min="1" max="100000" value="400" label="min align length" help="" /> | |
165 <param argument="-z" type="integer" min="1" max="100" value="10" label="scan window size" help="" /> | |
166 <param argument="-b" type="integer" min="1" max="100000" value="2000" label="block size" help="" /> | |
167 <param argument="-e" type="float" min="0" max="1" value="0.50" label="sequencing error" help="" /> | |
168 </section> | |
169 </xml> | |
170 | |
171 | |
172 <xml name="assembly_overlap_options"> | |
173 <section name="aov" title="Assembly Overlap Options (for oc2asmpm subprogram)" expanded="false" help="ASM_OVLP_OPTIONS. Passed to oc2asmpm. "> | |
174 <param argument="-n" type="integer" min="1" max="100000" value="100" label="number of candidates" help="" /> | |
175 <param argument="-a" type="integer" min="1" max="100000" value="400" label="min align length" help="" /> | |
176 <param argument="-z" type="integer" min="1" max="100" value="10" label="scan window size" help="" /> | |
177 <param argument="-b" type="integer" min="1" max="100000" value="2000" label="block size" help="" /> | |
178 <param argument="-e" type="float" min="0" max="1" value="0.50" label="sequencing error" help="" /> | |
179 </section> | |
180 </xml> | |
181 | |
182 | |
183 <xml name="assembly_overlap_filtering"> | |
184 <section name="fol" title="Assembly Overlap Filtering Options (for fsa_ol_filter subprogram)" expanded="false" help="Filters out low-quality overlaps for assembly. "> | |
185 <param argument="--min_length" type="integer" min="1" value="2500" label="min read length" help="" /> | |
186 <param argument="--max_length" type="integer" min="1" value="2147483647" label="max read length" help="" /> | |
187 <param argument="--min_identity" type="float" min="-1" value="-1" label="min identity of overlaps" help="" /> | |
188 <param argument="--min_aligned_length" type="integer" min="0" value="2500" label="min aligned length of overlaps" help="" /> | |
189 <param argument="--max_overhang" type="integer" min="-1" value="-1" label="max overhang" help="maximum overhang of overlaps, negative number = determined by the program. default: -1" /> | |
190 <param argument="--min_coverage" type="integer" min="-1" value="-1" label="min base coverage. " help="set automatically using '-1'" /> | |
191 <param argument="--max_coverage" type="integer" min="-1" value="-1" label="max base coverage. " help="set automatically using '-1'" /> | |
192 <param argument="--max_diff_coverage" type="integer" min="-1" value="-1" label="max difference of base coverage. " help="set automatically using '-1'" /> | |
193 <param argument="--coverage_discard" type="float" min="0" value="0.01" label="discard ratio of base coverage. If max_coverage or max_diff_coverage is negative, it will be reset to (100-coverage_discard)th percentile" help="" /> | |
194 <param argument="--bestn" type="integer" min="1" value="10" label="bestn" help="output best n overlaps on 5' or 3' end for each read." /> | |
195 <param argument="--genome_size" type="integer" min="0" value="0" label="genome size" help="Genome size. Determines the maximum length of reads with coverage together" /> | |
196 <param argument="--coverage" type="integer" min="0" value="40" label="coverage" help="determines the maximum length of reads with genome_size together" /> | |
197 <param argument="--identity_global_deviation1" type="integer" value="98" label="identity global deviation 1" help="If min_identity < 0, min_identity is set to min(m, deviation1) - 1.4826*mad*deviation2 default: 98" /> | |
198 <param argument="--identity_global_deviation2" type="integer" value="6" label="identity global deviation 2" help="If min_identity < 0, min_identity is set to min(m, deviation1) - 1.4826*mad*deviation2 default: 6" /> | |
199 <param argument="--overhang_global_deviation1" type="float" value="30" label="overhang global deviation 1" help="If max_overhang < 0, max_overhang is set to max(m, deviation1) + 1.4826*mad*deviation2 default: 30" /> | |
200 <param argument="--overhang_global_deviation2" type="float" value="6" label="overhang global deviation 2" help="If max_overhang < 0, max_overhang is set to max(m, deviation1) + 1.4826*mad*deviation2 default: 6" /> | |
201 <param argument="--identity_local_deviation1" type="float" min="0" value="99" label="identity local deviation 1" help="The local threshold of identity is set to min(m, deviation1) - 1.4826*mad*deviation2 default: 99" /> | |
202 <param argument="--identity_local_deviation2" type="float" min="0" value="6" label="identity local deviation 2" help="The local threshold of identity is set to min(m, deviation1) - 1.4826*mad*deviation2 default: 6" /> | |
203 <param argument="--overhang_local_deviation1" type="float" min="0" value="10" label="overhang local deviation 1" help="The local threshold of overhang is set to max(m, deviation1) + 1.253*mad*deviation2 default: 10" /> | |
204 <param argument="--overhang_local_deviation2" type="float" min="0" value="6" label="overhang local deviation 2" help="The local threshold of overhang is set to max(m, deviation1) + 1.253*mad*deviation2 default: 6" /> | |
205 <param argument="--identity_local_condition" type="integer" min="0" max="1" value="0" label="identity local condition" help="Local filtering conditions. 0 = overlap idenitity < threshold, 1 = overlap idenitity < threshold and query identity >= target identity default: 0" /> | |
206 <param argument="--local_low_coverage" type="integer" min="0" value="25" label="local low coverage" help="If the coverage of reads is less than local_low_coverage, min_identity and max_overhang are used to filter out low-quality overlaps. Otherwise, the local threshold is used. default: 25" /> | |
207 </section> | |
208 </xml> | |
209 | |
210 | |
211 <xml name="contig_assembly"> | |
212 <section name="fa" title="Contig Assembly Options (for fsa_assemble subprogram)" expanded="false" help="Passed to fsa_assemble subprogram. Constructs contigs from filtered overlaps and corrected reads. "> | |
213 <param argument="--min_length" type="integer" min="0" value="0" label="min read length" help="minimum length of reads" /> | |
214 <param argument="--min_identity" type="float" min="0" max="100" value="0" label="min overlap identity" help="minimum identity of overlaps" /> | |
215 <param argument="--min_contig_length" type="integer" min="1" value="500" label="min contig length" help="minimum length of contigs" /> | |
216 <param argument="--max_spur_length" type="integer" min="1" value="50000" label="max spur length" help="branches less the threshod are treated as spurs" /> | |
217 <param argument="--select_branch" type="boolean" truevalue="best" falsevalue="no" label="select branch" help="select the most probable branch. default is no." /> | |
218 </section> | |
219 </xml> | |
220 | |
221 | |
222 | |
223 <xml name="contig_bridging"> | |
224 <section name="fcb" title="Contig Bridging Options (for fsa_ctg_bridge subprogram)" expanded="false" help="Passed to fsa_ctg_bridge subprogram. Bridges contigs using long reads "> | |
225 <param argument="--read_min_length" type="integer" min="1" value="5000" label="read min length" help="minimum rawread length" /> | |
226 <param argument="--ctg_min_length" type="integer" min="1" value="500" label="contig min length" help="minimum contig length" /> | |
227 | |
228 <param argument="--ctg2ctg_min_identity" type="float" min="1" max="100" value="95" label="ctg2ctg_min_identity" help="minimum identity of overlaps between contigs" /> | |
229 <param argument="--ctg2ctg_max_overhang" type="integer" min="1" value="100" label="contig-contig max overhang" help="maximum overhang of overlaps between contigs" /> | |
230 <param argument="--ctg2ctg_min_aligned_length" type="integer" min="1" value="2000" label="contig-contig min aligned length" help="minimum aligned length of overlaps between contigs" /> | |
231 | |
232 <param argument="--read2ctg_min_identity" type="float" min="1" max="100" value="80" label="read-contig min identity" help="minimum identity of overlaps between rawreads and contigs" /> | |
233 <param argument="--read2ctg_max_overhang" type="integer" min="1" value="500" label="read-contig max overhang" help="maximum overhang of overlaps between rawreads and contigs" /> | |
234 <param argument="--read2ctg_min_aligned_length" type="integer" min="1" value="5000" label="read-contig min aligned length" help="minimum aligned length of overlaps between rawreads and contigs" /> | |
235 <param argument="--read2ctg_min_coverage" type="integer" min="1" value="3" label="read-contig min coverage" help="minimum coverage of links between rawreads and contigs" /> | |
236 | |
237 <param argument="--min_contig_length" type="integer" min="1" value="500" label="min contig length" help="minimum length of bridged contigs" /> | |
238 <param argument="--window_size" type="integer" min="1" value="1000" label="window size" help="threshold is used to group rawreads that bridge contigs" /> | |
239 <param argument="--select_branch" type="boolean" truevalue="best" falsevalue="no" label="select branch" help="select the most probable branch. default is no." /> | |
240 </section> | |
241 </xml> | |
242 | |
243 | |
244 | |
245 <xml name="citations"> | |
246 <citations> | |
247 <citation type="doi">10.1038/s41467-020-20236-7</citation> | |
248 </citations> | |
249 </xml> | |
250 </macros> |