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comparison macros.xml @ 0:cee311483327 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat commit 6946d81de9419c90e9bc4ea2f7bd5e4168dd6dd6
author iuc
date Fri, 25 Nov 2022 14:23:52 +0000
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-1:000000000000 0:cee311483327
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 &#60; 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 &#60; 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 &#60; 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 &#60; 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 &#60; threshold, 1 = overlap idenitity &#60; 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>