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comparison hifiasm_meta.xml @ 2:fa35f1106d3e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta commit bc8759245f44924d0122276e42f02fc1f1190e50
author iuc
date Mon, 06 Feb 2023 12:20:38 +0000
parents 15dbb444df71
children 213df31ba341
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1:15dbb444df71 2:fa35f1106d3e
15 ################# 15 #################
16 ## RUN HIFIASM ## 16 ## RUN HIFIASM ##
17 ################# 17 #################
18 18
19 hifiasm_meta 19 hifiasm_meta
20 --lowq-10 '$read_selection.lowq_10' 20
21 --lowq-3 '$read_selection.lowq_3' 21 ## bloom filter parameter
22 --lowq-5 '$read_selection.lowq_5'
23 -a '$assembly.a'
24 #if $f: 22 #if $f:
25 -f '$f' 23 -f '$f'
26 #end if 24 #end if
25
26 ## read selection parameters
27 #if $read_selection.forced_read_selection.force_rs == "yes":
28 --force-rs
29 --lowq-10 '$read_selection.forced_read_selection.lowq_10'
30 --lowq-3 '$read_selection.forced_read_selection.lowq_3'
31 --lowq-5 '$read_selection.forced_read_selection.lowq_5'
32 #else
33 $read_selection.forced_read_selection.S
34 #end if
35
36 -a '$assembly.a'
27 -k '$overlap_correction.k' 37 -k '$overlap_correction.k'
28 -o asm 38 -o asm
29 -r '$overlap_correction.r' 39 -r '$overlap_correction.r'
30 $read_selection.S
31 -t \${GALAXY_SLOTS:-4} 40 -t \${GALAXY_SLOTS:-4}
32 '$reads_fn' 41 '$reads_fn'
33 42
34 ]]></command> 43 ]]></command>
35 <inputs> 44 <inputs>
36 <param name="reads" format="fastqsanger,fastqsanger.gz" type="data" label="HiFi reads" help="Input reads for assembly" /> 45 <param name="reads" format="fastqsanger,fastqsanger.gz" type="data" label="HiFi reads" help="Input reads for assembly" />
37 <!-- This hidden parameter is only used to save RAM for planemo test. --> 46 <!-- This hidden parameter is only used to save RAM for planemo test. -->
38 <!-- See https://github.com/galaxyproject/tools-iuc/pull/5033#issuecomment-1382915060 --> 47 <!-- See https://github.com/galaxyproject/tools-iuc/pull/5033#issuecomment-1382915060 -->
39 <param type="hidden" optional="true" argument="-f" /> 48 <param type="hidden" optional="true" argument="-f" />
40 <section name="read_selection" title="Read selection" expanded="false"> 49 <section name="read_selection" title="Read selection" expanded="false">
41 <param argument='-S' type="boolean" checked="true" truevalue="-S" falsevalue="" label="Enable read selection" help="If enabled, hifiasm_meta will estimate the total number of read overlaps." /> 50 <conditional name="forced_read_selection">
42 <param argument='--lowq-10' type="integer" value='50' label="lower 10% runtime kmer frequency threshold." /> 51 <param argument="--force-rs" type="select" label="Force read selection" help="Drop reads according to configurable runtime kmer frequency thresholds">
43 <param argument='--lowq-5' type="integer" value='50' label="lower 5% runtime kmer frequency threshold." /> 52 <option value="no" selected="true">No</option>
44 <param argument='--lowq-3' type="integer" value='10' label="lower 3% runtime kmer frequency threshold." /> 53 <option value="yes">Yes</option>
54 </param>
55 <when value="yes">
56 <param argument='--lowq-10' type="integer" value='50' label="Lower 10% runtime kmer frequency threshold" />
57 <param argument='--lowq-5' type="integer" value='50' label="Lower 5% runtime kmer frequency threshold" />
58 <param argument='--lowq-3' type="integer" value='10' label="Lower 3% runtime kmer frequency threshold" />
59 </when>
60 <when value="no">
61 <param argument='-S' type="boolean" checked="false" truevalue="-S" falsevalue="" label="Enable read selection" help="If enabled, hifiasm_meta will estimate the total number of read overlaps. If the estimation seems acceptable, no read will be dropped; otherwise, reads will be dropped from the most redundant ones until the criteria are satisfied. This can only be enabled if forced read selection is disabled." />
62 </when>
63 </conditional>
45 </section> 64 </section>
46 <section name="overlap_correction" title="Overlap/Error correction" expanded="false"> 65 <section name="overlap_correction" title="Overlap/Error correction" expanded="false">
47 <param argument='-k' type="integer" value='51' min="1" max="63" label="k-mer length" /> 66 <param argument='-k' type="integer" value='51' min="1" max="63" label="k-mer length" />
48 <param argument='-r' type="integer" value='3' min="1" max="10" label="rounds of correction" /> 67 <param argument='-r' type="integer" value='3' min="1" max="10" label="rounds of correction" />
49 </section> 68 </section>
75 <output_collection name="contig_graphs" type="list"> 94 <output_collection name="contig_graphs" type="list">
76 <element name="Primary contigs" file="asm.p_ctg.gfa"/> 95 <element name="Primary contigs" file="asm.p_ctg.gfa"/>
77 <element name="Alternate contigs" file="asm.a_ctg.gfa"/> 96 <element name="Alternate contigs" file="asm.a_ctg.gfa"/>
78 </output_collection> 97 </output_collection>
79 </test> 98 </test>
99 <!-- 02: forced read selection -->
100 <test>
101 <param name="reads" value="tiny.fa.gz" />
102 <param name='f' value="0" />
103 <param name='force_rs' value='yes' />
104 <output_collection name="contig_graphs" type="list">
105 <element name="Primary contigs">
106 <assert_contents>
107 <has_size value="93053" delta="30000" />
108 </assert_contents>
109 </element>
110 </output_collection>
111 </test>
112 <!-- 03: read selection -->
113 <test>
114 <param name="reads" value="zymoD6331std-ecoli-ten-percent.42.1.fq.gz" />
115 <param name='f' value="0" />
116 <param name='force_rs' value='no' />
117 <param name='S' value='true' />
118 <output_collection name="contig_graphs" type="list">
119 <element name="Primary contigs" file="S.p_ctg.gfa"/>
120 <element name="Alternate contigs" file="S.a_ctg.gfa"/>
121 </output_collection>
122 </test>
80 </tests> 123 </tests>
81 <help><![CDATA[ 124 <help><![CDATA[
82 hifiasm_meta 125 hifiasm_meta
83 ------------ 126 ------------
84 127