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comparison salsa2.xml @ 2:e15025381b3b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 59c5c8edd0c2080d7685e312fee19de1da75097e"
author iuc
date Thu, 23 Sep 2021 19:35:46 +0000
parents 1bb6b39018e7
children 5af503c47367
comparison
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1:1bb6b39018e7 2:e15025381b3b
3 <xrefs> 3 <xrefs>
4 <xref type="bio.tools">SALSA</xref> 4 <xref type="bio.tools">SALSA</xref>
5 </xrefs> 5 </xrefs>
6 <macros> 6 <macros>
7 <token name="@TOOL_VERSION@">2.3</token> 7 <token name="@TOOL_VERSION@">2.3</token>
8 <token name="@VERSION_SUFFIX@">0</token> 8 <token name="@VERSION_SUFFIX@">1</token>
9 </macros> 9 </macros>
10 <requirements> 10 <requirements>
11 <requirement type="package" version="@TOOL_VERSION@">salsa2</requirement> 11 <requirement type="package" version="@TOOL_VERSION@">salsa2</requirement>
12 <requirement type="package" version="1.11">samtools</requirement> 12 <requirement type="package" version="1.11">samtools</requirement>
13 </requirements> 13 </requirements>
16 samtools faidx input.fasta && 16 samtools faidx input.fasta &&
17 17
18 run_pipeline.py 18 run_pipeline.py
19 -a '$fasta_in' 19 -a '$fasta_in'
20 -l input.fasta.fai 20 -l input.fasta.fai
21 #if $enzyme_conditional.enzyme_options == 'preconfigured':
22 #if $enzyme_conditional.preconfigured_enzymes == 'dovetail'
23 -e 'GATC'
24 #else if $enzyme_conditional.preconfigured_enzymes == 'arima1'
25 -e 'GATC,GANTC'
26 #else
27 -e 'GATC,GANTC,CTNAG,TTAA'
28 #end if
29 #else:
30 -e '${enzyme_conditional.manual_enzyme}'
31 #end if
21 -b '$bed_file' 32 -b '$bed_file'
22 -e '$enzyme'
23
24 #if str($cutoff): 33 #if str($cutoff):
25 -c '$cutoff' 34 -c '$cutoff'
26 #end if 35 #end if
27 #if $gfa_file: 36 #if $gfa_file:
28 -g '$gfa_file' 37 -g '$gfa_file'
35 <inputs> 44 <inputs>
36 <param name="fasta_in" type="data" format="fasta" label="Initial assembly file" help="Headers must not contain ':'."/> 45 <param name="fasta_in" type="data" format="fasta" label="Initial assembly file" help="Headers must not contain ':'."/>
37 <param name="bed_file" type="data" format="bed" label="Bed alignment" help="Sorted by read names"/> 46 <param name="bed_file" type="data" format="bed" label="Bed alignment" help="Sorted by read names"/>
38 <param name="cutoff" argument="-c" type="integer" min="1" label="Cutoff" optional="true" help="Minimum contig length to scaffold."/> 47 <param name="cutoff" argument="-c" type="integer" min="1" label="Cutoff" optional="true" help="Minimum contig length to scaffold."/>
39 <param name="gfa_file" argument="-g" type="data" format="gfa1,gfa2" optional="true" label="Sequence graphs" help="Sequence graphs encoded in GFA format."/> 48 <param name="gfa_file" argument="-g" type="data" format="gfa1,gfa2" optional="true" label="Sequence graphs" help="Sequence graphs encoded in GFA format."/>
40 <param name="enzyme" argument="-e" type="text" label="Restriction enzyme sequence(s)" 49 <conditional name="enzyme_conditional">
41 help="Restriction enzyme sequence. If multiple were used, include all as a comma separated list without spaces (ex. 'GATC,AAGCTT')."> 50 <param name="enzyme_options" type="select" label="Enzyme selection" help="TODO">
42 <validator type="expression" message="Only alphabetical letters and the comma can be used in to define restriction enzym sequences.">value.replace(',', '').isalpha()</validator> 51 <option value="preconfigured">Preconfigured restriction enzymes</option>
43 </param> 52 <option value="specific">Enter a specific sequence</option>
53 </param>
54 <when value="preconfigured">
55 <param name="preconfigured_enzymes" type="select" multiple="true" label="Preconfigured enzymes">
56 <option value="dovetail">Dovetail Chicago, Dovetail Hi-C or Phase: GATC</option>
57 <option value="arima1">Arima Hi-C 1.0: GATC, GANTC</option>
58 <option value="arima2">Arima Hi-C 2.0: GATC, GANTC, CTNAG, TTAA</option>
59 </param>
60 </when>
61 <when value="specific">
62 <param name="manual_enzyme" argument="-e" type="text" label="Restriction enzyme sequence(s)"
63 help="Restriction enzyme sequence. If multiple were used, include all as a comma separated list without spaces (ex. 'GATC,AAGCTT').">
64 <validator type="expression" message="Only alphabetical letters and the comma can be used in to define restriction enzym sequences.">value.replace(',', '').isalpha()</validator>
65 </param>
66 </when>
67 </conditional>
44 <param name="iter" argument="-i" type="integer" min="0" label="Iterations" optional="true" help="Number of iterations to run"/> 68 <param name="iter" argument="-i" type="integer" min="0" label="Iterations" optional="true" help="Number of iterations to run"/>
45 </inputs> 69 </inputs>
46 <outputs> 70 <outputs>
47 <data name="scaffolds_fasta" format="fasta" from_work_dir="out/scaffolds_FINAL.fasta" label="${tool.name} on ${on_string}: FASTA assembly"/> 71 <data name="scaffolds_fasta" format="fasta" from_work_dir="out/scaffolds_FINAL.fasta" label="${tool.name} on ${on_string}: FASTA assembly"/>
48 <data name="scaffolds_agp" format="tabular" from_work_dir="out/scaffolds_FINAL.agp" label="${tool.name} on ${on_string}: agp output"/> 72 <data name="scaffolds_agp" format="tabular" from_work_dir="out/scaffolds_FINAL.agp" label="${tool.name} on ${on_string}: agp output"/>
51 <test> 75 <test>
52 <param name="fasta_in" value="test.fasta"/> 76 <param name="fasta_in" value="test.fasta"/>
53 <param name="length" value="test.fai"/> 77 <param name="length" value="test.fai"/>
54 <param name="bed_file" value="test.bed"/> 78 <param name="bed_file" value="test.bed"/>
55 <param name="gfa_file" value="test.gfa1"/> 79 <param name="gfa_file" value="test.gfa1"/>
80 <conditional name="enzyme_conditional">
81 <param name="enzyme_options" value="specific"/>
82 <param name="manual_enzyme" value="GATC,GANTC"/>
83 </conditional>
56 <param name="enzyme" value="GATC,GANTC"/> 84 <param name="enzyme" value="GATC,GANTC"/>
57 <param name="cutoff" value="1000"/> 85 <param name="cutoff" value="1000"/>
58 <param name="iter" value="3"/> 86 <param name="iter" value="3"/>
59 <output name="scaffolds_fasta" file="out.fasta"/> 87 <output name="scaffolds_fasta" file="out.fasta"/>
60 <output name="scaffolds_agp" file="out.agp"/> 88 <output name="scaffolds_agp" file="out.agp"/>
61 </test> 89 </test>
90 <!--Test manual enzyme-->
62 <test> 91 <test>
63 <param name="fasta_in" value="test.fasta"/> 92 <param name="fasta_in" value="test.fasta"/>
64 <param name="bed_file" value="test.bed"/> 93 <param name="bed_file" value="test.bed"/>
65 <param name="gfa_file" value="test.gfa1"/> 94 <param name="gfa_file" value="test.gfa1"/>
66 <param name="enzyme" value="GATC,GANTC"/> 95 <conditional name="enzyme_conditional">
96 <param name="enzyme_options" value="specific"/>
97 <param name="manual_enzyme" value="GATC,GANTC"/>
98 </conditional>
99 <param name="cutoff" value="1000"/>
100 <param name="iter" value="3"/>
101 <output name="scaffolds_fasta" file="out.fasta"/>
102 <output name="scaffolds_agp" file="out.agp"/>
103 </test>
104 <!--Test predefined enzyme-->
105 <test>
106 <param name="fasta_in" value="test.fasta"/>
107 <param name="bed_file" value="test.bed"/>
108 <param name="gfa_file" value="test.gfa1"/>
109 <conditional name="enzyme_conditional">
110 <param name="enzyme_options" value="preconfigured"/>
111 <param name="preconfigured_enzymes" value="arima1"/>
112 </conditional>
67 <param name="cutoff" value="1000"/> 113 <param name="cutoff" value="1000"/>
68 <param name="iter" value="3"/> 114 <param name="iter" value="3"/>
69 <output name="scaffolds_fasta" file="out.fasta"/> 115 <output name="scaffolds_fasta" file="out.fasta"/>
70 <output name="scaffolds_agp" file="out.agp"/> 116 <output name="scaffolds_agp" file="out.agp"/>
71 </test> 117 </test>