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comparison salsa2.xml @ 0:575b4d5bd444 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 67cd735c6709a56ad1c4d65cd84e38fccd59603b"
author iuc
date Sun, 17 Jan 2021 13:24:22 +0000
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children ba7b0f11e470
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-1:000000000000 0:575b4d5bd444
1 <tool id="salsa" name="SALSA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description>scaffold long read assemblies with Hi-C</description>
3 <xrefs>
4 <xref type="bio.tools">SALSA</xref>
5 </xrefs>
6 <macros>
7 <token name="@TOOL_VERSION@">2.2</token>
8 <token name="@VERSION_SUFFIX@">0</token>
9 </macros>
10 <requirements>
11 <requirement type="package" version="@TOOL_VERSION@">salsa2</requirement>
12 <requirement type="package" version="1.11">samtools</requirement>
13 </requirements>
14 <command detect_errors="exit_code"><![CDATA[
15 ln -s '$fasta_in' input.fasta &&
16 samtools faidx input.fasta &&
17
18 run_pipeline.py
19 -a '$fasta_in'
20 -l input.fasta.fai
21 -b '$bed_file'
22 -e '$enzyme'
23
24 #if str($cutoff):
25 -c '$cutoff'
26 #end if
27 #if $gfa_file:
28 -g '$gfa_file'
29 #end if
30 #if $iter:
31 -i '$iter'
32 #end if
33 -o ./out
34 ]]></command>
35 <inputs>
36 <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"/>
38 <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."/>
40 <param name="enzyme" argument="-e" type="text" label="Restriction enzyme sequence(s)"
41 help="Restriction enzyme sequence. If multiple were used, include all as a comma separated list without spaces (ex. 'GATC,AAGCTT').">
42 <validator type="expression" message="Only alphabetical letters and the comma can be used in to define restriction enzym sequences.">value.replace(',', '').isalpha()</validator>
43 </param>
44 <param name="iter" argument="-i" type="integer" min="0" label="Iterations" optional="true" help="Number of iterations to run"/>
45 </inputs>
46 <outputs>
47 <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"/>
49 </outputs>
50 <tests>
51 <test>
52 <param name="fasta_in" value="test.fasta"/>
53 <param name="length" value="test.fai"/>
54 <param name="bed_file" value="test.bed"/>
55 <param name="gfa_file" value="test.gfa1"/>
56 <param name="enzyme" value="GATC,GANTC"/>
57 <param name="cutoff" value="1000"/>
58 <param name="iter" value="3"/>
59 <output name="scaffolds_fasta" file="out.fasta"/>
60 <output name="scaffolds_agp" file="out.agp"/>
61 </test>
62 <test>
63 <param name="fasta_in" value="test.fasta"/>
64 <param name="bed_file" value="test.bed"/>
65 <param name="gfa_file" value="test.gfa1"/>
66 <param name="enzyme" value="GATC,GANTC"/>
67 <param name="cutoff" value="1000"/>
68 <param name="iter" value="3"/>
69 <output name="scaffolds_fasta" file="out.fasta"/>
70 <output name="scaffolds_agp" file="out.agp"/>
71 </test>
72 </tests>
73 <help><![CDATA[
74 **What is does**
75
76 SALSA (Simple AssembLy ScAffolder) is a scaffolding tool based on a computational method that exploits the genomic proximity
77 information in Hi-C data sets for long range scaffolding of de novo genome assemblies.
78
79 ]]></help>
80 <citations>
81 <citation type="doi">10.1101/261149</citation>
82 <citation type="doi">10.1186/s12864-017-3879-z</citation>
83 </citations>
84 </tool>