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comparison tools/mira4/mira4_convert.xml @ 0:6a88b42ce6b9 draft

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Uploaded v0.0.4, previously only on the TestToolShed
author peterjc
date Fri, 21 Nov 2014 06:42:56 -0500
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1 <tool id="mira_4_0_convert" name="MIRA v4.0 miraconvert" version="0.0.5">
2 <description>Convert MIRA assembly to FASTA/SAM/BAM</description>
3 <requirements>
4 <requirement type="binary">miraconvert</requirement>
5 <requirement type="package" version="4.0">MIRA</requirement>
6 </requirements>
7 <version_command interpreter="python">mira4_convert.py --version</version_command>
8 <command interpreter="python">
9 mira4_convert.py
10 --input "$mira_file"
11 --min_length $min_length
12 --min_cover $min_cover
13 --min_reads $min_reads
14 #if str($maf_wanted)=="true":
15 --maf "$out_maf"
16 #end if
17 #if str($fasta_wanted)=="true":
18 --fasta "$out_fasta"
19 #end if
20 #if str($bam_wanted)=="true":
21 --bam "$out_bam"
22 #end if
23 ##Don't yet have a Galaxy datatype defined for ace:
24 ## #if str($ace_wanted)=="true":
25 ## --ace "$out_ace"
26 ## #end if
27 #if str($cstats_wanted)=="true":
28 --cstats "$out_cstats"
29 #end if
30 </command>
31 <stdio>
32 <!-- Assume anything other than zero is an error -->
33 <exit_code range="1:" />
34 <exit_code range=":-1" />
35 </stdio>
36 <inputs>
37 <param name="mira_file" type="data" format="mira" required="true" label="MIRA Assembly Format input" />
38 <!-- TODO - top level select for contig versus read output? Or two Galaxy tools in different XML files? -->
39 <param name="min_length" type="integer" required="false" value="0" min="0"
40 label="Minimum contig length"
41 help="e.g. Set to 1000 to exclude small contigs. Default is to keep all contigs (minimum zero)" />
42 <param name="min_cover" type="integer" required="false" value="0" min="0"
43 label="Minimum average contig coverage"
44 help="e.g. Set to 10 to exclude low coverage contigs. Default is to keep all contigs (minimum zero)" />
45 <param name="min_reads" type="integer" required="false" value="0" min="0"
46 label="Minimum reads per contig"
47 help="e.g. Set to 5 to exclude low coverage contigs with only a few reads. Default is to keep all contigs (minimum zero)." />
48 <param name="maf_wanted" type="boolean" label="Output assembly in MIRA's own format? (useful if filtering)" checked="False" />
49 <param name="fasta_wanted" type="boolean" label="Convert assembly into (unpadded) FASTA?" checked="True" />
50 <param name="bam_wanted" type="boolean" label="Convert assembly into (upadded) BAM format?" checked="False" />
51 <!-- Don't yet have a Galaxy datatype defined for ace:
52 <param name="ace_wanted" type="boolean" label="Convert assembly in ACE format?" checked="False" />
53 -->
54 <param name="cstats_wanted" type="boolean" label="Assembly statistics file?" checked="False" />
55 </inputs>
56 <outputs>
57 <data name="out_maf" format="mira" label="$mira_file.name (filtered)">
58 <filter>maf_wanted is True</filter>
59 </data>
60 <data name="out_fasta" format="fasta" label="$mira_file.name (as FASTA)">
61 <filter>fasta_wanted is True</filter>
62 </data>
63 <data name="out_bam" format="bam" label="$mira_file.name (as BAM)">
64 <filter>bam_wanted is True</filter>
65 </data>
66 <!--
67 <data name="out_ace" format="ace" label="$mira_file.name (as ACE)">
68 <filter>ace_wanted is True</filter>
69 </data>
70 -->
71 <data name="out_cstats" format="tabular" label="$mira_file.name (filtered stats)">
72 <filter>cstats_wanted is True</filter>
73 </data>
74 </outputs>
75 <tests>
76 <!-- TODO -->
77 </tests>
78 <help>
79 **What it does**
80
81 Runs the ``miraconvert`` utility from MIRA v4.0 to filter and/or convert
82 a MIRA Assembly Format file produced by a *mapping* or *de novo* assembly.
83
84 **Example Usage**
85
86 You want to remove all the low coverage contigs from a transcriptome
87 assembly to focus on those with higher coverage.
88
89 You want to convert your MIRA assembly into SAM/BAM to run a standard
90 SNP finding tool.
91
92 You've lost the FASTA consensus from your MIRA assembly and need to
93 regenerate it.
94
95
96 **Citation**
97
98 If you use this Galaxy tool in work leading to a scientific publication please
99 cite the following papers:
100
101 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
102 Galaxy tools and workflows for sequence analysis with applications
103 in molecular plant pathology. PeerJ 1:e167
104 http://dx.doi.org/10.7717/peerj.167
105
106 Bastien Chevreux, Thomas Wetter and Sándor Suhai (1999).
107 Genome Sequence Assembly Using Trace Signals and Additional Sequence Information.
108 Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
109 http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html
110
111 This wrapper is available to install into other Galaxy Instances via the Galaxy
112 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
113 </help>
114 </tool>