comparison minced.xml @ 0:20f12e7c279b draft

Imported from capsule None
author bgruening
date Mon, 05 May 2014 04:23:26 -0400
parents
children 6117712107bf
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-1:000000000000 0:20f12e7c279b
1 <tool id="crispr_recognition_tool" name="detect CRISPR sequences" version="0.1.5">
2 <description>(minced)</description>
3 <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="50" merge_outputs="output,output_region,output_ggf_full,output_ggf,output_fasta" />
4 <requirements>
5 <requirement type="package" version="0.1.5">minced</requirement>
6 <requirement type="set_environment">MINCED_SCRIPT_PATH</requirement>
7 </requirements>
8 <stdio>
9 <exit_code range=":-1" level="fatal" />
10 <exit_code range="1:" level="fatal" />
11 </stdio>
12 <command>
13 temp_output=\$(mktemp);
14 minced
15 -minNR $minNR
16 -minRL $minRL
17 -maxRL $maxRL
18 -minSL $minSL
19 -maxSL $maxSL
20 #if str($searchWL) != 'none':
21 -searchWL $searchWL
22 #end if
23 $input
24 \$temp_output
25 #if '-spacers' in str($outputs).split():
26 -spacers
27 #end if
28 #if '-gffFull' in str($outputs).split():
29 -gffFull
30 #end if
31 #if '-gff' in str($outputs).split():
32 -gff
33 #end if
34 ;
35
36 python \$MINCED_SCRIPT_PATH/reformat.py \$temp_output results.bed results.tab;
37 #if '-spacers' in str($outputs).split():
38 mv \$temp_output'_spacers.fa' $output_fasta;
39 #end if
40 </command>
41 <inputs>
42 <param format="fasta" name="input" type="data" label="Input sequence as FASTA"/>
43
44 <param name="minNR" type="integer" value="3" label="Minimum number of repeats a CRISPER must have"/>
45 <param name="minRL" type="integer" value="19" label="Minimum length of a CRISPER repeated region"/>
46 <param name="maxRL" type="integer" value="38" label="Maximum length of a CRISPER repeated region"/>
47 <param name="minSL" type="integer" value="19" label="Minimum length of CRISPER non repeated region" help="or spacer region"/>
48 <param name="maxSL" type="integer" value="48" label="Maximum length of CRISPER non repeated region" help="or spacer region"/>
49 <param name="searchWL" type="select" label="Length of search window to used to discover CRISPERs">
50 <option value="none" selected="true">default</option>
51 <option value="6">6</option>
52 <option value="7">7</option>
53 <option value="8">8</option>
54 <option value="9">9</option>
55 </param>
56
57 <param name="outputs" type="select" multiple="True" label="Additional output format" help="Please select a output format.">
58 <option value="-gff">summary results in gff format</option>
59 <option value="BED" selected="true">summary results in BED format</option>
60 <option value="-gffFull">detailed results in gff format</option>
61 <option value="TABULAR" selected="true">detailed results in tabular format</option>
62 <option value="-spacers">fasta formatted file containing the spacers</option>
63 <validator type="no_options" message="Please select at least one output file." />
64 </param>
65
66 </inputs>
67 <outputs>
68 <data format="tabular" name="output" from_work_dir="results.tab" label="${tool.name} on ${on_string}">
69 <filter>'TABULAR' in outputs</filter>
70 </data>
71 <data format="bed" name="output_region" from_work_dir="results.bed" label="${tool.name} on ${on_string} - BED file">
72 <filter>'BED' in outputs</filter>
73 </data>
74 <data format="gff3" name="output_ggf_full" from_work_dir="results_full.gff" label="${tool.name} on ${on_string} - GFF file extended">
75 <filter>'-gffFull' in outputs</filter>
76 </data>
77 <data format="gff3" name="output_gff" from_work_dir="results.gff" label="${tool.name} on ${on_string} - GFF file">
78 <filter>'-gff' in outputs</filter>
79 </data>
80 <data format="fasta" name="output_fasta" label="${tool.name} on ${on_string} - GFF file">
81 <filter>'-spacers' in outputs</filter>
82 </data>
83 </outputs>
84 <tests>
85 <test>
86 <param name="input" value="sequence.fasta" ftype="fasta" />
87 <param name="minNR" value="3" />
88 <param name="minRL" value="29" />
89 <param name="maxRL" value="38" />
90 <param name="minSL" value="19" />
91 <param name="maxSL" value="48" />
92 <param name="searchWL" value="none" />
93 <output name="output" file="minced.tabular" ftype="tabular" />
94 <output name="output_region" file="minced.bed" ftype="bed" />
95 </test>
96 </tests>
97 <help>
98 **What it does**
99
100 MinCED - Mining CRISPRs in Environmental Datasets
101
102
103 MinCED is a program to find Clustered Regularly Interspaced Short Palindromic
104 Repeats (CRISPRs) in full genomes or environmental datasets such as metagenomes,
105 in which sequence size can be anywhere from 100 to 800 bp. MinCED runs from the
106 command-line and was derived from CRT (http://www.room220.com/crt/).
107
108 https://github.com/ctSkennerton/minced
109
110 **Citation**
111
112 For the underlying tool, please cite `Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P:
113 CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics. 2007 Jun 18;8(1):209`
114
115 If you use this tool in Galaxy, please cite Gruening, BA et al. https://github.com/bgruening/galaxytools
116
117 </help>
118 </tool>
119