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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/minced commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
author bgruening
date Sun, 18 Sep 2016 06:18:17 -0400
parents 67b57e2f6c7b
children
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3:67b57e2f6c7b 4:08e4ca411ea6
1 <tool id="minced" name="detect CRISPR sequences" version="0.1.5"> 1 <tool id="minced" name="detect CRISPR sequences" version="0.2.0">
2 <description>(minced)</description> 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" /> 3 <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="250" merge_outputs="output,output_region,output_ggf_full,output_ggf,output_fasta" />
4 <requirements> 4 <requirements>
5 <requirement type="package" version="0.1.5">minced</requirement> 5 <requirement type="package" version="0.2.0">minced</requirement>
6 <requirement type="set_environment">MINCED_SCRIPT_PATH</requirement>
7 </requirements> 6 </requirements>
8 <stdio> 7 <stdio>
9 <exit_code range=":-1" level="fatal" /> 8 <exit_code range=":-1" level="fatal" />
10 <exit_code range="1:" level="fatal" /> 9 <exit_code range="1:" level="fatal" />
11 </stdio> 10 </stdio>
12 <command> 11 <command>
12 <![CDATA[
13 temp_output=\$(mktemp); 13 temp_output=\$(mktemp);
14 minced 14 minced
15 -minNR $minNR 15 -minNR $minNR
16 -minRL $minRL 16 -minRL $minRL
17 -maxRL $maxRL 17 -maxRL $maxRL
22 #end if 22 #end if
23 $input 23 $input
24 \$temp_output 24 \$temp_output
25 #if '-spacers' in str($outputs).split(): 25 #if '-spacers' in str($outputs).split():
26 -spacers 26 -spacers
27 #end if 27 #end if
28 #if '-gffFull' in str($outputs).split(): 28 #if '-gffFull' in str($outputs).split():
29 -gffFull 29 -gffFull
30 #end if 30 #end if
31 #if '-gff' in str($outputs).split(): 31 #if '-gff' in str($outputs).split():
32 -gff 32 -gff
33 #end if 33 #end if
34 ; 34 ;
35 35
36 python \$MINCED_SCRIPT_PATH/reformat.py \$temp_output results.bed results.tab; 36 python $__tool_directory__/reformat.py \$temp_output results.bed results.tab;
37 #if '-spacers' in str($outputs).split(): 37 #if '-spacers' in str($outputs).split():
38 mv \$temp_output'_spacers.fa' $output_fasta; 38 mv \$temp_output'_spacers.fa' $output_fasta;
39 #end if 39 #end if
40 ]]>
40 </command> 41 </command>
41 <inputs> 42 <inputs>
42 <param format="fasta" name="input" type="data" label="Input sequence as FASTA"/> 43 <param format="fasta" name="input" type="data" label="Input sequence as FASTA"/>
43 44
44 <param name="minNR" type="integer" value="3" label="Minimum number of repeats a CRISPER must have"/> 45 <param name="minNR" type="integer" value="3" label="Minimum number of repeats a CRISPER must have"/>
93 <output name="output" file="minced.tabular" ftype="tabular" /> 94 <output name="output" file="minced.tabular" ftype="tabular" />
94 <output name="output_region" file="minced.bed" ftype="bed" /> 95 <output name="output_region" file="minced.bed" ftype="bed" />
95 </test> 96 </test>
96 </tests> 97 </tests>
97 <help> 98 <help>
99 <![CDATA[
98 **What it does** 100 **What it does**
99 101
100 MinCED - Mining CRISPRs in Environmental Datasets 102 MinCED - Mining CRISPRs in Environmental Datasets
101 103
102 104
105 in which sequence size can be anywhere from 100 to 800 bp. MinCED runs from the 107 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/). 108 command-line and was derived from CRT (http://www.room220.com/crt/).
107 109
108 https://github.com/ctSkennerton/minced 110 https://github.com/ctSkennerton/minced
109 111
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`
114 112
115 If you use this tool in Galaxy, please cite Gruening, BA et al. https://github.com/bgruening/galaxytools 113 If you use this tool in Galaxy, please cite Gruening, BA et al. https://github.com/bgruening/galaxytools
116 114
115 ]]>
117 </help> 116 </help>
117 <citations>
118 <citation type="doi">10.1186/1471-2105-8-209 </citation>
119 </citations>
118 </tool> 120 </tool>
119 121