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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan commit 608bf2d6f11fe6dceaa0060f729bdbb66cfee867
author rnateam
date Sun, 12 Nov 2017 06:10:23 -0500
parents 6845ddcd5588
children
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1 <tool id="rbc_gotohscan" name="GotohScan" version="1.3.0">
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2 <description>Find subsequences in db</description>
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3 <requirements>
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4 <requirement type="package" version="1.3">gotohscan</requirement>
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5 </requirements>
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6 <version_command><![CDATA[GotohScan --version | sed -n -e 2p]]></version_command>
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7 <command detect_errors="aggressive"><![CDATA[
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8 GotohScan
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9 -d '$dbase'
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10 -q '$query'
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11
1
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12 #if $split
0
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13 --split $split
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14 #end if
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15
1
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16 #if $e
0
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17 -e $e
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18 #end if
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19
1
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20 #if $p
0
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21 -p $p
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22 #end if
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23
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24 $s
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25 -o $o
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26 >
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27
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28 #if $o.value == '0'
1
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29 '$output0'
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30 #elif $o.value == '1'
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31 '$output1'
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32 #elif $o.value == '2'
1
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33 '$output2'
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34 #elif $o.value == '3'
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35 '$output3'
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36 #elif $o.value == '4'
1
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37 '$output4'
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38 #elif $o.value == '5'
1
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39 '$output5'
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40 #end if
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41 ]]></command>
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42 <inputs>
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43 <param argument="-d" name="dbase" type="data" format="fasta" label="Input Database"/>
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44 <param argument="-q" name="query" type="data" format="fasta" label="Input Query"/>
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45 <param argument="--split" name="split" type="integer" optional="true" label="Database is split into subsequences of size:" help="default: 10000"/>
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46 <param argument="-e" name="e" type="float" optional="true" label="E-value" help="Value should be &lt; 10. default: 1e-3"/>
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47 <param argument="-p" name="p" type="float" optional="true" label="Percent identity of aligned sequences" help="Value should be in [0.0,100.00]"/>
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48 <param argument="-s" name="s" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Print score distribution data for each query to a file"/>
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49 <param argument="-o" name="o" type="select" label="Output Format">
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50 <option value="0" selected="true">Blast tabular output</option>
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51 <option value="1">Blast tabular output + aligned sequences</option>
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52 <option value="2">FASTA format. NOTE: Hit sequence only, without gaps !</option>
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53 <option value="3">MAF format. NOTE: Header truncated to 30 characters!</option>
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54 <option value="4">BED + aligned sequences</option>
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55 <option value="5">GFF + aligned sequences</option>
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56 </param>
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57 </inputs>
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58 <outputs>
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59 <data name="output0" format="tabular" label="${tool.name} on ${on_string}">
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60 <filter>o == '0'</filter>
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61 </data>
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62 <data name="output1" format="tabular" label="${tool.name} on ${on_string}">
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63 <filter>o == '1'</filter>
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64 </data>
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65 <data name="output2" format="fasta" label="${tool.name} on ${on_string}">
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66 <filter>o == '2'</filter>
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67 </data>
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68 <data name="output3" format="maf" label="${tool.name} on ${on_string}">
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69 <filter>o == '3'</filter>
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70 </data>
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71 <data name="output4" format="bed" label="${tool.name} on ${on_string}">
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72 <filter>o == '4'</filter>
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73 </data>
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74 <data name="output5" format="gff" label="${tool.name} on ${on_string}">
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75 <filter>o == '5'</filter>
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76 </data>
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77 </outputs>
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78 <tests>
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79 <test>
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80 <param name="dbase" value="NC_000913.fna"/>
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81 <param name="query" value="C0299.fa"/>
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82 <param name="o" value="2"/>
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83 <output name="" ftype="fasta" file="gotohscan.result1"/>
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84 </test>
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85 </tests>
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86 <help>
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87 <![CDATA[
1
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88
0
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89 **GotohScan** is a search tool that finds shorter sequences
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90 (usually genes) in large database sequences (chromosomes, genomes, ..)
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91 by computing all semi-global alignments. Thus, the query sequence is
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92 never truncated or split into subsequences, but always mapped to the
6845ddcd5588 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan commit d18a08287799b0aa6ca50242ebcc218820923fb2-dirty
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93 database over its complete length. The alignment is computed via the
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94 Gotoh-alignment algorithm using affine gap costs.
1
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95
0
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96 ]]></help>
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97 <citations>
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98 <citation type="doi">10.1093/nar/gkn1084</citation>
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99 </citations>
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100 </tool>