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annotate gotohscan.xml @ 0:6845ddcd5588 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan commit d18a08287799b0aa6ca50242ebcc218820923fb2-dirty
author rnateam
date Thu, 02 Jul 2015 12:06:30 -0400
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children c172fed9eb75
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6845ddcd5588 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan commit d18a08287799b0aa6ca50242ebcc218820923fb2-dirty
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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 <stdio>
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7 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error"/>
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8 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error"/>
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9 </stdio>
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10 <version_command><![CDATA[GotohScan --version | sed -n -e 2p]]></version_command>
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11 <command><![CDATA[
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12 GotohScan
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13
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14 -d $dbase
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15 -q $query
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16
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17 #if $split and $split is not None
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18 --split $split
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19 #end if
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21 #if $e and $e is not None
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22 -e $e
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23 #end if
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25 #if $p and $p is not None
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26 -p $p
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27 #end if
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29 $s
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30 -o $o
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31 >
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32
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33 #if $o.value == '0'
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34 $output0
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35 #elif $o.value == '1'
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36 $output1
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37 #elif $o.value == '2'
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38 $output2
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39 #elif $o.value == '3'
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40 $output3
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41 #elif $o.value == '4'
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42 $output4
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43 #elif $o.value == '5'
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44 $output5
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45 #end if
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46 ]]></command>
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47 <inputs>
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48 <param argument="-d" name="dbase" type="data" format="fasta" label="Input Database"/>
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49 <param argument="-q" name="query" type="data" format="fasta" label="Input Query"/>
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50 <param argument="--split" name="split" type="integer" optional="true" label="Database is split into subsequences of size:" help="default: 10000"/>
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51 <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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52 <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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53 <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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54 <param argument="-o" name="o" type="select" label="Output Format">
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55 <option value="0" selected="true">Blast tabular output</option>
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56 <option value="1">Blast tabular output + aligned sequences</option>
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57 <option value="2">FASTA format. NOTE: Hit sequence only, without gaps !</option>
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58 <option value="3">MAF format. NOTE: Header truncated to 30 characters!</option>
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59 <option value="4">BED + aligned sequences</option>
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60 <option value="5">GFF + aligned sequences</option>
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61 </param>
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62 </inputs>
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63 <outputs>
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64 <data name="output0" format="tabular" label="${tool.name} on ${on_string}">
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65 <filter>o == '0'</filter>
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66 </data>
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67 <data name="output1" format="tabular" label="${tool.name} on ${on_string}">
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68 <filter>o == '1'</filter>
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69 </data>
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70 <data name="output2" format="fasta" label="${tool.name} on ${on_string}">
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71 <filter>o == '2'</filter>
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72 </data>
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73 <data name="output3" format="maf" label="${tool.name} on ${on_string}">
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74 <filter>o == '3'</filter>
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75 </data>
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76 <data name="output4" format="bed" label="${tool.name} on ${on_string}">
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77 <filter>o == '4'</filter>
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78 </data>
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79 <data name="output5" format="gff" label="${tool.name} on ${on_string}">
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80 <filter>o == '5'</filter>
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81 </data>
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82 </outputs>
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83 <tests>
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84 <test>
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85 <param name="dbase" value="NC_000913.fna"/>
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86 <param name="query" value="C0299.fa"/>
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87 <param name="o" value="2"/>
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88 <output name="" ftype="fasta" file="gotohscan.result1"/>
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89 </test>
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90 </tests>
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91 <help>
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92 <![CDATA[
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93 **GotohScan** is a search tool that finds shorter sequences
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94 (usually genes) in large database sequences (chromosomes, genomes, ..)
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95 by computing all semi-global alignments. Thus, the query sequence is
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96 never truncated or split into subsequences, but always mapped to the
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97 database over its complete length. The alignment is computed via the
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98 Gotoh-alignment algorithm using affine gap costs.
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99 ]]></help>
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100 <citations>
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101 <citation type="doi">10.1093/nar/gkn1084</citation>
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102 </citations>
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103 </tool>