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annotate fraggenescan.xml @ 0:1f0a3e4497d4 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/fraggenescan/ commit 59ac8955ccb33e3fcd6649c61779bb3ae9ccb6d4
author iuc
date Wed, 06 Sep 2017 13:23:14 -0400
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children 2dfb2fba4081
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1f0a3e4497d4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/fraggenescan/ commit 59ac8955ccb33e3fcd6649c61779bb3ae9ccb6d4
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1 <tool id="fraggenescan" name="FragGeneScan" version="@WRAPPER_VERSION@.0">
1f0a3e4497d4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/fraggenescan/ commit 59ac8955ccb33e3fcd6649c61779bb3ae9ccb6d4
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2 <description>for finding (fragmented) genes in short reads</description>
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3 <macros>
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4 <token name="@WRAPPER_VERSION@">1.30</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@WRAPPER_VERSION@">fraggenescan</requirement>
1f0a3e4497d4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/fraggenescan/ commit 59ac8955ccb33e3fcd6649c61779bb3ae9ccb6d4
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8 </requirements>
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9 <version_command>@WRAPPER_VERSION@</version_command>
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10 <command detect_errors="aggressive"><![CDATA[
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11 run_FragGeneScan.pl
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12 -genome='$genome'
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13 -out="output_file_name"
1f0a3e4497d4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/fraggenescan/ commit 59ac8955ccb33e3fcd6649c61779bb3ae9ccb6d4
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14 -complete='$complete'
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15 -train='$train'
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16 -thread=\${GALAXY_SLOTS:-4}
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17 ]]></command>
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18 <inputs>
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19 <param argument="-genome" type="data" format="fasta" label="Input equence file"/>
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20 <param argument="-complete" type="boolean" truevalue="1" falsevalue="0" label="Does the sequence file have complete genomic sequences?"/>
1f0a3e4497d4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/fraggenescan/ commit 59ac8955ccb33e3fcd6649c61779bb3ae9ccb6d4
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21 <param argument="-train" type="select" label="Model">
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22 <option value="454_5">454 pyrosequencing reads with about 0.5% error rate (454_5)</option>
1f0a3e4497d4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/fraggenescan/ commit 59ac8955ccb33e3fcd6649c61779bb3ae9ccb6d4
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23 <option value="454_10">454 pyrosequencing reads with about 1% error rate (454_10)</option>
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24 <option value="454_30">454 pyrosequencing reads with about 3% error rate (454_30)</option>
1f0a3e4497d4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/fraggenescan/ commit 59ac8955ccb33e3fcd6649c61779bb3ae9ccb6d4
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25 <option value="complete">complete genomic sequences or short sequence reads without sequencing error (complete)</option>
1f0a3e4497d4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/fraggenescan/ commit 59ac8955ccb33e3fcd6649c61779bb3ae9ccb6d4
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26 <option value="gene">gene</option>
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27 <option value="illumina_1">Illumina sequencing reads with about 0.01% error rate (illumina_1)</option>
1f0a3e4497d4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/fraggenescan/ commit 59ac8955ccb33e3fcd6649c61779bb3ae9ccb6d4
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28 <option value="illumina_5">Illumina sequencing reads with about 0.5% error rate (illumina_5)</option>
1f0a3e4497d4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/fraggenescan/ commit 59ac8955ccb33e3fcd6649c61779bb3ae9ccb6d4
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29 <option value="illumina_10">Illumina sequencing reads with about 1% error rate (illumina_10)</option>
1f0a3e4497d4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/fraggenescan/ commit 59ac8955ccb33e3fcd6649c61779bb3ae9ccb6d4
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30 <option value="noncoding">noncoding</option>
1f0a3e4497d4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/fraggenescan/ commit 59ac8955ccb33e3fcd6649c61779bb3ae9ccb6d4
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31 <option value="pwm">pwm</option>
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32 <option value="rgene">rgene</option>
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33 <option value="sanger_5">Sanger sequencing reads with about 0.5% error rate (sanger_5)</option>
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34 <option value="sanger_10">Sanger sequencing reads with about 1% error rate (sanger_10)</option>
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35 <option value="start">start</option>
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36 <option value="start1">start1</option>
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37 <option value="stop">stop</option>
1f0a3e4497d4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/fraggenescan/ commit 59ac8955ccb33e3fcd6649c61779bb3ae9ccb6d4
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38 <option value="stop1">stop1</option>
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39 </param>
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40 </inputs>
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41 <outputs>
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42 <data name="coord" format="tabular" from_work_dir="output_file_name.out" label="${tool.name} on ${on_string}: Coordinates of putative genes"/>
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43 <data name="nt_seq" format="fasta" from_work_dir="output_file_name.ffn" label="${tool.name} on ${on_string}: Nucleotide equences of putative genes"/>
1f0a3e4497d4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/fraggenescan/ commit 59ac8955ccb33e3fcd6649c61779bb3ae9ccb6d4
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44 <data name="prot_seq" format="fasta" from_work_dir="output_file_name.faa" label="${tool.name} on ${on_string}: Protein equences of putative genes"/>
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45 <data name="gff" format="gff" from_work_dir="output_file_name.gff" label="${tool.name} on ${on_string}"/>
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46 </outputs>
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47 <tests>
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48 <test>
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49 <param name="genome" value="contigs.fasta"/>
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50 <param name="complete" value="False"/>
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51 <param name="train" value="complete"/>
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52 <output name="coord" ftype="tabular" value="contigs.out"/>
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53 <output name="nt_seq" ftype="fasta" value="contigs.ffn"/>
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54 <output name="prot_seq" ftype="fasta" value="contigs.faa"/>
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55 <output name="gff" ftype="gff" value="contigs.gff"/>
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56 </test>
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57 <test>
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58 <param name="genome" value="NC_000913.fasta"/>
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59 <param name="complete" value="True"/>
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60 <param name="train" value="complete"/>
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61 <output name="coord" ftype="tabular" value="NC_000913.out"/>
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62 <output name="nt_seq" ftype="fasta" value="NC_000913.ffn"/>
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63 <output name="prot_seq" ftype="fasta" value="NC_000913.faa"/>
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64 <output name="gff" ftype="gff" value="NC_000913.gff"/>
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65 </test>
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66 <test>
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67 <param name="genome" value="NC_000913-454.fasta"/>
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68 <param name="complete" value="False"/>
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69 <param name="train" value="454_10"/>
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70 <output name="coord" ftype="tabular" value="NC_000913-454.out"/>
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71 <output name="nt_seq" ftype="fasta" value="NC_000913-454.ffn"/>
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72 <output name="prot_seq" ftype="fasta" value="NC_000913-454.faa"/>
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73 <output name="gff" ftype="gff" value="NC_000913-454.gff"/>
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74 </test>
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75 </tests>
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76 <help><![CDATA[
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77 **What it does**
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78
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79 FragGeneScan is an application for finding (fragmented) genes in short reads.
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80 It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes.
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81
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82 ]]></help>
1f0a3e4497d4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/fraggenescan/ commit 59ac8955ccb33e3fcd6649c61779bb3ae9ccb6d4
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83 <citations>
1f0a3e4497d4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/fraggenescan/ commit 59ac8955ccb33e3fcd6649c61779bb3ae9ccb6d4
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84 <citation type="doi">10.1093/nar/gkq747</citation>
1f0a3e4497d4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/fraggenescan/ commit 59ac8955ccb33e3fcd6649c61779bb3ae9ccb6d4
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85 </citations>
1f0a3e4497d4 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/fraggenescan/ commit 59ac8955ccb33e3fcd6649c61779bb3ae9ccb6d4
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86 </tool>