Mercurial > repos > yating-l > psltobigpsl

annotate psltobigpsl.xml @ 4:beb6e2ef1b45 draft

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planemo upload for repository https://github.com/Yating-L/psltobigpsl.git commit 6815597fe564030e70de3ffe147374e8c6dfcdf5-dirty
author yating-l
date Fri, 03 Feb 2017 13:03:59 -0500
parents 107373c01472
children 4776e061493a
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1 <tool id="pslToBigPsl" name="pslToBigPsl" version="0.1.0">
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2 <requirements>
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3 </requirements>
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4 <stdio>
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5 <exit_code range="1:" />
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6 </stdio>
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7 <command><![CDATA[
4
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8 $__tool_directory__/pslToBigPsl
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9 '${input}'
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10 #if $add_input.input_type == "both"
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11 -cds='${input_cds}'
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12 -fa='${input_fa}'
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13 #elif $add_input.input_type == "fa"
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14 -fa='${input_fa}'
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15 #elif $add_input.input_type == "cds"
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16 -cds='${input_cds}'
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17 #end if
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18 output
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19 && sort -k1,1 -k2,2n output > '${output_sorted}'
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20 ]]></command>
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21 <inputs>
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22 <param name="input" label="Psl file" type="data" format="psl" />
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23 <conditional name="add_input">
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24 <param name="input_type" type="select" label="Provide FASTA and CDS files">
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25 <option value="no">No</option>
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26 <option value="both">Provide both FASTA and CDS files</option>
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27 <option value="fa">Provide FASTA file</option>
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28 <option value="cds">Provide CDS file</option>
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29 </param>
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30 <when value="both">
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31 <param name="input_fa" type="data" format="fasta" label="Input FASTA file" />
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32 <param name="input_cds" type="data" format="tabular" label="Input CDS file" />
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33 </when>
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34 <when value="fa">
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35 <param name="input_fa" type="data" format="fasta" label="Input FASTA file" />
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36 </when>
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37 <when value="cds">
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38 <param name="input_cds" type="data" format="tabular" label="Input CDS file" />
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39 </when>
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40 <when value="no">
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41 </when>
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42 </conditional>
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43 </inputs>
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44 <outputs>
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45 <data name="output_sorted" format="bed" />
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46 </outputs>
4
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47 <tests>
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48 <test>
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49 <param name="input" value="amaVit1_Gallus_gallus.psl" />
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50 <param name="input_type" value="no" />
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51 <output name="output_sorted" value="out.bigpsl" />
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52 </test>
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53 <test>
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54 <param name="input" value="amaVit1_Gallus_gallus.psl" />
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55 <param name="input_type" value="fa" />
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56 <param name="input_fa" value="Gallus_gallus_RefSeq.fa" />
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57 <output name="output_sorted" value="out_fa.bigpsl" />
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58 </test>
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59 <test>
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60 <param name="input" value="amaVit1_Gallus_gallus.psl" />
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61 <param name="input_type" value="cds" />
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62 <param name="input_cds" value="Gallus_gallus_RefSeq.cds" />
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63 <output name="output_sorted" value="out_cds.bigpsl" />
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64 </test>
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65 <test>
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66 <param name="input" value="amaVit1_Gallus_gallus.psl" />
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67 <param name="input_type" value="both" />
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68 <param name="input_fa" value="Gallus_gallus_RefSeq.fa" />
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69 <param name="input_cds" value="Gallus_gallus_RefSeq.cds" />
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70 <output name="output_sorted" value="out_both.bigpsl" />
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71 </test>
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72 </tests>
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73 <help><![CDATA[
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74 Transform a Psl format file to a Bed format file.
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75 Input: Psl File
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76 Ouput: BigPsl File
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77 ]]></help>
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78 <citations>
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79 <citation type="bibtex">@article{kent2002blat,
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80 title={BLAT—the BLAST-like alignment tool},
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81 author={Kent, W James},
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82 journal={Genome research},
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83 volume={12},
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84 number={4},
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85 pages={656--664},
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86 year={2002},
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87 publisher={Cold Spring Harbor Lab}
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88 }</citation>
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89 </citations>
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90 </tool>