Mercurial > repos > rmarenco > bedclip

annotate bedclip.xml @ 0:3275f20f1368 draft default tip

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planemo upload for repository https://github.com/remimarenco/bedclip
author rmarenco
date Sat, 23 Jul 2016 03:20:57 -0400
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0
3275f20f1368 planemo upload for repository https://github.com/remimarenco/bedclip
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1 <tool id="bedclip" name="bedClip" version="0.1.0">
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2 <requirements>
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3 <requirement type="package" version="332">ucsc-fatotwobit</requirement>
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4 <requirement type="package" version="324">ucsc-twobitinfo</requirement>
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5 <requirement type="package" version="332">ucsc-bedclip</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" />
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9 </stdio>
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10 <command><![CDATA[
3275f20f1368 planemo upload for repository https://github.com/remimarenco/bedclip
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11 faToTwoBit "$ref_genome" two_bit_ref_genome;
3275f20f1368 planemo upload for repository https://github.com/remimarenco/bedclip
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12 twoBitInfo two_bit_ref_genome chrom_sizes;
3275f20f1368 planemo upload for repository https://github.com/remimarenco/bedclip
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13 bedClip "$bed_file" chrom_sizes "$bed_clipped";
3275f20f1368 planemo upload for repository https://github.com/remimarenco/bedclip
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14 ]]></command>
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15 <inputs>
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16 <param type="data" name="ref_genome" format="fasta" />
3275f20f1368 planemo upload for repository https://github.com/remimarenco/bedclip
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17 <param type="data" name="bed_file" format="bed" />
3275f20f1368 planemo upload for repository https://github.com/remimarenco/bedclip
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18 </inputs>
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19 <outputs>
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20 <data name="bed_clipped" format="bed" />
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="ref_genome" value="input.fasta"/>
3275f20f1368 planemo upload for repository https://github.com/remimarenco/bedclip
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25 <param name="bed_file" value="input.bed"/>
3275f20f1368 planemo upload for repository https://github.com/remimarenco/bedclip
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26 <output name="bed_clipped" file="output.bed"/>
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27 </test>
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28 </tests>
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29 <help><![CDATA[
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30 ]]></help>
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31 </tool>