Mercurial > repos > ryotas > export2sam

annotate export2sam.xml @ 0:61f3089ddc74 default tip

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author ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
date Tue, 30 Dec 2014 18:53:23 +0900
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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1 <tool id="export2sam" name="Export to SAM" version="0.1">
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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2 <description></description>
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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3 <parallelism method="basic"></parallelism>
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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4 <command interpreter="sh">
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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5 export2sam.sh
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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6 -a $read1
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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7 #if $pairCondition.pairSelect == "yes"
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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8 -b $read2
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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9 #end if
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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10 -o $output
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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11 $gunzip
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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12 $remove
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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13 </command>
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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14 <inputs>
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15 <param name="read1" type="data" format="eland_export" label="ELAND export file" help="" />
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16 <param name="gunzip" type="boolean" truevalue="-g" falsevalue="" checked="True" label="Input file is gzipped" help="" />
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17 <param name="remove" type="boolean" truevalue="-r" falsevalue="" checked="True" label="Remove (chr).fa and chr_fragments.fa/" help="" />
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18 <conditional name="pairCondition">
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19 <param name="pairSelect" type="select" label="Pair end?">
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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20 <option value="yes">Yes</option>
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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21 <option value="no" selected="True">No</option>
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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22 </param>
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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23 <when value="yes">
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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24 <param name="read2" type="data" format="eland_export" label="ELAND export file" help="" />
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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25 </when>
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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26 <when value="no"></when>
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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27 </conditional>
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28 </inputs>
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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29 <outputs>
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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30 <data format="sam" name="output" label="${tool.name} on ${on_string}"/>
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31 </outputs>
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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32 <help>If thou thyself canst do it, attend no other's help or hand.</help>
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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33 </tool>