Mercurial > repos > morinlab > read_counter

annotate read_counter.xml @ 0:cac6401377d2 draft default tip

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planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
author morinlab
date Tue, 11 Oct 2016 14:29:02 -0400
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cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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1 <tool id="read_counter" name="readCounter" version="0.1.1">
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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2 <description>
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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3 Get Binned Read Distribution for a Sequence Alignment File
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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4 </description>
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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5 <requirements>
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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6 <requirement type="package" version="0.1.1">hmmcopy</requirement>
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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7 </requirements>
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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8 <command>
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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9 <![CDATA[
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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10
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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11 ln -s $input_bam input.bam;
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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12 ln -s $input_bam.metadata.bam_index input.bam.bai;
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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13
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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14 #if $interval
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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15 for i in \$( cat $interval ); do
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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16 #end if
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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17
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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18 readCounter
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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19
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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20 #if $interval
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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21 -c \$i
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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22 #end if
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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23
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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24 input.bam >> $output
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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25
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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26 #if $interval
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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27 ; done
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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28 #end if
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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29
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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30 ]]>
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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31 </command>
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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32 <inputs>
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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33 <param type="data" format="bam" name="input_bam" label="Specify BAM Alignment File"/>
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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34 <param type="data" format="bed,txt" name="interval" label="Specify Interval" optional="true"/>
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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35 </inputs>
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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36 <outputs>
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37 <data format="wig" name="output"/>
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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38 </outputs>
cac6401377d2 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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39 </tool>