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1 <tool id="sam2counts" name="SAM To Counts">
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2 <description>Produce count data from SAM files</description>
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3
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4 <requirements>
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5 <requirement type="python-module">sam2counts_galaxy.py</requirement>
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6 </requirements>
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7
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8 <command interpreter="python">
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9 sam2counts_galaxy.py
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10
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11 ${first_input}
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12 #for $input_file in $input_files:
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13 ${input_file.additional_input}
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14 #end for
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15
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16 -o $counts
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17 -l $colnames
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18 </command>
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19
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20 <inputs>
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21 <param name="colnames" type="text" size="30" label="Short names for samples" help="A comma-separated list of short names for the samples in order">
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22 <validator type="empty_field"/>
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23 <validator type="regex" message="Must be a comma-separated tuple with no spaces">^(\w+,)+\w+$</validator>
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24 </param>
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25
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26 <param format="sam" name="first_input" type="data" label="SAM file" help=""/>
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27 <repeat name="input_files" title="Additional SAM Files">
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28 <param format="sam" name="additional_input" type="data" label="SAM file" help=""/>
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29 </repeat>
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30 </inputs>
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31
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32 <outputs>
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33 <data format="tabular" name="counts"/>
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34 </outputs>
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35
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36 <help>
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37 </help>
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38
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39 </tool>
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