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1 <tool id="fetch_interval" name="Fetch Interval" version="1.0.0">
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2 <description> Creates Interval files used to parallelize certain Galaxy Tools </description>
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3 <requirements>
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4 <requirement type="package" version="1.0.0">fetch_interval</requirement>
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5 <requirement type="set_environment">FETCH_REPOSITORY_DIR</requirement>
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6 </requirements>
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7 <command>
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8 <![CDATA[
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9
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10 mkdir outputs;
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11 #if $output_option.output_option_selector == "collection":
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12 python \$FETCH_REPOSITORY_DIR/fetch_interval.py --mode by_rname --input $input --order $order --output output.txt --chromosome --group_according_to_largest_chromosome --prefixes_to_ignore GL NC MT;
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13
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14 #else:
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15 python \$FETCH_REPOSITORY_DIR/fetch_interval.py --mode by_rname --input $input --output $order --chromosome --prefixes_to_ignore GL NC MT;
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16 cat $order > ./outputs/samp1.bed;
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17
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18 #end if
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19
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20 ]]>
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21 </command>
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22 <inputs>
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23 <conditional name="output_option">
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24 <param type="select" name="output_option_selector" label="How to Output?">
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25 <option value="collection">Collection</option>
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26 <option value="file">Single File</option>
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27 </param>
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28 </conditional>
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29 <param type="data" format="bam" name="input" label="BAM Alignment File" help="Information is pulled from the header, ensure consistent across BAMs"/>
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30 </inputs>
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31 <outputs>
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32 <collection name="list_output" type="list" description="Interval Files">
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33 <discover_datasets pattern="__name_and_ext__" directory="outputs"/>
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34 </collection>
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35 <data format="txt" name="order"/>
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36 </outputs>
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37 </tool>
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