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1 <tool id="sort_bam" name="sort_bam" version="1.1">
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2 <description>Sort bam file based on chromosomal coordinates.</description>
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3 <requirements>
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4 <requirement type="set_environment">LINKYX_PATH</requirement>
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5 <requirement type="set_environment">SAMTOOLS</requirement>
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6 <requirement type="package" version="0.1.19">samtools-fpic</requirement>
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7 <requirement type="package" version="1.6.922">bioperl</requirement>
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8 </requirements>
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9 <command interpreter="bash">sort_bam.sh $output $input1</command>
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10 <inputs>
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11 <param format="bam" name="input1" type="data" label="Alignment file"/>
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12 </inputs>
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13 <outputs>
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14 <data format="bam" name="output" />
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15 </outputs>
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16
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17 <tests>
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18 <test>
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19 </test>
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20 </tests>
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21
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22 <help>
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23 Sort bam file based on chromosomal coordinates.
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24 </help>
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25
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26 </tool>
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