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1 <tool id="bam_to_psl" name="Convert BAM to PSL format" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 #if $input.ext == 'bam':
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9 samtools view -o 'input.sam' -h '$input' &&
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10 #else:
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11 ln -s '$input' 'input.sam' &&
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12 #end if
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13 python '${__tool_directory__}/bam_to_psl.py'
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14 --input_file 'input.sam'
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15 --output_file '$output'
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16 ]]></command>
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17 <inputs>
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18 <param name="input" type="data" format="bam,sam" label="BAM or SAM file"/>
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19 </inputs>
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20 <outputs>
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21 <data name="output" format="psl"/>
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="input" value="input_1.sam" ftype="sam"/>
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26 <output name="output" value="output_1.psl" ftype="psl" compare="contains"/>
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27 </test>
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28 <test>
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29 <param name="input" value="input_2.bam" ftype="bam"/>
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30 <output name="output" value="output_2.psl" ftype="psl" compare="contains"/>
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31 </test>
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32 </tests>
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33 <help>
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34 **What it does**
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35
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36 Converts a BAM or SAM dataset to PSL format - https://genome.ucsc.edu/FAQ/FAQformat.html#format2.
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37 </help>
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38 <expand macro="citations"/>
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39 </tool>
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40
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