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1 <tool id="get_cov_stats" name="get statistics from bam file" version="1">
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2 <description>
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3 From bam file, get some statistics
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="3.6.0">r</requirement>
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7 <requirement type="package" version="1.14">samtools</requirement>
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8 <requirement type="package" version="3.7.12">python</requirement>
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9 </requirements>
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10 <stdio>
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11 <exit_code range="1:" />
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12 </stdio>
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13 <command><![CDATA[
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14 python '$__tool_directory__/get_cov_stats.py'
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15 -bam "$bamfile"
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16 #if $typeofreads.p_or_s == "paired":
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17 -p
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18 #end if
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19 > "$output"
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20 ]]></command>
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21 <inputs>
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22 <param name="bamfile" type="data" format="bam" label="Bam file" help="Bam file of an aligment"/>
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23 <conditional name="typeofreads">
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24 <param name="p_or_s" type="select" label="Read option">
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25 <option value="single" selected="True">Single-end</option>
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26 <option value="paired">Paired-end</option>
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27 </param>
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28 </conditional>
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29 </inputs>
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30 <outputs>
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31 <data format="txt" name="output" label="${tool.name} on ${on_string}"/>
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32 </outputs>
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33 <help>
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34 <![CDATA[
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35
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36 Homemade script to get some statistics about and bam file.
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37
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38 ]]>
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39 </help>
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40 </tool>
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