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1 <tool id="samtools_index" name="Samtools index" version="2.0.4" profile="@PROFILE@">
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2 <description>order of storing aligned sequences</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 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
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10 @ADDTHREADS@
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11 @ADDMEMORY@
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12 samtools index
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13 -@ \$addthreads
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14 -m \$addmemory"M"
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15 $prim_key_cond.prim_key_select
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16 '${input1}'
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17 '${output1}'
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18 ]]></command>
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19 <inputs>
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20 <param name="input1" type="data" format="sam,unsorted.bam,cram" label="BAM File" />
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21 <conditional name="prim_key_cond">
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22 <param name="prim_key_select" type="select" label="Index type">
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23 <option value="-b" selected="True">BAI (-b)</option>
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24 <option value="-c" selected="True">CSI (-c)</option>
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25 </param>
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26 <when value="-b"/>
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27 <when value="-c"/>
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28 </conditional>
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29 </inputs>
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30 <outputs>
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31 <data name="output1" format="bam">
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32 <change_format>
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33 <when input="prim_key_cond.prim_key_select" value="-b" format="bai" />
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34 <when input="prim_key_cond.prim_key_select" value="-c" format="csi" />
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35 </change_format>
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36 </data>
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37 </outputs>
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38 <tests>
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39 <test>
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40 <param name="input1" value="1.bam" ftype="bam" />
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41 <param name="prim_key_cond.prim_key_select" value="-c" />
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42 <output name="output1" file="1.bam.bai" ftype="bai" lines_diff="4" />
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43 </test>
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44 </tests>
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45 <help>
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46 **What it does**
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47
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48 Indexes a BAM file
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49 </help>
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50 <expand macro="citations"/>
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51 </tool>
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