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comparison samtools_index/samtools_index.xml @ 0:5bdc8418c378 draft

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author jackcurragh
date Wed, 23 Mar 2022 12:51:35 +0000
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1 <tool id="samtools_index" name="Samtools index" version="2.0.4" profile="@PROFILE@">
2 <description>order of storing aligned sequences</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @ADDTHREADS@
11 @ADDMEMORY@
12 samtools index
13 -@ \$addthreads
14 -m \$addmemory"M"
15 $prim_key_cond.prim_key_select
16 '${input1}'
17 '${output1}'
18 ]]></command>
19 <inputs>
20 <param name="input1" type="data" format="sam,unsorted.bam,cram" label="BAM File" />
21 <conditional name="prim_key_cond">
22 <param name="prim_key_select" type="select" label="Index type">
23 <option value="-b" selected="True">BAI (-b)</option>
24 <option value="-c" selected="True">CSI (-c)</option>
25 </param>
26 <when value="-b"/>
27 <when value="-c"/>
28 </conditional>
29 </inputs>
30 <outputs>
31 <data name="output1" format="bam">
32 <change_format>
33 <when input="prim_key_cond.prim_key_select" value="-b" format="bai" />
34 <when input="prim_key_cond.prim_key_select" value="-c" format="csi" />
35 </change_format>
36 </data>
37 </outputs>
38 <tests>
39 <test>
40 <param name="input1" value="1.bam" ftype="bam" />
41 <param name="prim_key_cond.prim_key_select" value="-c" />
42 <output name="output1" file="1.bam.bai" ftype="bai" lines_diff="4" />
43 </test>
44 </tests>
45 <help>
46 **What it does**
47
48 Indexes a BAM file
49 </help>
50 <expand macro="citations"/>
51 </tool>