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comparison 01_RemoveSNPs/RemoveSNPs.xml @ 7:cd9c123ab04f draft default tip

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author dktanwar
date Mon, 16 Oct 2017 14:20:00 -0400
parents 11377edbbea2
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6:11377edbbea2 7:cd9c123ab04f
1 <tool id="RemoveSNPs" name="Remove Mismatches (SNPs) from SAM Alignment file" version="0.1.0"> 1 <tool id="RemoveSNPs" name="Remove Mismatches (SNPs) from SAM Alignment file" version="0.1.0">
2 <requirements> 2 <requirements>
3 </requirements> 3 </requirements>
4 <command detect_errors="exit_code"><![CDATA[ 4 <command detect_errors="exit_code"><![CDATA[
5 bash $__tool_directory__/RemoveSNPs "$SAM alignment files" 3 > "$output1" 5 bash $__tool_directory__/RemoveSNPs "$SAM_files" "$SNPs_allowed" > "$output1"
6 ]]></command> 6 ]]></command>
7 <inputs> 7 <inputs>
8 <param type="data" name="SAM alignment files" format="sam" /> 8 <param type="data" name="SAM_files" format="sam" />
9 <param type="integer" name="SNPs/ mismatches allowed" value="3" /> 9 <param type="integer" name="SNPs_allowed" value="3" />
10 </inputs> 10 </inputs>
11 <outputs> 11 <outputs>
12 <data name="output1" format="sam" /> 12 <data name="output1" format="sam" />
13 </outputs> 13 </outputs>
14 <tests> 14 <tests>
15 <test> 15 <test>
16 <param name="SAM alignment files" value="input.sam"/> 16 <param name="SAM_files" value="input.sam"/>
17 <output name="output1" file="output.sam"/> 17 <output name="output1" file="output.sam"/>
18 </test> 18 </test>
19 </tests> 19 </tests>
20 <help><![CDATA[ 20 <help><![CDATA[
21 This program will remove mismatches from sam file. 21 This program will remove mismatches from sam file.