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1 <tool id="vcf_snp" name="vcf to snp" version="0.1">
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2 <description>vcf to snp for fasta</description>
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3 <requirements>
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4 <!-- Should just use the filter snp that's installed in the path -->
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5
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6 </requirements>
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7
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8 ## The command is a Cheetah template which allows some Python based syntax.
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9 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
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10 ## ! We only have a simple single command here.
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11
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12 <command interpreter="python">
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13 vcf_snp.py
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14 -s ${vcf}
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15 -o output.txt;
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16 cut -f1 output.txt > header.txt | cut -f2- output.txt > seq.txt;
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17 cat seq.txt | sed 's/[[:blank:]]//g' >seq2.txt;
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18 paste header.txt seq2.txt >tab.txt;
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19
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20
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21 </command>
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22
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23 <inputs>
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24 <param name="vcf" type="data" label="vcf" help=""/>
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25
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26 </inputs>
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27
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28 <outputs>
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29 <data format="tabular" name="output_file" label="${vcf}" from_work_dir="tab.txt">
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30 </data>
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31 </outputs>
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32
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33 <tests>
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34 <!-- Empty -->
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35 </tests>
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36
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37 <help>
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38
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39 .. class:: infomark
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40
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41 **What it does**
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42
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43 Transforms a vcf into a snp tab file
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44
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45 -------------
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46
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47 .. class:: infomark
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48
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49 **Tool Author**
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50
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51 Brigida Rusconi
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52
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53
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54 </help>
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55 </tool> |