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41
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1 <tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.8.2">
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26
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2 <description>Generates a TAB Delimited chrom.sizes File from an Inputted FASTA</description>
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41
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3 <requirement type="package" version="1.13">samtools</requirement>
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4
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1
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5 <command>
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33
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6
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7 #if $refGenomeSource.genomeSource == "builtin":
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41
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8 samtools index ${refGenomeSource.input1_builtin.fields.path}
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9 cut -f 1,2 ${refGenomeSource.input1_builtin.fields.path}.fai > $output1
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33
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10 #else:
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41
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11 samtools index ${refGenomeSource.input1_file}
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12 cut -f 1,2 ${refGenomeSource.input1_file}.fai > $output1
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29
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13 #end if
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14
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1
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15 </command>
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0
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16 <inputs>
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4
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17 <conditional name="refGenomeSource">
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18 <param name="genomeSource" type="select" label="Will you select a reference from your history or use a built-in FASTA?">
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19 <option value="builtin">Use a built-in FASTA</option>
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20 <option value="history">Use one from the history</option>
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21 </param>
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22 <when value="builtin">
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12
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23 <param name="input1_builtin" type="select" format="fasta" label="Select a reference" help="if your reference of interest is not listed - contact RiboGalaxy team">
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4
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24 <options from_data_table="builtin_fastas">
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25 <filter type="sort_by" column="2" />
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26 <validator type="no_options" message="No built-ins are available" />
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27 </options>
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28 </param>
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29 </when>
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30 <when value="history">
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6
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31 <param name="input1_file" type="data" format="fasta" label="FASTA File" />
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4
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32 </when>
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33 </conditional>
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39
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34
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35 <param name="input2" type="text" label="Chromosome Column Prefix (add chr if absent from FASTA file for GWIPS upload)" />
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3
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36
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0
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37 </inputs>
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38 <outputs>
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39 <data name="output1" format="tabular"/>
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40 </outputs>
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41 <tests>
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42 <test>
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1
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43 <param name="input1" value="test.fasta" ftype="fasta" />
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3
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44 <param name="input2" value="chr"/>
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0
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45 <output name="output1" file="test.fasta.sizes" ftype="tabular" lines_diff="4" />
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46 </test>
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47 </tests>
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48 <help>
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49 **What it does**
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50
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25
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51 Creates a chromosome sizes file from a fasta file. This is needed for creating ribosome profiles.
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52
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53 Some commonly used genomes are provided to save on storage.
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0
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54 </help>
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55 <citations/>
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56 </tool>
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