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29
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1 <tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.5">
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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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1
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3 <command>
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28
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4 <!-- python $__tool_directory__/calculating_chrom.sizes.py ${refGenomeSource.genomeSource} ${input2}
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13
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5 #if $refGenomeSource.genomeSource == "builtin":
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23
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6 none ${refGenomeSource.input1_builtin.fields.path} ${output1}
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13
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7 #else:
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23
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8 ${refGenomeSource.input1_file} none ${output1}
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28
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9 #end if -->
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27
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10
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11 #if $refGenomeSource.genomeSource == "builtin":
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29
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12 if ${input2} == "chr":
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13 cat ${refGenomeSource.input1_builtin.fields.path} | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0; printf "chr" substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END {print c; }' | cat > $output1
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14 else:
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15 cat ${refGenomeSource.input1_builtin.fields.path} | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0; printf substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END {print c; }' | cat > $output1
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16 #else:
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17 if ${input2} == "chr":
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18 cat ${refGenomeSource.input1_file} | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0; printf "chr" substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END {print c; }' | cat > $output1
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19 else:
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20 cat ${refGenomeSource.input1_file} | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0; printf substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END {print c; }' | cat > $output1
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21 #end if
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22
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23
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24
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25 cat ${refGenomeSource.input1_builtin.fields.path} | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0; printf ${input2} substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END {print c; }' | cat > $output1
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27
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26 #else:
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27 cat ${refGenomeSource.input1_file} | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0; printf ${input2} substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END {print c; }' | cat > $output1
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28 #end if
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1
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29 </command>
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0
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30 <inputs>
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4
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31 <conditional name="refGenomeSource">
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32 <param name="genomeSource" type="select" label="Will you select a reference from your history or use a built-in FASTA?">
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33 <option value="builtin">Use a built-in FASTA</option>
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34 <option value="history">Use one from the history</option>
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35 </param>
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36 <when value="builtin">
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12
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37 <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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38 <options from_data_table="builtin_fastas">
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39 <filter type="sort_by" column="2" />
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40 <validator type="no_options" message="No built-ins are available" />
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41 </options>
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42 </param>
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43 </when>
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44 <when value="history">
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6
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45 <param name="input1_file" type="data" format="fasta" label="FASTA File" />
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4
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46 </when>
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47 </conditional>
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48 <param name="input2" type="select" label="Chromosome Column Prefix (eg. chr)">
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49 <option value="chr">'chr' (required for upload to GWIPS-Viz)</option>
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50 <option value="none" selected='true'>None - do not add a prefix</option>
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51 </param>
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3
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52
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0
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53 </inputs>
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54 <outputs>
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55 <data name="output1" format="tabular"/>
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56 </outputs>
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57 <tests>
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58 <test>
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1
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59 <param name="input1" value="test.fasta" ftype="fasta" />
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3
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60 <param name="input2" value="chr"/>
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0
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61 <output name="output1" file="test.fasta.sizes" ftype="tabular" lines_diff="4" />
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62 </test>
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63 </tests>
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64 <help>
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65 **What it does**
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66
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25
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67 Creates a chromosome sizes file from a fasta file. This is needed for creating ribosome profiles.
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68
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69 Some commonly used genomes are provided to save on storage.
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0
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70 </help>
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71 <citations/>
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72 </tool>
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