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author yating-l
date Mon, 10 Jul 2017 12:43:51 -0400
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1 <?xml version="1.0"?>
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2 <tool id="hg_gc_percent" name="hgGcPercent" version="1.0">
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3 <description>Calculates GC percentages of a twoBit file</description>
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4
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5 <macros>
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6 <import>ucsc_macros.xml</import>
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7 </macros>
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8
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9 <expand macro="requirements_twobit">
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10 <requirement type="package" version="340">ucsc_gcpercent</requirement>
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11 <requirement type="package" version="340">ucsc_bigwig</requirement>
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12 </expand>
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13
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14 <command detect_errors="exit_code">
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15 <![CDATA[
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16 ## This tool generates a bigWig file instead of a gzip wiggle file in order
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17 ## to facilitate testing. Support for comparing gzip files will be added to
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18 ## Galaxy in 17.05: https://github.com/galaxyproject/galaxy/pull/3550
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19
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20 twoBitInfo "${twobit_input}" "${twobit_input}.chromInfo" &&
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21
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22 hgGcPercent -doGaps -noDots -verbose=0 -wigOut
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23 -win=${window_size}
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24 -overlap=${overlap}
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25 -file=stdout
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26
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27 #if str($region_type.region_type_selector) == "chrom":
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28 -chr="${region_type.chrom_name}"
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29 #end if
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30
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31 db_placeholder "${twobit_input}" |
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32
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33 wigToBigWig stdin "${twobit_input}.chromInfo" "${bw_output}"
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34 ]]>
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35 </command>
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36 <inputs>
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37 <param name="twobit_input" type="data" format="twobit" label="twoBit input file" />
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38
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39 <param name="window_size" type="integer" min="1" value="5"
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40 label="Window size"
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41 help="Size of the sliding window for calculating GC percentages (-win)" />
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42
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43 <param name="overlap" type="integer" min="0" value="0"
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44 label="Overlap size"
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45 help="Size of overlap for the sliding window (-overlap)" />
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46
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47 <conditional name="region_type">
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48 <param name="region_type_selector" type="select"
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49 label="Choose the analysis region">
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50 <option value="all" selected="true">All scaffolds</option>
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51 <option value="chrom">Chromosome</option>
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52 </param>
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53
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54 <when value="all"></when>
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55
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56 <when value="chrom">
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57 <param name="chrom_name" type="text" label="Sequence name"
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58 help="Process only this sequence in the twoBit file" />
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59 </when>
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60 </conditional>
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61 </inputs>
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62 <outputs>
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63 <data name="bw_output" format="bigwig" />
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64 </outputs>
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65 <tests>
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66 <test>
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67 <!-- Test hgGcPercent with default settings -->
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68 <param name="twobit_input" value="contigs.unmasked.2bit" ftype="twobit" />
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69 <output name="bw_output" file="contigs_gc5Base.bw" />
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70 </test>
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71 <test>
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72 <!-- Test hgGcPercent with custom window and overlap -->
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73 <param name="twobit_input" value="contigs.unmasked.2bit" ftype="twobit" />
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74 <param name="window_size" value="100" />
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75 <param name="overlap" value="10" />
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76 <output name="bw_output" file="contigs_gc100Base_10overlap.bw" />
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77 </test>
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78 <test>
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79 <!-- Test hgGcPercent with only one chromosome -->
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80 <param name="twobit_input" value="contigs.unmasked.2bit" ftype="twobit" />
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81 <param name="region_type_selector" value="chrom" />
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82 <param name="chrom_name" value="contig12" />
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83 <output name="bw_output" file="contig12_gc5Base.bw" />
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84 </test>
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85 </tests>
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86 <help>
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87 <![CDATA[
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88 **What it does**
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89
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90 hgGcPercent uses a sliding window to calculate the GC percentages
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91 of a genome assembly.
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92
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93 ]]></help>
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94
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95 <expand macro="citations" />
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96 </tool>