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1 <tool id="pscan_chip" name="PscanChIP" version="1.0.0">
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2 <description>PscanChIP</description>
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3 <requirements>
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4 <requirement type="binary">twoBitToFa</requirement>
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5 <requirement type="binary">pscan_chip_g</requirement>
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6 </requirements>
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7
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8 <!--command>
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9 read_distrib $input_map_file $input_pos_file $region_size $bin_size $shift_size '$output_freq' '$output_freq_all'
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10 </command-->
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11 <command>
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12 #if $profile_type.profiles == "/home/galaxy/galaxy-dist/tools/ngs_beacon/pscan_chip/jaspar_vertebrates.wil"
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13 #if $profile_type.BG_Jaspar.value == "none"
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14 #if $selected.value == ""
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15 pscan_chip_g -r $input_bed_file -M $profile_type.profiles -g $genomeSource -go $main_output -2bit -quiet
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16 #else
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17 pscan_chip_g -r $input_bed_file -M $profile_type.profiles -g $genomeSource -go $main_output -2bit -quiet -m $selected
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18 #end if
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19 #else
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20 #if $selected.value == ""
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21 pscan_chip_g -r $input_bed_file -M $profile_type.profiles -g $genomeSource -go $main_output -2bit -quiet -bg /home/galaxy/galaxy-dist/tools/ngs_beacon/pscan_chip/BG/$profile_type.BG_Jaspar
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22 #else
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23 pscan_chip_g -r $input_bed_file -M $profile_type.profiles -g $genomeSource -go $main_output -2bit -quiet -bg /home/galaxy/galaxy-dist/tools/ngs_beacon/pscan_chip/BG/$profile_type.BG_Jaspar -m $selected
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24 #end if
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25 #end if
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26 #else if $profile_type.profiles == "/home/galaxy/galaxy-dist/tools/ngs_beacon/pscan_chip/transfac_vertebrates.wil"
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27 #if $profile_type.BG_Transfac.value == "none"
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28 #if $selected.value == ""
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29 pscan_chip_g -r $input_bed_file -M $profile_type.profiles -g $genomeSource -go $main_output -2bit -quiet
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30 #else
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31 pscan_chip_g -r $input_bed_file -M $profile_type.profiles -g $genomeSource -go $main_output -2bit -quiet -m '$selected'
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32 #end if
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33 #else
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34 #if $selected.value == ""
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35 pscan_chip_g -r $input_bed_file -M $profile_type.profiles -g $genomeSource -go $main_output -2bit -quiet -bg /home/galaxy/galaxy-dist/tools/ngs_beacon/pscan_chip/BG/$profile_type.BG_Transfac
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36 #else
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37 pscan_chip_g -r $input_bed_file -M $profile_type.profiles -g $genomeSource -go $main_output -2bit -quiet -bg /home/galaxy/galaxy-dist/tools/ngs_beacon/pscan_chip/BG/$profile_type.BG_Transfac -m '$selected'
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38 #end if
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39 #end if
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40 #else
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41 #if $selected.value == ""
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42 pscan_chip_g -r $input_bed_file -M $profile_type.custom_matrix_file -g $genomeSource -go $main_output -2bit -quiet
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43 #else
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44 pscan_chip_g -r $input_bed_file -M $profile_type.custom_matrix_file -g $genomeSource -go $main_output -2bit -quiet -m $selected
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45 #end if
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46 #end if
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47 </command>
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48
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49
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50 <inputs>
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51 <param name="input_bed_file" type="data" format="bed" label="ChIP-Seq Peaks File" />
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52 <param name="genomeSource" type="select" label="Use a built in reference genome.">
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53 <options from_data_table="2bit_genomes">
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54 <validator type="no_options" message="No genomes are available for the selected input dataset"/>
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55 </options>
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56 </param>
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57 <conditional name="profile_type">
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58 <param name="profiles" type="select" label="Select binding profiles descriptors">
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59 <option value="/home/galaxy/galaxy-dist/tools/ngs_beacon/pscan_chip/jaspar_vertebrates.wil" selected="true">Jaspar (vertebrates)</option>
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60 <option value="/home/galaxy/galaxy-dist/tools/ngs_beacon/pscan_chip/transfac_vertebrates.wil">Transfac (vertebrates)</option>
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61 <option value="data">From file</option>
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62 </param>
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63
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64 <when value="/home/galaxy/galaxy-dist/tools/ngs_beacon/pscan_chip/jaspar_vertebrates.wil">
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65 <param name="BG_Jaspar" type="select" label="Select background">
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66 <options from_data_table="jaspar_pchip_bg">
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67 </options>
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68 </param>
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69 </when>
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70
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71 <when value="/home/galaxy/galaxy-dist/tools/ngs_beacon/pscan_chip/transfac_vertebrates.wil">
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72 <param name="BG_Transfac" type="select" label="Select Background">
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73 <options from_data_table="transfac_pchip_bg">
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74 </options>
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75 </param>
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76 </when>
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77
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78 <when value="data">
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79 <param name="custom_matrix_file" type="data" label="Select dataset"/>
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80 </when>
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81 </conditional>
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82 <param name="selected" type="text" size="16" value="" label="Matrix ID (leave blank to perform standard run)" >
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83 <sanitizer sanitize="false"/>
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84 </param>
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85 </inputs>
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86 <outputs>
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87 <data name="main_output" metadata_source="input_bed_file" format="tabular" label="${tool.name} on ${on_string} results"/>
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88 </outputs>
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89
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90
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91 <help>
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92 PscanChIP Galaxy plug-in. Visit Pscan-ChIP home page at http://www.beaconlab.it/pscan_chip_dev to learn more on Pscan-ChIP.
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93 </help>
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94 </tool>
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