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1 <tool name="MISP: Motif-based Interval Screener with PSSM" id="misp" version="0.1.0">
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2 <description>Input one or more motifs, find all hits in peak regions</description>
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3 <requirements>
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4 <requirement type="package" version="2013-11-28">misp</requirement>
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5 <requirement type="package" version="2.19.1">bedtools</requirement>
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6 </requirements>
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7 <command>
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8 #if $motifopt.motifopt_select == "upload"
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9 #set $motif_db = str($motifopt.motif_file)
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10 #else
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11 #set $motif_db = "\${MISP_DATABASE_PATH}/motif/cistrome.db"
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12 #end if
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13 #set $motif_id = str($motifopt.motif_id)
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14 #if $refGenomeSource.genomeSource == "history":
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15 #set $genome_file = $refGenomeSource.ownFile
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16 #else:
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17 #set $genome_file = $refGenomeSource.index.fields.path
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18 #end if
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19 bedtools getfasta -fi $genome_file -bed $bedfile -fo out.fasta > /dev/null &&
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20 misp out.fasta $motif_db $pvalue $motif_id output &> $log &&
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21 cat output* > $outputtxt
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22 </command>
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23 <stdio>
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24 <exit_code range="1:" level="fatal" description="Error" />
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25 </stdio>
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26 <inputs>
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27 <param format="bed" name="bedfile" type="data" label="bed file for regions">
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28 <validator type="unspecified_build" />
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29 </param>
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30 <conditional name="refGenomeSource">
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31 <param name="genomeSource" type="select" label="Use a built in reference genome or own from your history" help="Built-ins genomes were created using default options">
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32 <option value="cached" selected="True">Use a built-in genome</option>
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33 <option value="history">Use a genome from history</option>
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34 </param>
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35 <when value="cached">
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36 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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37 <options from_data_table="all_fasta">
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38 <filter type="data_meta" ref="bedfile" key="dbkey" column="1" multiple="True" separator="," />
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39 <validator type="no_options" message="No reference build available for selected input" />
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40 </options>
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41 </param>
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42 </when>
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43 <when value="history">
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44 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
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45 </when> <!-- history -->
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46 </conditional> <!-- refGenomeSource -->
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47 <conditional name="motifopt">
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48 <param name="motifopt_select" type="select" label="upload a motif or select from our database.">
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49 <option value="upload">Use uploaded motif</option>
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50 <option value="database">Use motif in cistrome database.</option>
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51 </param>
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52 <when value="upload">
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53 <param name="motif_file" type="data" label="motif file" />
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54 <param name="motif_id" type="text" label="The motif id in uploaded motif file. Or write 'all' to run all motifs in the file." />
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55 </when>
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56 <when value="database">
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57 <param name="motif_id" type="text" label="The motif id in Cistrome motif collection. Or write 'all' to run all motifs in the file." />
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58 </when>
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59 </conditional>
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60 <param name="pvalue" type="float" label="p-value cutoff for the motif screen" value="0.001">
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61 <validator type="in_range" max="1" min="0" message="pvalue is out of range, width has to be between 0 to 1" />
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62 </param>
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63 </inputs>
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64 <outputs>
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65 <data format="txt" name="outputtxt" label="MISP hits on ${bedfile.name}"/>
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66 <data format="txt" name="log" label="Log of MISP on ${bedfile.name}"/>
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67 </outputs>
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68 <tests>
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69 <test>
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70 <param name="bedfile" type="bed" value="test.bed" dbkey="mm9"/>
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71 <param name="genomeSource" value="history" />
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72 <param name="ownFile" type="fasta" value="mm9_chr19_part.fasta" dbkey="mm9"/>
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73 <param name="motifopt_select" value="upload" />
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74 <param name="motif_file" value="misp_motif" />
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75 <param name="motif_id" value="M00139" />
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76 <param name="pvalue" value="0.001" />
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77 <output name="outputtxt" file="misp.hits"/>
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78 <output name="log" file="misp.log"/>
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79 </test>
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80 </tests>
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81 <help>
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82 Given a motif, this tool will find all hits of the motif in specified region.
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83
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84 -----
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85
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86 **Formula**
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87
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88 .. image:: ./static/cistrome_icons/misp_formula.png
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89
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90 -----
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91
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92 **TIP:** The source code of misp is available at bitbucket_
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93
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94 .. _bitbucket: https://bitbucket.org/hanfeisun/misp/overview
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95
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96
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97 **TIP:** To check the motif id in our database, click here_
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98
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99 .. _here: http://cistrome.org/motif/
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100
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101 -----
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102
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103 Left to right shoule be:
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104
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105 T
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106
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107 C
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108
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109 G
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110
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111 A
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112
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113 **Example of the format of uploaded motif database.**
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114
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115 M00139
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116
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117 0.667 0.111 0.667 0.01 0.01 0.01 0.01 0.01 0.333 0.01 0.01 0.333 0.444 0.222 0.01 0.01 0.01 0.01
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118
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119 0.01 0.546 0.111 0.97 0.01 0.97 0.01 0.97 0.111 0.01 0.444 0.444 0.536 0.333 0.222 0.111 0.01 0.222
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120
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121 0.01 0.333 0.111 0.01 0.01 0.01 0.97 0.01 0.222 0.01 0.536 0.111 0.01 0.333 0.758 0.556 0.667 0.667
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122
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123 0.313 0.01 0.111 0.01 0.97 0.01 0.01 0.01 0.334 0.97 0.01 0.112 0.01 0.112 0.01 0.323 0.313 0.101
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124
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125 hPDI060
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126
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127 0.01 0.01 0.01 0.625 0.01 0.01
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128
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129 0.97 0.97 0.97 0.01 0.5 0.97
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130
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131 0.01 0.01 0.01 0.01 0.48 0.01
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132
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133 0.01 0.01 0.01 0.355 0.01 0.01
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134 </help>
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135
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136 </tool>
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