Mercurial > repos > jjohnson > cistrome_beta

annotate beta_macros.xml @ 5:c119110a5b47 draft default tip

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/cistrome_beta commit d824634e1b43fd7f2628631d2d4443ca1cd1ecce-dirty
author jjohnson
date Thu, 22 Mar 2018 11:17:52 -0400
parents 52ed4957ace9
children
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2 <macros>
2
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3 <macro name="requirements">
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4 <requirements>
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5 <requirement type="package" version="1.0.7">beta</requirement>
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6 </requirements>
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7 </macro>
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8 <token name="@VERSION@">1.0.7</token>
2
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9 <macro name="stdio">
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10 <stdio>
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11 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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12 <exit_code range="1:" level="fatal" description="Error" />
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13 </stdio>
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14 </macro>
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16 <macro name="common_params">
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17 <param format="bed" name="peakfile" type="data" label="BED file for Peaks">
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18 <validator type="unspecified_build" />
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19 </param>
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20 <param name="output_dir" type="hidden" label="Name for the output files" value="BETA_OUTPUT"/>
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21 <param name="name" type="hidden" label="Name for the output files" value="NA"/>
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22 <param name="distance" type="integer" label="the distance from gene TSS within which peaks will be selected" value="100000">
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23 <validator type="in_range" max="20000000" min="0" message="The Relative distance is out of range, the parameter has to be between 0 to 20000000" />
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24 </param>
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25 <param name="peaknumber" type="integer" label="Peaks considered to contribute to the genes" value="10000">
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26 <validator type="in_range" max="200000" min="100" message="The Relative distance is out of range, the parameter has to be between 100 to 10000" />
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27 </param>
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28 </macro>
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30 <macro name="boundary">
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31 <conditional name="boundary">
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32 <param name="boundaryLimit" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Use CTCF boundary to filter peaks around a gene"/>
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33 <when value="no"/>
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34 <when value="yes">
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35 <yield />
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36 </when>
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37 </conditional>
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38 </macro>
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39
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40 <macro name="genome_params">
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41 <conditional name="refGenome">
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42 <param name="genomeName" type="select" label="genome reference">
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43 <option value="hg19">hg19 (built-in)</option>
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44 <option value="mm9">mm9 (built-in)</option>
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45 <option value="other">other</option>
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46 </param>
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47 <when value="hg19">
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48 <expand macro="boundary" />
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49 </when>
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50 <when value="mm9">
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51 <expand macro="boundary" />
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52 </when>
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53 <when value="other">
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54 <param name="refseq" type="data" format="tabular" label="UCSC Refseq Genes (From UCSC Table Browser)"
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55 help="Columns: name,chrom,strand,txStart,txEnd,name"/>
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56 <expand macro="boundary">
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57 <param name="bl_bed" type="data" format="bed" label="BED format boundary file"/>
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58 </expand>
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59 </when>
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60 </conditional>
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61 </macro>
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62
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63 <macro name="refGenomeSourceConditional">
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64 <conditional name="refGenomeSource">
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65 <param name="genomeSource" type="select" label="Use a built in reference genome or one from your history" help="Genome Reference Fasta sequence">
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66 <option value="cached" selected="True">Use a built-in genome</option>
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67 <option value="history">Use a genome from history</option>
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68 </param>
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69 <when value="cached">
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70 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
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71 <options from_data_table="all_fasta"/>
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72 </param>
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73 </when>
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74 <when value="history">
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75 <param name="ownFile" type="data" format="fasta" label="Select the reference genome" />
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76 </when> <!-- history -->
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77 </conditional> <!-- refGenomeSource -->
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78 </macro>
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79
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80 <macro name="extended_params">
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81 <param format="txt" name="exprefile" type="data" label="TEXT file for differential expression data">
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82 <validator type="unspecified_build" />
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83 </param>
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84 <conditional name="expression">
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85 <param name="kind" type="select" label="Expression FIle Type" help="Preset columns for Cuffdiff, LIMMA, and BETA Specific Format">
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86 <option value="CUF">RNA-seq data with Cuffdiff default format</option>
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87 <option value="LIM">MicroArray data with LIMMA default format</option>
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88 <option value="BSF">BETA Specific Format</option>
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89 <option value="O">Other tools processed data with BETA specific format</option>
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90 </param>
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91 <when value="CUF">
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92 <param name="expreinfo" type="text" value="2,10,13" label="Column number of the geneid, regulate status and statistics value"/>
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93 </when>
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94 <when value="LIM">
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95 <param name="expreinfo" type="text" value="2,5,7" label="Column number of the geneid, regulate status and statistics value"/>
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96 </when>
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97 <when value="BSF">
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98 <param name="expreinfo" type="text" value="1,2,3" label="Column number of the geneid, regulate status and statistics value"/>
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99 </when>
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100 <when value="O">
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101 <param name="expreinfo" type="text" value="" label="Column number of the geneid, regulate status and statistics value is required">
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102 <validator type="regex" message="Enter column numbers:geneid,test_stat,value">^\d+,\d+,\d+$</validator>
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103 </param>
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104 </when>
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105 </conditional>
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106 <param name="gname2" type="select" label="TRUE if gene ID in expression file identified by official gene symbol">
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107 <option value="Refseq">Refseq</option>
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108 <option value="Gene_Symbol">Gene Symbol</option>
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109 </param>
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110 <param name="diff_fdr" type="float" label="get the most significant expression differentially changed genes by this cutoff based on fdr or pvalue" value="1.0">
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111 <validator type="in_range" max="1.0" min="0" message="The Relative distance is out of range, the parameter has to be between 0 to 1.0" />
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112 </param>
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113 <param name="diff_amount" type="float" label="get the most significant expression differentially changed genes by amount" value="0.5">
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114 <validator type="in_range" max="20000" min="0" message="The Relative distance is out of range, the parameter has to be between 0 to 20000" />
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115 </param>
5
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116 <param name="method" type="select" label="method to do the TF/CR function prediction">
2
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117 <option value="score">regulatory potential</option>
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118 <option value="distance">distance to the nearest peak</option>
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119 </param>
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120 </macro>
0
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121
2
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122 <template name="common_opts">
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123 -p "$peakfile"
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124 -d $distance --pn $peaknumber -o $output_dir -n $name
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125 </template>
0
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126
2
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127 <template name="genome_opts">
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128 #if $refGenome.genomeName == 'hg19':
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129 -g $refGenome.genomeName
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130 ## -r \$BETA_LIB_PATH/BETA/references/hg19.refseq
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131 #if $refGenome.boundary.boundaryLimit:
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132 --bl
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133 ## --bf \$BETA_LIB_PATH/BETA/references/hg19_CTCF_bound.bed
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134 #end if
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135 #elif $refGenome.genomeName == 'mm9':
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136 -g $refGenome.genomeName
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137 ## -r \$BETA_LIB_PATH/BETA/references/mm9.refseq
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138 #if $refGenome.boundary.boundaryLimit:
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139 --bl
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140 ## --bf \$BETA_LIB_PATH/BETA/references/mm9_CTCF_bound.bed
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141 #end if
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142 #else
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143 -r $refGenome.refseq
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144 #if $refGenome.boundary.boundaryLimit:
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145 --bl
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146 --bf $refGenome.boundary.bl_bed
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147 #end if
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148 #end if
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149 </template>
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150 <template name="ref_genome_seq_opts">
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151 #if $refGenomeSource.genomeSource == 'cached':
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152 --gs $refGenomeSource.all_fasta_source.fields.path
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153 #else
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154 --gs $refGenomeSource.ownFile
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155 #end if
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156 </template>
0
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157
2
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158 <template name="extended_opts">
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159 -e "$exprefile"
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160 -k $expression.kind --info $expression.expreinfo --method $method
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161 --da $diff_amount --df $diff_fdr -c 1
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162 #if $gname2 == "Gene_Symbol":
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163 --gname2"
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164 #end if
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165 </template>
4
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166 <template name="write_log">
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167 | tee $log | grep 'total time' > /dev/null
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168 </template>
0
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169
2
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170 <token name="@EXTERNAL_DOCUMENTATION@">
0
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171
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172 For details about this application, please go to:
2
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173 http://cistrome.org/BETA/index.html
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174
2
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175 </token>
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176 <token name="@CITATION_SECTION@">
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177
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178 **Citation**
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179
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180 For the underlying tool, please cite the following publication:
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181 Wang, S., Sun, H., Ma, J., Zang, C., Wang, C., Wang, J., Tang Q, Meyer CA, Zhang Y, Liu, X. S. (2013). Target analysis by integration of transcriptome and ChIP-seq data with BETA. Nature protocols, 8(12), 2502-2515.
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182 PMID: 24263090
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183 </token>
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184 <xml name="citations">
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185 <citations>
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186 <citation type="doi">10.1038/nprot.2013.150</citation>
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187 </citations>
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188 </xml>
0
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189 </macros>
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190