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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 6767a5ffb02052c844e9d862c79912f998f39d8e
author rnateam
date Mon, 20 Nov 2017 05:04:27 -0500
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4bff424dfa47 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="footprint" name="footprint" version="1.0.0">
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3 <requirements>
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4 <requirement type="package" version="1.0.0">footprint</requirement>
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5 </requirements>
1
0d94a529f925 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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6 <command detect_errors="aggressive"><![CDATA[
0d94a529f925 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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7 ln -s '$bam_file' ./bam_file.bam
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8 &&
0d94a529f925 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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9 find_footprints.sh
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10 ./bam_file.bam
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11 '$chrom_sizes'
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12 '$motif_coords'
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13 ## genome source
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14 #if $refGenomeSource.genomeSource == "history":
0d94a529f925 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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15 '$refGenomeSource.ownFile'
0d94a529f925 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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16 #else
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17 '$refGenomeSource.builtin.fields.path'
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18 #end if
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19 '$factor_name'
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20 '$bias_file'
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21 '$peak_file'
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22 $no_of_components
0d94a529f925 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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23 $background
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24 $fixed_bg
0d94a529f925 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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25 &&
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26 mv *.PARAM PARAM &&
0d94a529f925 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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27 mv *.RESULTS RESULTS &&
0d94a529f925 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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28 mv *.plot2.png plot2.png &&
0d94a529f925 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 6767a5ffb02052c844e9d862c79912f998f39d8e
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29 mv *.plot1.png plot1.png
0
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30
4bff424dfa47 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
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31 ]]>
4bff424dfa47 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
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32 </command>
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33 <inputs>
4bff424dfa47 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
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34 <param name="bam_file" type="data" format="BAM" label="alignment bam file" help="" />
4bff424dfa47 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
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35 <param name="chrom_sizes" type="data" format="tablular" label="chromosome length" help="" />
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36 <param name="motif_coords" type="data" format="BED" label="coordinates of motif" help="" />
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37 <conditional name="refGenomeSource">
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38 <param name="genomeSource" type="select"
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39 label="Will you select a reference genome from your
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40 history or use a built-in genome?"
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41 help="The version of genome against which the reads were aligned.">
4bff424dfa47 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
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42 <option value="fai" selected="True">
4bff424dfa47 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
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43 Use a built-in genome</option>
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44 <option value="history">
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45 Use a genome from my current history</option>
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46 </param>
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47 <when value="fai">
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48 <param name="builtin" type="select"
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49 label="Select a reference genome">
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50 <options from_data_table="sam_fa_indices">
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51 <filter type="sort_by" column="1" />
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52 <validator type="no_options"
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53 message="A built-in reference genome is not available
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54 for the build associated with the selected input file"/>
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55 </options>
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56 </param>
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57 </when>
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58 <when value="history">
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59 <param name="ownFile" type="data" format="fasta"
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60 label="Select the reference genome" help="Genome sequences in FASTA format" />
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61 </when>
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62 </conditional>
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63 <param name="factor_name" type="text" label="transcription factor" help="e.g. CTCF" />
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64 <param name="bias_file" type="data" format="tabular,txt" label="cleavage/transposition bias" help="" />
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65 <param name="peak_file" type="data" format="tabular" label="coordinates of ChIP-seq peaks" help="" />
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66 <param name="no_of_components" type="select" label="number of components">
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67 <option value="2" selected="true">2</option>
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68 <option value="3">3</option>
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69 </param>
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70 <param name="background" type="select" label="background components">
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71 <option value="Seq" selected="true">Seq</option>
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72 <option value="Flat">Flat</option>
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73 </param>
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74 <param name="fixed_bg" type="select" label="fixed background component">
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75 <option value="TRUE" selected="true">TRUE</option>
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76 <option value="FALSE">FALSE</option>
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77 </param>
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78 </inputs>
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79 <outputs>
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80 <data name="RESULTS" format="tabular" from_work_dir="RESULTS" label="${tool.name} on ${on_string}: results" />
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81 <data name="PARAM" format="txt" from_work_dir="PARAM" label="${tool.name} on ${on_string}: parameters" />
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82 <data name="plot1" format="png" from_work_dir="plot1.png" label="${tool.name} on ${on_string}: plot 1" />
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83 <data name="plot2" format="png" from_work_dir="plot2.png" label="${tool.name} on ${on_string}: plot 2" />
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84 </outputs>
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85 <tests>
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86 <test>
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87 <param name="bam_file" value="input_ATAC_HEK293_hg19_chr1.bam" />
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88 <param name="chrom_sizes" value="input_hg19.chr1.chrom.size" />
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89 <param name="motif_coords" value="input_CTCF_motifs_hg19_chr1.bed" />
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90 <param name="genomeSource" value="history" />
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91 <param name="ownFile" value="input_hg19_chr1.fa" />
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92 <param name="factor_name" value="CTCF" />
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93 <param name="bias_file" value="input_SeqBias_ATAC.txt" />
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94 <param name="peak_file" value="input_CTCF_HEK293_chip_hg19_chr1.bed" />
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95 <param name="no_of_components" value="2" />
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96 <param name="background" value="Seq" />
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97 <param name="fixed_bg" value="TRUE" />
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98 <output name="RESULTS" file="output.RESULTS" ftype="tabular" compare="sim_size"/>
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99 <output name="PARAM" file="output.PARAM" ftype="txt" compare="sim_size"/>
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100 <output name="plot1" file="output_plot1.png" ftype="png" compare="sim_size" delta="15000" />
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101 <output name="plot2" file="output_plot2.png" ftype="png" compare="sim_size" delta="15000" />
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102 </test>
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103 </tests>
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104 <help><![CDATA[.. class:: infomark
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105
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106 **Purpose**
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107
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108 This is a pipeline to find transcription factor footprints in ATAC-seq or DNase-seq data.
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109
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110 -----
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111
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112 .. class:: infomark
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113
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114 **Inputs**
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115
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116 alignment bam file
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117 * A bam file from the ATAC-seq or DNase-seq experiment.
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118
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119 chromosome length
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120 * A tab delimited file with 2 columns.
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121 * The first column is the chromosome name and the second column is the chromosome length for the appropriate organism and genome build.
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122 * Example: chr1 10000000
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123
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124 coordinates of motif
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125 * A 6-column bed file with the coordinates of motif matches (eg resulting from scanning the genome with a PWM) for the transcription factor of interest.
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126 * The 6 columns should contain chromosome, start coordinate, end coordinate, name, score and strand information in this order. The coordinates should be closed (1-based).
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127 * Example: chr1 24782 24800 . 11.60 -
1
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128 * There should not be any additional columns.
0
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129
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130 transcription factor
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131 * The name of the transcription factor of interest supplied by the user, e.g. CTCF.
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132
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133 cleavage/transposition bias
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134 * The cleavage/transposition bias of the different protocols, for all 6-mers.
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135 * Provided `options`_: ATAC, DNase double hit or DNase single hit protocols.
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136
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137 .. _options: https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/
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138
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139 coordinates of ChIP-seq peaks
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140 * A file with the coordinates of the ChIP-seq peaks for the transcription factor of interest.
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141 * The format is flexible as long as the first 3 columns (chromosome, start coordinate, end coordinate) are present.
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142 * Example: chr1 237622 237882
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143
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144 number of components
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145 * Total number of footprint and background components that should be learned from the data.
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146 * Options are 2 (1 fp and 1 bg) and 3 (2 fp and 1 bg) components.
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147
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148 background components
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149 * The mode of initialization for the background component. Options are "Flat" or "Seq".
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150 * Choosing "Flat" initializes this component as a uniform distribution.
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151 * Choosing "Seq" initializes it as the signal profile that would be expected solely due to the protocol bias (given by the cleavage/transposition bias file).
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152
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153 fixed background component
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154 * Whether the background component should be kept fixed.
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155 * Options are TRUE or FALSE.
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156 * Setting "TRUE" keeps this component fixed, whereas setting "FALSE" lets it be reestimated during training.
1
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157 * In general, if the background is estimated from bias (option "Seq"), it is recommended to keep it fixed.
0
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158
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159 -----
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160
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161 .. class:: infomark
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162
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163 **Outputs**
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164
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165 results
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166 * The results of the footprinting analysis.
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167 * The first 6 columns harbor the motif information (identical to the 'coordinates of motif').
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168 * The 7th column has the footprint score (log-odds of footprint versus background) for each motif instance.
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169 * The following columns show the probabilities for the individual footprint and background components.
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170
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171 parameters
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172 * Gives the trained parameters for the footprint and background components.
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173 * It includes as many lines as components (eg the first line has the parameters for the first component).
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174
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175 plot 1
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176 * A plot with two panels, showing the initial components above and the final trained components below.
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177 * The plotted values for the final components are given in the 'parameters' output file explained above.
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178
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179 plot 2
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180 * A plot only with the final trained components.
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181 * In a model where 2 components are used, this plot is identical to the bottom panel in plot1.
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182 * When 3 components are used, this plot shows the weighted average of the 2 footprint components as the final footprint profile.
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183
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184 ]]></help>
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185 <citations>
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186 <citation type="bibtex">@ARTICLE{footprint,
1
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187 author = {Aslihan Karabacak, Galip Gurkan Yardimci, Ricardo Wurmus, Dilmurat Yusuf, Uwe Ohler},
0
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188 title = {To submit},
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189 journal = {},
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190 year = {},
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191 volume = {},
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192 pages = {}
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193 }</citation>
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194 </citations>
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195 </tool>