annotate deepTools_macros.xml @ 6:5742b322f956 draft default tip

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author greg
date Tue, 10 Dec 2013 10:09:39 -0500
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1 <macros>
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2 <macro name="bamCorrelate_mode_actions">
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3 <conditional name="advancedOpt">
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4 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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5 <option value="no" selected="true">no</option>
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6 <option value="yes">yes</option>
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7 </param>
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8 <when value="no" />
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9 <when value="yes">
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10 <param name="region" type="text" value=""
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11 label="Region of the genome to limit the operation to"
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12 help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" />
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13
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14 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
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15 label="Do not extend paired ends"
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16 help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/>
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17
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18 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
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19 label="Ignore duplicates"
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20 help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." />
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21
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22 <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
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23 label="Minimum mapping quality"
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24 help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
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25
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26 <param name="includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
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27 label ="Include zeros"
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28 help ="If set, then regions with zero counts for *all* BAM files given are included. The default behavior is to ignore those cases." />
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29
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30 <param name="zMin" type="integer" value="" optional="true" label="Minimum value for the heatmap intensities"
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31 help="If not specified the value is set automatically."/>
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32
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33 <param name="zMax" type="integer" value="" optional="true" label="Maximum value for the heatmap intensities"
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34 help="If not specified the value is set automatically."/>
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35
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36 <expand macro="colormap" />
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37 </when>
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38 </conditional>
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39 </macro>
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40 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
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41 <macro name="requirements">
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42 <requirements>
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43 <requirement type="package" >samtools</requirement>
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44 <requirement type="package" >deepTools</requirement>
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45 <requirement type="package" >ucsc_tools</requirement>
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46 <requirement type="package" version="1.5.4_fada41ab04f78c4c78d10c7a216e5c3160e8c36e">deepTools</requirement>
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47 <requirement type="package" version="0.1">ucsc_tools</requirement>
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48 <requirement type="package" version="1.7.1">numpy</requirement>
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49 <requirement type="package" version="0.7.7">pysam</requirement>
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50 <requirement type="package" version="1.2.1">matplotlib</requirement>
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51 <requirement type="package" version="0.1.19">samtools</requirement>
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52 <requirement type="package" version="12-2013">bx-python</requirement>
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53 <yield />
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54 </requirements>
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55 </macro>
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56
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57 <token name="@REFERENCES@">
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58
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59 For more informations, please visit our `project site`_.
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60
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61 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
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62
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63 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
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64
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65
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66 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
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67 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
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68 .. _project site: https://github.com/fidelram/deepTools
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69
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70 </token>
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71
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72 <macro name="multiple_input_bams">
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73 <repeat name="input_files" title="Input files" min="2">
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74 <param name="bamfile" type="data" format="bam"
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75 label="Bam file"
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76 help="The BAM file must be sorted."/>
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77 <param name="label" type="text" size="30" optional="true" value=""
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78 label="Label"
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79 help="Label to use in the output. If not given the dataset name will be used instead."/>
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80 </repeat>
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81 </macro>
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82
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83 <token name="@multiple_input_bams@">
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84 #for $i in $input_files:
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85 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
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86 #set $temp_input_path = $temp_input_handle.name
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87 #silent $temp_input_handle.close()
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88 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
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89 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
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90 #silent $files.append('%s.bam' % $temp_input_path)
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91
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92 ##set $files += [str($i.bamfile)]
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93 #if str($i.label.value) != "":
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94 #set $labels += ["\"%s\"" % ($i.label.value)]
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95 #else
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96 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
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97 #end if
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98 #end for
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99 </token>
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100
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101 <macro name="reference_genome_source">
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102 <conditional name="source">
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103 <param name="ref_source" type="select" label="Reference genome">
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104 <option value="cached">locally cached</option>
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105 <option value="history">in your history</option>
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106 </param>
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107 <when value="cached">
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108 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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109 <options from_data_table="deepTools_seqs">
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110 <filter type="sort_by" column="1" />
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111 <validator type="no_options" message="No indexes are available." />
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112 </options>
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113 </param>
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114 </when>
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115 <when value="history">
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116 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
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117 </when>
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118 </conditional>
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119 </macro>
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120
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121 <token name="@reference_genome_source@">
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122 #if $source.ref_source=="history":
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123 --genome $source.input1
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124 #else:
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125 --genome "${source.input1_2bit.fields.path}"
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126 #end if
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127 </token>
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128
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129 <macro name="effectiveGenomeSize">
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130 <conditional name="effectiveGenomeSize">
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131 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
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132 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded.
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133 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
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134 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
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135 <option value="2150570000">mm9</option>
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136 <option value="2451960000">hg19</option>
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137 <option value="121400000">dm3</option>
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138 <option value="93260000">ce10</option>
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139 <option value="specific">user specified</option>
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140 </param>
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141 <when value="specific">
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142 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" />
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143 </when>
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144 </conditional>
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145 </macro>
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146
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147 <macro name="graphic_output_settings">
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148 <conditional name="output" >
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149 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
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150 <option value="no" selected="true">no</option>
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151 <option value="yes">yes</option>
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152 </param>
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153 <when value="no" />
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154 <when value="yes">
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155 <param name="outFileFormat" type="select" label="Image file format">
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156 <option value="png" selected="true">png</option>
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157 <option value="pdf">pdf</option>
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158 <option value="svg">svg</option>
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159 <option value="eps">eps</option>
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160 <option value="emf">emf</option>
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161 </param>
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162 <param name="saveData" type="boolean" label="Save the data underlying data for the average profile"/>
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163 <param name="saveMatrix" type="boolean" label="Save the the matrix of values underlying the heatmap"/>
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164 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
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165 </when>
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166 </conditional>
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167 </macro>
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168
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169 <macro name="colormap">
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170
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171 <param name="colorMap" type="select" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">
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172 <option value="RdYlBu" selected="true">RdYlBu</option>
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173 <option value="Accent">Accent</option>
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174 <option value="Spectral">Spectral</option>
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175 <option value="Set1">Set1</option>
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176 <option value="Set2">Set2</option>
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177 <option value="Set3">Set3</option>
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178 <option value="Dark2">Dark2</option>
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179 <option value="Reds">Reds</option>
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180 <option value="Oranges">Oranges</option>
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181 <option value="Greens">Greens</option>
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182 <option value="Blues">Blues</option>
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183 <option value="Greys">Greys</option>
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184 <option value="Purples">Purples</option>
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185 <option value="Paired">Paired</option>
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186 <option value="Pastel1">Pastel1</option>
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187 <option value="Pastel2">Pastel2</option>
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188 <option value="spring">spring</option>
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189 <option value="summer">summer</option>
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190 <option value="autumn">autumn</option>
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191 <option value="winter">winter</option>
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192 <option value="hot">hot</option>
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193 <option value="coolwarm">coolwarm</option>
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194 <option value="cool">cool</option>
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195 <option value="seismic">seismic</option>
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196 <option value="terrain">terrain</option>
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197 <option value="ocean">ocean</option>
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198 <option value="rainbow">rainbow</option>
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199 <option value="bone">bone</option>
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200 <option value="flag">flag</option>
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201 <option value="prism">prism</option>
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202 <option value="cubehelix">cubehelix</option>
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203 <option value="binary">binary</option>
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204 <option value="pink">pink</option>
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205 <option value="gray">gray</option>
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206 <option value="copper">copper</option>
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207 <option value="BrBG">BrBG</option>
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diff changeset
208 <option value="BuGn">BuGn</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
209 <option value="BuPu">BuPu</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
210 <option value="GnBu">GnBu</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
211 <option value="OrRd">OrRd</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
212 <option value="PiYG">PiYG</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
213 <option value="PRGn">PRGn</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
214 <option value="PuOr">PuOr</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
215 <option value="PuRd">PuRd</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
216 <option value="PuBu">PuBu</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
217 <option value="RdBu">RdBu</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
218 <option value="RdGy">RdGy</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
219 <option value="RdPu">RdPu</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
220 <option value="YlGn">YlGn</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
221 <option value="PuBuGn">PuBuGn</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
222 <option value="RdYlGn">RdYlGn</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
223 <option value="YlGnBu">YlGnBu</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
224 <option value="YlOrBr">YlOrBr</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
225 <option value="YlOrRd">YlOrRd</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
226 <option value="gist_gray">gist_gray</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
227 <option value="gist_stern">gist_stern</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
228 <option value="gist_earth">gist_earth</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
229 <option value="gist_yarg">gist_yarg</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
230 <option value="gist_ncar">gist_ncar</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
231 <option value="gist_rainbow">gist_rainbow</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
232 <option value="gist_heat">gist_heat</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
233 <option value="gnuplot">gnuplot</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
234 <option value="gnuplot2">gnuplot2</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
235 <option value="CMRmap">CMRmap</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
236 <option value="bwr">bwr</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
237 <option value="hsv">hsv</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
238 <option value="brg">brg</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
239 <option value="jet">jet</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
240 <option value="afmhot">afmhot</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
241 <option value="Accent_r">Accent reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
242 <option value="Spectral_r">Spectral reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
243 <option value="Set1_r">Set1 reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
244 <option value="Set2_r">Set2 reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
245 <option value="Set3_r">Set3 reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
246 <option value="Dark2_r">Dark2 reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
247 <option value="Reds_r">Reds reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
248 <option value="Oranges_r">Oranges reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
249 <option value="Greens_r">Greens reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
250 <option value="Blues_r">Blues reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
251 <option value="Greys_r">Greys reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
252 <option value="Purples_r">Purples reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
253 <option value="Paired_r">Paired reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
254 <option value="Pastel1_r">Pastel1 reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
255 <option value="Pastel2_r">Pastel2 reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
256 <option value="spring_r">spring reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
257 <option value="summer_r">summer reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
258 <option value="autumn_r">autumn reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
259 <option value="winter_r">winter reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
260 <option value="hot_r">hot reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
261 <option value="coolwarm_r">coolwarm reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
262 <option value="cool_r">cool reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
263 <option value="seismic_r">seismic reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
264 <option value="terrain_r">terrain reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
265 <option value="ocean_r">ocean reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
266 <option value="rainbow_r">rainbow reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
267 <option value="bone_r">bone reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
268 <option value="flag_r">flag reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
269 <option value="prism_r">prism reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
270 <option value="cubehelix_r">cubehelix reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
271 <option value="binary_r">binary reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
272 <option value="pink_r">pink reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
273 <option value="gray_r">gray reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
274 <option value="copper_r">copper reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
275 <option value="BrBG_r">BrBG reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
276 <option value="BuGn_r">BuGn reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
277 <option value="BuPu_r">BuPu reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
278 <option value="GnBu_r">GnBu reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
279 <option value="OrRd_r">OrRd reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
280 <option value="PiYG_r">PiYG reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
281 <option value="PRGn_r">PRGn reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
282 <option value="PuOr_r">PuOr reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
283 <option value="PuRd_r">PuRd reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
284 <option value="PuBu_r">PuBu reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
285 <option value="RdBu_r">RdBu reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
286 <option value="RdGy_r">RdGy reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
287 <option value="RdPu_r">RdPu reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
288 <option value="YlGn_r">YlGn reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
289 <option value="PuBuGn_r">PuBuGn reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
290 <option value="RdYlBu_r">RdYlBu reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
291 <option value="RdYlGn_r">RdYlGn reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
292 <option value="YlGnBu_r">YlGnBu reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
293 <option value="YlOrBr_r">YlOrBr reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
294 <option value="YlOrRd_r">YlOrRd reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
295 <option value="gist_gray_r">gist_gray reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
296 <option value="gist_stern_r">gist_stern reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
297 <option value="gist_earth_r">gist_earth reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
298 <option value="gist_yarg_r">gist_yarg reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
299 <option value="gist_ncar_r">gist_ncar reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
300 <option value="gist_rainbow_r">gist_rainbow reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
301 <option value="gist_heat_r">gist_heat reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
302 <option value="gnuplot_r">gnuplot reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
303 <option value="gnuplot2_r">gnuplot2 reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
304 <option value="CMRmap_r">CMRmap reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
305 <option value="bwr_r">bwr reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
306 <option value="hsv_r">hsv reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
307 <option value="brg_r">brg reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
308 <option value="jet_r">jet reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
309 <option value="afmhot_r">afmhot reversed</option>
5742b322f956 Uploaded
greg
parents:
diff changeset
310 </param>
5742b322f956 Uploaded
greg
parents:
diff changeset
311
5742b322f956 Uploaded
greg
parents:
diff changeset
312 </macro>
5742b322f956 Uploaded
greg
parents:
diff changeset
313
5742b322f956 Uploaded
greg
parents:
diff changeset
314 </macros>