annotate deepTools_macros.xml @ 5:c54d31467be4 draft

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author bgruening
date Fri, 29 Nov 2013 08:59:04 -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="" 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="" 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="1.5.1_323fa6bf083c9d40e5092a6364a4ab8fee57507a">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="0.1.19">samtools</requirement>
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51 <yield />
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52 </requirements>
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53 </macro>
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54
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55 <token name="@REFERENCES@">
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56
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57 For more informations, please visit our `project site`_.
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58
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59 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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60
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61 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
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62
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63
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64 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
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65 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
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66 .. _project site: https://github.com/fidelram/deepTools
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67
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68 </token>
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69
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70 <macro name="multiple_input_bams">
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71 <repeat name="input_files" title="Input files" min="2">
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72 <param name="bamfile" type="data" format="bam"
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73 label="Bam file"
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74 help="The BAM file must be sorted."/>
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75 <param name="label" type="text" size="30" optional="true" value=""
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76 label="Label"
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77 help="Label to use in the output. If not given the dataset name will be used instead."/>
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78 </repeat>
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79 </macro>
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80
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81 <token name="@multiple_input_bams@">
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82 #for $i in $input_files:
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83 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
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84 #set $temp_input_path = $temp_input_handle.name
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85 #silent $temp_input_handle.close()
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86 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
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87 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
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88 #silent $files.append('%s.bam' % $temp_input_path)
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89
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90 ##set $files += [str($i.bamfile)]
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91 #if str($i.label.value) != "":
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92 #set $labels += ["\"%s\"" % ($i.label.value)]
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93 #else
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94 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
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95 #end if
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96 #end for
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97 </token>
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98
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99 <macro name="reference_genome_source">
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100 <conditional name="source">
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101 <param name="ref_source" type="select" label="Reference genome">
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102 <option value="cached">locally cached</option>
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103 <option value="history">in your history</option>
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104 </param>
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105 <when value="cached">
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106 <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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107 <options from_data_table="deepTools_seqs" />
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108 </param>
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109 </when>
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110 <when value="history">
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111 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
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112 </when>
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113 </conditional>
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114 </macro>
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115
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116 <token name="@reference_genome_source@">
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117 #if $source.ref_source=="history":
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118 --genome $source.input1
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119 #else:
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120 --genome "${source.input1_2bit.fields.path}"
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121 #end if
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122 </token>
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123
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124 <macro name="effectiveGenomeSize">
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125 <conditional name="effectiveGenomeSize">
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126 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
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127 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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128 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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129 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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130 <option value="2150570000">mm9</option>
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131 <option value="2451960000">hg19</option>
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132 <option value="121400000">dm3</option>
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133 <option value="93260000">ce10</option>
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134 <option value="specific">user specified</option>
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135 </param>
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136 <when value="specific">
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137 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" />
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138 </when>
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139 </conditional>
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140 </macro>
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141
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142 <macro name="graphic_output_settings">
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143 <conditional name="output" >
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144 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
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145 <option value="no" selected="true">no</option>
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146 <option value="yes">yes</option>
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147 </param>
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148 <when value="no" />
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149 <when value="yes">
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150 <param name="outFileFormat" type="select" label="Image file format">
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151 <option value="png" selected="true">png</option>
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152 <option value="pdf">pdf</option>
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153 <option value="svg">svg</option>
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154 <option value="eps">eps</option>
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155 <option value="emf">emf</option>
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156 </param>
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157 <param name="saveData" type="boolean" label="Save the data underlying data for the average profile"/>
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158 <param name="saveMatrix" type="boolean" label="Save the the matrix of values underlying the heatmap"/>
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159 <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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160 </when>
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161 </conditional>
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162 </macro>
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163
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164 <macro name="colormap">
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165
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166 <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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167 <option value="RdYlBu" selected="true">RdYlBu</option>
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168 <option value="Accent">Accent</option>
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169 <option value="Spectral">Spectral</option>
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170 <option value="Set1">Set1</option>
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171 <option value="Set2">Set2</option>
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172 <option value="Set3">Set3</option>
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173 <option value="Dark2">Dark2</option>
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174 <option value="Reds">Reds</option>
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175 <option value="Oranges">Oranges</option>
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176 <option value="Greens">Greens</option>
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177 <option value="Blues">Blues</option>
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178 <option value="Greys">Greys</option>
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179 <option value="Purples">Purples</option>
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180 <option value="Paired">Paired</option>
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181 <option value="Pastel1">Pastel1</option>
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182 <option value="Pastel2">Pastel2</option>
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183 <option value="spring">spring</option>
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184 <option value="summer">summer</option>
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185 <option value="autumn">autumn</option>
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186 <option value="winter">winter</option>
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187 <option value="hot">hot</option>
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diff changeset
188 <option value="coolwarm">coolwarm</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
189 <option value="cool">cool</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
190 <option value="seismic">seismic</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
191 <option value="terrain">terrain</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
192 <option value="ocean">ocean</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
193 <option value="rainbow">rainbow</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
194 <option value="bone">bone</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
195 <option value="flag">flag</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
196 <option value="prism">prism</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
197 <option value="cubehelix">cubehelix</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
198 <option value="binary">binary</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
199 <option value="pink">pink</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
200 <option value="gray">gray</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
201 <option value="copper">copper</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
202 <option value="BrBG">BrBG</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
203 <option value="BuGn">BuGn</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
204 <option value="BuPu">BuPu</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
205 <option value="GnBu">GnBu</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
206 <option value="OrRd">OrRd</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
207 <option value="PiYG">PiYG</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
208 <option value="PRGn">PRGn</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
209 <option value="PuOr">PuOr</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
210 <option value="PuRd">PuRd</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
211 <option value="PuBu">PuBu</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
212 <option value="RdBu">RdBu</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
213 <option value="RdGy">RdGy</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
214 <option value="RdPu">RdPu</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
215 <option value="YlGn">YlGn</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
216 <option value="PuBuGn">PuBuGn</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
217 <option value="RdYlGn">RdYlGn</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
218 <option value="YlGnBu">YlGnBu</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
219 <option value="YlOrBr">YlOrBr</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
220 <option value="YlOrRd">YlOrRd</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
221 <option value="gist_gray">gist_gray</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
222 <option value="gist_stern">gist_stern</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
223 <option value="gist_earth">gist_earth</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
224 <option value="gist_yarg">gist_yarg</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
225 <option value="gist_ncar">gist_ncar</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
226 <option value="gist_rainbow">gist_rainbow</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
227 <option value="gist_heat">gist_heat</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
228 <option value="gnuplot">gnuplot</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
229 <option value="gnuplot2">gnuplot2</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
230 <option value="CMRmap">CMRmap</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
231 <option value="bwr">bwr</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
232 <option value="hsv">hsv</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
233 <option value="brg">brg</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
234 <option value="jet">jet</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
235 <option value="afmhot">afmhot</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
236 <option value="Accent_r">Accent reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
237 <option value="Spectral_r">Spectral reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
238 <option value="Set1_r">Set1 reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
239 <option value="Set2_r">Set2 reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
240 <option value="Set3_r">Set3 reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
241 <option value="Dark2_r">Dark2 reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
242 <option value="Reds_r">Reds reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
243 <option value="Oranges_r">Oranges reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
244 <option value="Greens_r">Greens reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
245 <option value="Blues_r">Blues reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
246 <option value="Greys_r">Greys reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
247 <option value="Purples_r">Purples reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
248 <option value="Paired_r">Paired reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
249 <option value="Pastel1_r">Pastel1 reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
250 <option value="Pastel2_r">Pastel2 reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
251 <option value="spring_r">spring reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
252 <option value="summer_r">summer reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
253 <option value="autumn_r">autumn reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
254 <option value="winter_r">winter reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
255 <option value="hot_r">hot reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
256 <option value="coolwarm_r">coolwarm reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
257 <option value="cool_r">cool reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
258 <option value="seismic_r">seismic reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
259 <option value="terrain_r">terrain reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
260 <option value="ocean_r">ocean reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
261 <option value="rainbow_r">rainbow reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
262 <option value="bone_r">bone reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
263 <option value="flag_r">flag reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
264 <option value="prism_r">prism reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
265 <option value="cubehelix_r">cubehelix reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
266 <option value="binary_r">binary reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
267 <option value="pink_r">pink reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
268 <option value="gray_r">gray reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
269 <option value="copper_r">copper reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
270 <option value="BrBG_r">BrBG reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
271 <option value="BuGn_r">BuGn reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
272 <option value="BuPu_r">BuPu reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
273 <option value="GnBu_r">GnBu reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
274 <option value="OrRd_r">OrRd reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
275 <option value="PiYG_r">PiYG reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
276 <option value="PRGn_r">PRGn reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
277 <option value="PuOr_r">PuOr reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
278 <option value="PuRd_r">PuRd reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
279 <option value="PuBu_r">PuBu reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
280 <option value="RdBu_r">RdBu reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
281 <option value="RdGy_r">RdGy reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
282 <option value="RdPu_r">RdPu reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
283 <option value="YlGn_r">YlGn reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
284 <option value="PuBuGn_r">PuBuGn reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
285 <option value="RdYlBu_r">RdYlBu reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
286 <option value="RdYlGn_r">RdYlGn reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
287 <option value="YlGnBu_r">YlGnBu reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
288 <option value="YlOrBr_r">YlOrBr reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
289 <option value="YlOrRd_r">YlOrRd reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
290 <option value="gist_gray_r">gist_gray reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
291 <option value="gist_stern_r">gist_stern reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
292 <option value="gist_earth_r">gist_earth reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
293 <option value="gist_yarg_r">gist_yarg reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
294 <option value="gist_ncar_r">gist_ncar reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
295 <option value="gist_rainbow_r">gist_rainbow reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
296 <option value="gist_heat_r">gist_heat reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
297 <option value="gnuplot_r">gnuplot reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
298 <option value="gnuplot2_r">gnuplot2 reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
299 <option value="CMRmap_r">CMRmap reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
300 <option value="bwr_r">bwr reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
301 <option value="hsv_r">hsv reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
302 <option value="brg_r">brg reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
303 <option value="jet_r">jet reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
304 <option value="afmhot_r">afmhot reversed</option>
d957e25e18a3 Uploaded
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parents:
diff changeset
305 </param>
d957e25e18a3 Uploaded
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parents:
diff changeset
306
d957e25e18a3 Uploaded
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parents:
diff changeset
307 </macro>
d957e25e18a3 Uploaded
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parents:
diff changeset
308
d957e25e18a3 Uploaded
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parents:
diff changeset
309 </macros>