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1 <?xml version="1.0"?>
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2 <toolbox>
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3 <label text="Sharp lab tools" id="sharplab" />
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4 <section name="Single interval manipulation" id="singleinterval">
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5 <tool file="mytools/bedclean.xml"/>
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6 <tool file="mytools/bedsort.xml"/>
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7 <tool file="mytools/collapseBed.xml" />
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8 <tool file="mytools/makewindow.xml" />
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9 <tool file="mytools/resize.xml" />
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10 <tool file="mytools/random_interval.xml"/>
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11 <tool file="mytools/shuffleBed.xml"/>
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12 <tool file="mytools/genomeView.xml"/>
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13 </section>
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14 <section name="Meta-Analysis" id="xuebing">
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15 <tool file="mytools/genomeView.xml"/>
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16 <tool file="mytools/intersectbed.xml"/>
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17 <tool file="mytools/closestBed.xml"/>
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18 <tool file="mytools/spatial_proximity.xml"/>
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19 <tool file="mytools/bwBinavg.xml"/>
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20 <tool file="mytools/metaintv.xml" />
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21 <tool file="mytools/metaintv_ext.xml" />
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22 <tool file="mytools/alignr.xml" />
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23 <tool file="mytools/align2multiple.xml" />
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24 <tool file="mytools/align2database.xml" />
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25 <tool file="mytools/intersectSig.xml" />
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26 <tool file="mytools/bigWigAverageOverBed.xml" />
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27 <tool file="mytools/endbias.xml" />
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28 </section>
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29 <section name="Statistics/Visualization" id="sharpvis">
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30 <tool file="mytools/genomeView.xml"/>
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31 <tool file="mytools/intervalSize.xml" />
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32 <tool file="mytools/intersectSig.xml" />
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33 <tool file="mytools/cdf.xml" />
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34 <tool file="mytools/binaverage.xml" />
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35 <tool file="mytools/alignvis.xml" />
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36 <tool file="mytools/plotmatrix.xml" />
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37 <tool file="mytools/venn.xml"/>
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38 </section>
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39 <section name="Text/Format manipulation" id="sharptext">
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40 <tool file="mytools/collapseTab.xml" />
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41 <tool file="mytools/fastqdump.xml" />
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42 <tool file="mytools/bowtie2bed.xml" />
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43 <tool file="mytools/sampline.xml" />
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44 <tool file="mytools/headtail.xml" />
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45 <tool file="mytools/convertEnsembl.xml" />
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46 <tool file="mytools/removeDuplicate.xml" />
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47 <tool file="mytools/bed_to_bam.xml" />
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48 <tool file="mytools/makebigwig.xml" />
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49
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50 </section>
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51 <section name="Sequence/Motif" id="sharpsequence">
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52 <tool file="extract/extract_genomic_dna.xml" />
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53 <tool file="mytools/revcompl.xml" />
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54 <tool file="mytools/fastashuffle1.xml" />
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55 <tool file="mytools/fastashuffle2.xml" />
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56 <tool file="mytools/iupac2meme.xml" />
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57 <tool file="mytools/seq2meme.xml" />
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58 <tool file="mytools/memelogo.xml" />
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59 <tool file="mytools/fastamarkov.xml" />
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60 <tool file="mytools/meme.xml"/>
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61 <tool file="mytools/dreme.xml"/>
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62 <tool file="mytools/fimo2.xml"/>
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63 <tool file="mytools/fimo2bed.xml"/>
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64 <tool file="rgenetics/rgWebLogo3.xml" />
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65 <tool file="mytools/splicesite.xml" />
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66 </section>
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67
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68 <section name="Conservation/Other scores" id="score">
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69 <tool file="mytools/phastCons.xml" />
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70 </section>
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71
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72 <label text="selected tools" id="selectedtools" />
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73 <section name="Get Data" id="sharpgetext">
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74 <tool file="data_source/upload.xml"/>
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75 <tool file="data_source/ucsc_tablebrowser.xml" />
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76 <tool file="data_source/biomart.xml" />
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77 </section>
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78 <section name="Operate on Genomic Intervals" id="sharpbxops">
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79 <tool file="new_operations/intersect.xml" />
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80 <tool file="new_operations/subtract.xml" />
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81 <tool file="new_operations/merge.xml" />
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82 <tool file="new_operations/concat.xml" />
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83
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84 <tool file="mytools/closestBed.xml" />
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85 <tool file="mytools/flankBed.xml" />
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86 <tool file="mytools/shuffleBed.xml" />
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87 <tool file="mytools/sortBed.xml" />
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88
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89 <tool file="new_operations/basecoverage.xml" />
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90 <tool file="new_operations/coverage.xml" />
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91 <tool file="new_operations/complement.xml" />
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92 <tool file="new_operations/cluster.xml" id="cluster" />
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93 <tool file="new_operations/join.xml" />
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94 <tool file="new_operations/get_flanks.xml" />
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95 <tool file="new_operations/flanking_features.xml" />
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96 <tool file="annotation_profiler/annotation_profiler.xml" />
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97 </section>
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98 <section name="Unix Tools" id="unix_tools">
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99 <tool file="unix_tools/awk_tool.xml" />
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100 <tool file="unix_tools/sed_tool.xml" />
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101 <tool file="unix_tools/grep_tool.xml" />
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102 <tool file="unix_tools/sort_tool.xml" />
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103 <tool file="unix_tools/uniq_tool.xml" />
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104 <tool file="unix_tools/cut_tool.xml" />
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105 <tool file="unix_tools/join_tool.xml" />
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106 <tool file="unix_tools/word_list_grep.xml" />
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107 <tool file="unix_tools/remove_ending.xml" />
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108 <tool file="unix_tools/find_and_replace.xml" />
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109 </section>
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110 <section name="Lift-Over" id="liftOver">
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111 <tool file="extract/liftOver_wrapper.xml" />
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112 </section>
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113 <section name="Text Manipulation" id="textutil">
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114 <tool file="filters/fixedValueColumn.xml" />
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115 <tool file="stats/column_maker.xml" />
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116 <tool file="filters/catWrapper.xml" />
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117 <tool file="filters/cutWrapper.xml" />
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118 <tool file="filters/mergeCols.xml" />
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119 <tool file="filters/convert_characters.xml" />
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120 <tool file="filters/CreateInterval.xml" />
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121 <tool file="filters/cutWrapper.xml" />
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122 <tool file="filters/changeCase.xml" />
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123 <tool file="filters/pasteWrapper.xml" />
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124 <tool file="filters/remove_beginning.xml" />
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125 <tool file="filters/randomlines.xml" />
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126 <tool file="filters/headWrapper.xml" />
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127 <tool file="filters/tailWrapper.xml" />
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128 <tool file="filters/trimmer.xml" />
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129 <tool file="filters/wc_gnu.xml" />
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130 <tool file="stats/dna_filtering.xml" />
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131 <tool file="new_operations/tables_arithmetic_operations.xml" />
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132 </section>
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133 <section name="Filter and Sort" id="filter">
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134 <tool file="stats/filtering.xml" />
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135 <tool file="filters/sorter.xml" />
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136 <tool file="filters/grep.xml" />
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137 <label text="GFF" id="gff" />
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138 <tool file="filters/gff/extract_GFF_Features.xml" />
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139 <tool file="filters/gff/gff_filter_by_attribute.xml" />
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140 <tool file="filters/gff/gff_filter_by_feature_count.xml" />
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141 <tool file="filters/gff/gtf_filter_by_attribute_values_list.xml" />
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142 </section>
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143 <section name="Join, Subtract and Group" id="group">
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144 <tool file="filters/joiner.xml" />
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145 <tool file="filters/compare.xml"/>
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146 <tool file="new_operations/subtract_query.xml"/>
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147 <tool file="stats/grouping.xml" />
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148 <tool file="new_operations/column_join.xml" />
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149 </section>
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150 <section name="Convert Formats" id="convert">
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151 <tool file="filters/axt_to_concat_fasta.xml" />
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152 <tool file="filters/axt_to_fasta.xml" />
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153 <tool file="filters/axt_to_lav.xml" />
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154 <tool file="filters/bed2gff.xml" />
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155 <tool file="fasta_tools/fasta_to_tabular.xml" />
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156 <tool file="filters/gff2bed.xml" />
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157 <tool file="filters/lav_to_bed.xml" />
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158 <tool file="maf/maf_to_bed.xml" />
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159 <tool file="maf/maf_to_interval.xml" />
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160 <tool file="maf/maf_to_fasta.xml" />
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161 <tool file="fasta_tools/tabular_to_fasta.xml" />
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162 <tool file="fastq/fastq_to_fasta.xml" />
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163 <tool file="filters/wiggle_to_simple.xml" />
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164 <tool file="filters/sff_extractor.xml" />
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165 <tool file="filters/gtf2bedgraph.xml" />
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166 <tool file="filters/wig_to_bigwig.xml" />
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167 <tool file="filters/bed_to_bigbed.xml" />
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168 <tool file="samtools/sam_to_bam.xml" />
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169 <tool file="samtools/bam_to_sam.xml" />
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170 <tool file="mytools/bedToBam.xml" />
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171 <tool file="mytools/bamToBed.xml" />
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172 </section>
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173
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174
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175
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176 <section name="FASTA manipulation" id="fasta_manipulation">
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177 <tool file="fasta_tools/fasta_compute_length.xml" />
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178 <tool file="fasta_tools/fasta_filter_by_length.xml" />
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179 <tool file="fasta_tools/fasta_concatenate_by_species.xml" />
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180 <tool file="fasta_tools/fasta_to_tabular.xml" />
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181 <tool file="fasta_tools/tabular_to_fasta.xml" />
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182 <tool file="fastx_toolkit/fasta_formatter.xml" />
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183 <tool file="fastx_toolkit/fasta_nucleotide_changer.xml" />
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184 <tool file="fastx_toolkit/fastx_collapser.xml" />
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185 </section>
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186 <section name="NGS: QC and manipulation" id="NGS_QC">
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187 <label text="FastQC: fastq/sam/bam" id="fastqcsambam" />
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188 <tool file="rgenetics/rgFastQC.xml" />
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189 <label text="Illumina fastq" id="illumina" />
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190 <tool file="fastq/fastq_groomer.xml" />
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191 <tool file="fastq/fastq_paired_end_splitter.xml" />
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192 <tool file="fastq/fastq_paired_end_joiner.xml" />
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193 <tool file="fastq/fastq_stats.xml" />
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194 <label text="Roche-454 data" id="454" />
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195 <tool file="metag_tools/short_reads_figure_score.xml" />
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196 <tool file="metag_tools/short_reads_trim_seq.xml" />
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197 <tool file="fastq/fastq_combiner.xml" />
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198 <label text="AB-SOLiD data" id="solid" />
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199 <tool file="next_gen_conversion/solid2fastq.xml" />
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200 <tool file="solid_tools/solid_qual_stats.xml" />
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201 <tool file="solid_tools/solid_qual_boxplot.xml" />
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202 <label text="Generic FASTQ manipulation" id="generic_fastq" />
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203 <tool file="fastq/fastq_filter.xml" />
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204 <tool file="fastq/fastq_trimmer.xml" />
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205 <tool file="fastq/fastq_trimmer_by_quality.xml" />
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206 <tool file="fastq/fastq_masker_by_quality.xml" />
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207 <tool file="fastq/fastq_paired_end_interlacer.xml" />
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208 <tool file="fastq/fastq_paired_end_deinterlacer.xml" />
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209 <tool file="fastq/fastq_manipulation.xml" />
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210 <tool file="fastq/fastq_to_fasta.xml" />
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211 <tool file="fastq/fastq_to_tabular.xml" />
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212 <tool file="fastq/tabular_to_fastq.xml" />
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213 <label text="FASTX-Toolkit for FASTQ data" id="fastx_toolkit" />
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214 <tool file="fastx_toolkit/fastq_quality_converter.xml" />
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215 <tool file="fastx_toolkit/fastx_quality_statistics.xml" />
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216 <tool file="fastx_toolkit/fastq_quality_boxplot.xml" />
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217 <tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" />
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218 <tool file="fastx_toolkit/fastq_to_fasta.xml" />
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219 <tool file="fastx_toolkit/fastq_quality_filter.xml" />
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220 <tool file="fastx_toolkit/fastq_to_fasta.xml" />
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221 <tool file="fastx_toolkit/fastx_artifacts_filter.xml" />
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222 <tool file="fastx_toolkit/fastx_barcode_splitter.xml" />
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223 <tool file="fastx_toolkit/fastx_clipper.xml" />
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224 <tool file="fastx_toolkit/fastx_collapser.xml" />
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225 <tool file="fastx_toolkit/fastx_renamer.xml" />
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226 <tool file="fastx_toolkit/fastx_reverse_complement.xml" />
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227 <tool file="fastx_toolkit/fastx_trimmer.xml" />
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228 </section>
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229 <section name="NGS: Mapping" id="solexa_tools">
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230 <tool file="sr_mapping/bowtie_wrapper.xml" />
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231 </section>
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232 <section name="NGS: SAM Tools" id="samtools">
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233 <tool file="samtools/sam_bitwise_flag_filter.xml" />
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234 <tool file="samtools/sam2interval.xml" />
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235 <tool file="samtools/sam_merge.xml" />
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236 <tool file="samtools/sam_pileup.xml" />
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237 <tool file="samtools/pileup_parser.xml" />
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238 <tool file="samtools/pileup_interval.xml" />
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239 <tool file="samtools/samtools_flagstat.xml" />
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240 </section>
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241 <section name="Functional Enrichment" id="enrichment">
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242 <tool file="human_genome_variation/linkToDavid.xml"/>
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243 </section>
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244
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245 <label text="other galaxy tools" id="galaxy_tools"/>
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246 <section name="Extract Features" id="features">
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247 <tool file="filters/ucsc_gene_bed_to_exon_bed.xml" />
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248 </section>
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249 <section name="Fetch Alignments" id="fetchAlign">
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250 <tool file="maf/interval2maf_pairwise.xml" />
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251 <tool file="maf/interval2maf.xml" />
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252 <tool file="maf/maf_split_by_species.xml"/>
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253 <tool file="maf/interval_maf_to_merged_fasta.xml" />
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254 <tool file="maf/genebed_maf_to_fasta.xml"/>
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255 <tool file="maf/maf_stats.xml"/>
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256 <tool file="maf/maf_thread_for_species.xml"/>
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257 <tool file="maf/maf_limit_to_species.xml"/>
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258 <tool file="maf/maf_limit_size.xml"/>
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259 <tool file="maf/maf_by_block_number.xml"/>
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260 <tool file="maf/maf_reverse_complement.xml"/>
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261 <tool file="maf/maf_filter.xml"/>
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262 </section>
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263 <section name="Get Genomic Scores" id="scores">
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264 <tool file="stats/wiggle_to_simple.xml" />
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265 <tool file="stats/aggregate_binned_scores_in_intervals.xml" />
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266 <tool file="extract/phastOdds/phastOdds_tool.xml" />
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267 </section>
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268 <section name="Operate on Genomic Intervals" id="bxops">
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269 <tool file="new_operations/intersect.xml" />
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270 <tool file="new_operations/subtract.xml" />
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271 <tool file="new_operations/merge.xml" />
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272 <tool file="new_operations/concat.xml" />
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273 <tool file="new_operations/basecoverage.xml" />
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274 <tool file="new_operations/coverage.xml" />
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275 <tool file="new_operations/complement.xml" />
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276 <tool file="new_operations/cluster.xml" id="cluster" />
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277 <tool file="new_operations/join.xml" />
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278 <tool file="new_operations/get_flanks.xml" />
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279 <tool file="new_operations/flanking_features.xml" />
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280 <tool file="annotation_profiler/annotation_profiler.xml" />
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281 </section>
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282 <section name="Statistics" id="stats">
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283 <tool file="stats/gsummary.xml" />
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284 <tool file="filters/uniq.xml" />
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285 <tool file="stats/cor.xml" />
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286 <tool file="stats/generate_matrix_for_pca_lda.xml" />
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287 <tool file="stats/lda_analy.xml" />
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288 <tool file="stats/plot_from_lda.xml" />
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289 <tool file="regVariation/t_test_two_samples.xml" />
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290 <tool file="regVariation/compute_q_values.xml" />
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291 <label text="GFF" id="gff" />
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292 <tool file="stats/count_gff_features.xml" />
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293 </section>
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294 <section name="Wavelet Analysis" id="dwt">
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295 <tool file="discreteWavelet/execute_dwt_var_perFeature.xml" />
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296 <!--
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297 Keep this section/tools commented until all of the tools have functional tests
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298 <tool file="discreteWavelet/execute_dwt_IvC_all.xml" />
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299 <tool file="discreteWavelet/execute_dwt_cor_aVa_perClass.xml" />
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300 <tool file="discreteWavelet/execute_dwt_cor_aVb_all.xml" />
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301 <tool file="discreteWavelet/execute_dwt_var_perClass.xml" />
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302 -->
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303 </section>
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304 <section name="Graph/Display Data" id="plots">
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305 <tool file="plotting/histogram2.xml" />
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306 <tool file="plotting/scatterplot.xml" />
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307 <tool file="plotting/bar_chart.xml" />
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308 <tool file="plotting/xy_plot.xml" />
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309 <tool file="plotting/boxplot.xml" />
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310 <tool file="visualization/GMAJ.xml" />
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311 <tool file="visualization/LAJ.xml" />
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312 <tool file="visualization/build_ucsc_custom_track.xml" />
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313 <tool file="maf/vcf_to_maf_customtrack.xml" />
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314 <tool file="mutation/visualize.xml" />
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315 </section>
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316 <section name="Regional Variation" id="regVar">
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317 <tool file="regVariation/windowSplitter.xml" />
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318 <tool file="regVariation/featureCounter.xml" />
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319 <tool file="regVariation/quality_filter.xml" />
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320 <tool file="regVariation/maf_cpg_filter.xml" />
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321 <tool file="regVariation/getIndels_2way.xml" />
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322 <tool file="regVariation/getIndels_3way.xml" />
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323 <tool file="regVariation/getIndelRates_3way.xml" />
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324 <tool file="regVariation/substitutions.xml" />
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325 <tool file="regVariation/substitution_rates.xml" />
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326 <tool file="regVariation/microsats_alignment_level.xml" />
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327 <tool file="regVariation/microsats_mutability.xml" />
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328 <tool file="regVariation/delete_overlapping_indels.xml" />
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329 <tool file="regVariation/compute_motifs_frequency.xml" />
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330 <tool file="regVariation/compute_motif_frequencies_for_all_motifs.xml" />
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331 <tool file="regVariation/categorize_elements_satisfying_criteria.xml" />s
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332 <tool file="regVariation/draw_stacked_barplots.xml" />
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333 <tool file="regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml" />
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334 <tool file="regVariation/microsatellite_birthdeath.xml" />
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335 </section>
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336 <section name="Multiple regression" id="multReg">
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337 <tool file="regVariation/linear_regression.xml" />
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338 <tool file="regVariation/best_regression_subsets.xml" />
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339 <tool file="regVariation/rcve.xml" />
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340 </section>
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341 <section name="Multivariate Analysis" id="multVar">
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342 <tool file="multivariate_stats/pca.xml" />
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343 <tool file="multivariate_stats/cca.xml" />
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344 <tool file="multivariate_stats/kpca.xml" />
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345 <tool file="multivariate_stats/kcca.xml" />
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346 </section>
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347 <section name="Evolution" id="hyphy">
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348 <tool file="hyphy/hyphy_branch_lengths_wrapper.xml" />
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349 <tool file="hyphy/hyphy_nj_tree_wrapper.xml" />
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350 <tool file="hyphy/hyphy_dnds_wrapper.xml" />
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351 <tool file="evolution/mutate_snp_codon.xml" />
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352 <tool file="evolution/codingSnps.xml" />
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353 <tool file="evolution/add_scores.xml" />
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354 </section>
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355 <section name="Multiple Alignments" id="clustal">
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356 <tool file="rgenetics/rgClustalw.xml" />
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357 </section>
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358 <section name="Metagenomic analyses" id="tax_manipulation">
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359 <tool file="taxonomy/gi2taxonomy.xml" />
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360 <tool file="taxonomy/t2t_report.xml" />
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361 <tool file="taxonomy/t2ps_wrapper.xml" />
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362 <tool file="taxonomy/find_diag_hits.xml" />
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363 <tool file="taxonomy/lca.xml" />
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364 <tool file="taxonomy/poisson2test.xml" />
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365 </section>
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366 <section name="FASTA manipulation" id="fasta_manipulation">
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367 <tool file="fasta_tools/fasta_compute_length.xml" />
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|
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368 <tool file="fasta_tools/fasta_filter_by_length.xml" />
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369 <tool file="fasta_tools/fasta_concatenate_by_species.xml" />
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370 <tool file="fasta_tools/fasta_to_tabular.xml" />
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371 <tool file="fasta_tools/tabular_to_fasta.xml" />
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372 <tool file="fastx_toolkit/fasta_formatter.xml" />
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|
|
373 <tool file="fastx_toolkit/fasta_nucleotide_changer.xml" />
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374 <tool file="fastx_toolkit/fastx_collapser.xml" />
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375 </section>
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|
376 <section name="NCBI BLAST+" id="ncbi_blast_plus_tools">
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377 <tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" />
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|
378 <tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" />
|
|
|
379 <tool file="ncbi_blast_plus/ncbi_blastx_wrapper.xml" />
|
|
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380 <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" />
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|
|
381 <tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" />
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|
|
382 <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" />
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|
|
383 </section>
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|
|
384 <section name="NGS: QC and manipulation" id="NGS_QC">
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|
|
385 <label text="FastQC: fastq/sam/bam" id="fastqcsambam" />
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|
|
386 <tool file="rgenetics/rgFastQC.xml" />
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|
|
387 <label text="Illumina fastq" id="illumina" />
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|
|
388 <tool file="fastq/fastq_groomer.xml" />
|
|
|
389 <tool file="fastq/fastq_paired_end_splitter.xml" />
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|
|
390 <tool file="fastq/fastq_paired_end_joiner.xml" />
|
|
|
391 <tool file="fastq/fastq_stats.xml" />
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|
|
392 <label text="Roche-454 data" id="454" />
|
|
|
393 <tool file="metag_tools/short_reads_figure_score.xml" />
|
|
|
394 <tool file="metag_tools/short_reads_trim_seq.xml" />
|
|
|
395 <tool file="fastq/fastq_combiner.xml" />
|
|
|
396 <label text="AB-SOLiD data" id="solid" />
|
|
|
397 <tool file="next_gen_conversion/solid2fastq.xml" />
|
|
|
398 <tool file="solid_tools/solid_qual_stats.xml" />
|
|
|
399 <tool file="solid_tools/solid_qual_boxplot.xml" />
|
|
|
400 <label text="Generic FASTQ manipulation" id="generic_fastq" />
|
|
|
401 <tool file="fastq/fastq_filter.xml" />
|
|
|
402 <tool file="fastq/fastq_trimmer.xml" />
|
|
|
403 <tool file="fastq/fastq_trimmer_by_quality.xml" />
|
|
|
404 <tool file="fastq/fastq_masker_by_quality.xml" />
|
|
|
405 <tool file="fastq/fastq_paired_end_interlacer.xml" />
|
|
|
406 <tool file="fastq/fastq_paired_end_deinterlacer.xml" />
|
|
|
407 <tool file="fastq/fastq_manipulation.xml" />
|
|
|
408 <tool file="fastq/fastq_to_fasta.xml" />
|
|
|
409 <tool file="fastq/fastq_to_tabular.xml" />
|
|
|
410 <tool file="fastq/tabular_to_fastq.xml" />
|
|
|
411 <label text="FASTX-Toolkit for FASTQ data" id="fastx_toolkit" />
|
|
|
412 <tool file="fastx_toolkit/fastq_quality_converter.xml" />
|
|
|
413 <tool file="fastx_toolkit/fastx_quality_statistics.xml" />
|
|
|
414 <tool file="fastx_toolkit/fastq_quality_boxplot.xml" />
|
|
|
415 <tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" />
|
|
|
416 <tool file="fastx_toolkit/fastq_to_fasta.xml" />
|
|
|
417 <tool file="fastx_toolkit/fastq_quality_filter.xml" />
|
|
|
418 <tool file="fastx_toolkit/fastq_to_fasta.xml" />
|
|
|
419 <tool file="fastx_toolkit/fastx_artifacts_filter.xml" />
|
|
|
420 <tool file="fastx_toolkit/fastx_barcode_splitter.xml" />
|
|
|
421 <tool file="fastx_toolkit/fastx_clipper.xml" />
|
|
|
422 <tool file="fastx_toolkit/fastx_collapser.xml" />
|
|
|
423 <tool file="fastx_toolkit/fastx_renamer.xml" />
|
|
|
424 <tool file="fastx_toolkit/fastx_reverse_complement.xml" />
|
|
|
425 <tool file="fastx_toolkit/fastx_trimmer.xml" />
|
|
|
426 </section>
|
|
|
427 <section name="NGS: Picard (beta)" id="picard_beta">
|
|
|
428 <label text="QC/Metrics for sam/bam" id="qcsambam"/>
|
|
|
429 <tool file="picard/picard_BamIndexStats.xml" />
|
|
|
430 <tool file="picard/rgPicardASMetrics.xml" />
|
|
|
431 <tool file="picard/rgPicardGCBiasMetrics.xml" />
|
|
|
432 <tool file="picard/rgPicardLibComplexity.xml" />
|
|
|
433 <tool file="picard/rgPicardInsertSize.xml" />
|
|
|
434 <tool file="picard/rgPicardHsMetrics.xml" />
|
|
|
435 <label text="bam/sam Cleaning" id="picard-clean" />
|
|
|
436 <tool file="picard/picard_AddOrReplaceReadGroups.xml" />
|
|
|
437 <tool file="picard/picard_ReorderSam.xml" />
|
|
|
438 <tool file="picard/picard_ReplaceSamHeader.xml" />
|
|
|
439 <tool file="picard/rgPicardFixMate.xml" />
|
|
|
440 <tool file="picard/rgPicardMarkDups.xml" />
|
|
|
441 </section>
|
|
|
442 <!--
|
|
|
443 Keep this section commented until it includes tools that
|
|
|
444 will be hosted on test/main. The velvet wrappers have been
|
|
|
445 included in the distribution but will not be hosted on our
|
|
|
446 public servers for the current time.
|
|
|
447 <section name="NGS: Assembly" id="ngs_assembly">
|
|
|
448 <label text="Velvet" id="velvet"/>
|
|
|
449 <tool file="sr_assembly/velvetg.xml" />
|
|
|
450 <tool file="sr_assembly/velveth.xml" />
|
|
|
451 </section>
|
|
|
452 -->
|
|
|
453 <section name="NGS: Mapping" id="solexa_tools">
|
|
|
454 <tool file="sr_mapping/lastz_wrapper.xml" />
|
|
|
455 <tool file="sr_mapping/lastz_paired_reads_wrapper.xml" />
|
|
|
456 <tool file="sr_mapping/bowtie_wrapper.xml" />
|
|
|
457 <tool file="sr_mapping/bowtie_color_wrapper.xml" />
|
|
|
458 <tool file="sr_mapping/bwa_wrapper.xml" />
|
|
|
459 <tool file="sr_mapping/bwa_color_wrapper.xml" />
|
|
|
460 <tool file="sr_mapping/bfast_wrapper.xml" />
|
|
|
461 <tool file="metag_tools/megablast_wrapper.xml" />
|
|
|
462 <tool file="metag_tools/megablast_xml_parser.xml" />
|
|
|
463 <tool file="sr_mapping/PerM.xml" />
|
|
|
464 <tool file="sr_mapping/srma_wrapper.xml" />
|
|
|
465 <tool file="sr_mapping/mosaik.xml"/>
|
|
|
466 </section>
|
|
|
467 <section name="NGS: Indel Analysis" id="indel_analysis">
|
|
|
468 <tool file="indels/sam_indel_filter.xml" />
|
|
|
469 <tool file="indels/indel_sam2interval.xml" />
|
|
|
470 <tool file="indels/indel_table.xml" />
|
|
|
471 <tool file="indels/indel_analysis.xml" />
|
|
|
472 </section>
|
|
|
473 <section name="NGS: RNA Analysis" id="ngs-rna-tools">
|
|
|
474 <label text="RNA-seq" id="rna_seq" />
|
|
|
475 <tool file="ngs_rna/tophat_wrapper.xml" />
|
|
|
476 <tool file="ngs_rna/tophat_color_wrapper.xml" />
|
|
|
477 <tool file="ngs_rna/cufflinks_wrapper.xml" />
|
|
|
478 <tool file="ngs_rna/cuffcompare_wrapper.xml" />
|
|
|
479 <tool file="ngs_rna/cuffdiff_wrapper.xml" />
|
|
|
480 <label text="De novo Assembly" id="de_novo_assembly "/>
|
|
|
481 <tool file="ngs_rna/trinity_all.xml" />
|
|
|
482 <label text="Filtering" id="filtering" />
|
|
|
483 <tool file="ngs_rna/filter_transcripts_via_tracking.xml" />
|
|
|
484 </section>
|
|
|
485 <section name="NGS: SAM Tools" id="samtools">
|
|
|
486 <tool file="samtools/sam_bitwise_flag_filter.xml" />
|
|
|
487 <tool file="samtools/sam2interval.xml" />
|
|
|
488 <tool file="samtools/sam_to_bam.xml" />
|
|
|
489 <tool file="samtools/bam_to_sam.xml" />
|
|
|
490 <tool file="samtools/sam_merge.xml" />
|
|
|
491 <tool file="samtools/sam_pileup.xml" />
|
|
|
492 <tool file="samtools/pileup_parser.xml" />
|
|
|
493 <tool file="samtools/pileup_interval.xml" />
|
|
|
494 <tool file="samtools/samtools_flagstat.xml" />
|
|
|
495 </section>
|
|
|
496 <section name="NGS: GATK Tools" id="gatk">
|
|
|
497 <label text="Realignment" id="gatk_realignment" />
|
|
|
498 <tool file="gatk/realigner_target_creator.xml" />
|
|
|
499 <tool file="gatk/indel_realigner.xml" />
|
|
|
500 <label text="Base Recalibration" id="gatk_recalibration" />
|
|
|
501 <tool file="gatk/count_covariates.xml" />
|
|
|
502 <tool file="gatk/table_recalibration.xml" />
|
|
|
503 <tool file="gatk/analyze_covariates.xml" />
|
|
|
504 <label text="Genotyping" id="gatk_genotyping" />
|
|
|
505 <tool file="gatk/unified_genotyper.xml" />
|
|
|
506 </section>
|
|
|
507 <section name="NGS: Peak Calling" id="peak_calling">
|
|
|
508 <tool file="peak_calling/macs_wrapper.xml" />
|
|
|
509 <tool file="peak_calling/sicer_wrapper.xml" />
|
|
|
510 <tool file="peak_calling/ccat_wrapper.xml" />
|
|
|
511 <tool file="genetrack/genetrack_indexer.xml" />
|
|
|
512 <tool file="genetrack/genetrack_peak_prediction.xml" />
|
|
|
513 </section>
|
|
|
514 <section name="NGS: Simulation" id="ngs-simulation">
|
|
|
515 <tool file="ngs_simulation/ngs_simulation.xml" />
|
|
|
516 </section>
|
|
|
517 <section name="SNP/WGA: Data; Filters" id="rgdat">
|
|
|
518 <label text="Data: Import and upload" id="rgimport" />
|
|
|
519 <tool file="data_source/upload.xml"/>
|
|
|
520 <tool file="data_source/access_libraries.xml" />
|
|
|
521 <label text="Data: Filter and Clean" id="rgfilter" />
|
|
|
522 <tool file="rgenetics/rgClean.xml"/>
|
|
|
523 <tool file="rgenetics/rgPedSub.xml"/>
|
|
|
524 <tool file="rgenetics/rgLDIndep.xml"/>
|
|
|
525 <label text="Simulate" id="rgsim" />
|
|
|
526 <tool file="rgenetics/rgfakePhe.xml"/>
|
|
|
527 <tool file="rgenetics/rgfakePed.xml"/>
|
|
|
528 </section>
|
|
|
529 <section name="SNP/WGA: QC; LD; Plots" id="rgqcplot">
|
|
|
530 <label text="QC; Eigenstrat" id="rgvisual" />
|
|
|
531 <tool file="rgenetics/rgQC.xml"/>
|
|
|
532 <tool file="rgenetics/rgEigPCA.xml"/>
|
|
|
533 <label text="LD; Manhattan/QQ; GRR" id="rgld" />
|
|
|
534 <tool file="rgenetics/rgHaploView.xml"/>
|
|
|
535 <tool file="rgenetics/rgManQQ.xml"/>
|
|
|
536 <tool file="rgenetics/rgGRR.xml"/>
|
|
|
537 </section>
|
|
|
538 <section name="SNP/WGA: Statistical Models" id="rgmodel">
|
|
|
539 <tool file="rgenetics/rgCaCo.xml"/>
|
|
|
540 <tool file="rgenetics/rgTDT.xml"/>
|
|
|
541 <tool file="rgenetics/rgGLM.xml"/>
|
|
|
542 <tool file="rgenetics/rgManQQ.xml"/>
|
|
|
543 </section>
|
|
|
544 <section name="Human Genome Variation" id="hgv">
|
|
|
545 <tool file="evolution/codingSnps.xml" />
|
|
|
546 <tool file="evolution/add_scores.xml" />
|
|
|
547 <tool file="human_genome_variation/sift.xml" />
|
|
|
548 <tool file="human_genome_variation/linkToGProfile.xml" />
|
|
|
549 <tool file="human_genome_variation/linkToDavid.xml"/>
|
|
|
550 <tool file="human_genome_variation/ctd.xml" />
|
|
|
551 <tool file="human_genome_variation/funDo.xml" />
|
|
|
552 <tool file="human_genome_variation/snpFreq.xml" />
|
|
|
553 <tool file="human_genome_variation/ldtools.xml" />
|
|
|
554 <tool file="human_genome_variation/pass.xml" />
|
|
|
555 <tool file="human_genome_variation/gpass.xml" />
|
|
|
556 <tool file="human_genome_variation/beam.xml" />
|
|
|
557 <tool file="human_genome_variation/lps.xml" />
|
|
|
558 <tool file="human_genome_variation/hilbertvis.xml" />
|
|
|
559 <tool file="human_genome_variation/freebayes.xml" />
|
|
|
560 </section>
|
|
|
561 <section name="Genome Diversity" id="gd">
|
|
|
562 <tool file="genome_diversity/extract_primers.xml" />
|
|
|
563 <tool file="genome_diversity/select_snps.xml" />
|
|
|
564 <tool file="genome_diversity/select_restriction_enzymes.xml" />
|
|
|
565 <tool file="genome_diversity/extract_flanking_dna.xml" />
|
|
|
566 </section>
|
|
|
567 <section name="VCF Tools" id="vcf_tools">
|
|
|
568 <tool file="vcf_tools/intersect.xml" />
|
|
|
569 <tool file="vcf_tools/annotate.xml" />
|
|
|
570 <tool file="vcf_tools/filter.xml" />
|
|
|
571 <tool file="vcf_tools/extract.xml" />
|
|
|
572 </section>
|
|
|
573 <section name="PacBio/Illumina Assembly" id="hybrid">
|
|
|
574 <tool file="ilmn_pacbio/quake.xml"/>
|
|
|
575 <tool file="ilmn_pacbio/quake_pe.xml"/>
|
|
|
576 <tool file="ilmn_pacbio/soap_denovo.xml"/>
|
|
|
577 <!--
|
|
|
578 Uncomment this tool when we support the HDF5 format
|
|
|
579 <tool file="ilmn_pacbio/smrtpipe_filter.xml"/>
|
|
|
580 -->
|
|
|
581 <tool file="ilmn_pacbio/smrtpipe_hybrid.xml"/>
|
|
|
582 <tool file="ilmn_pacbio/assembly_stats.xml"/>
|
|
|
583 </section>
|
|
|
584 <!--
|
|
|
585 TODO: uncomment the following EMBOSS section whenever
|
|
|
586 moving to test, but comment it in .sample to eliminate
|
|
|
587 it from buildbot functional tests since these tools
|
|
|
588 rarely change.
|
|
|
589 -->
|
|
|
590 <!--
|
|
|
591 <section name="EMBOSS" id="EMBOSSLite">
|
|
|
592 <tool file="emboss_5/emboss_antigenic.xml" />
|
|
|
593 <tool file="emboss_5/emboss_backtranseq.xml" />
|
|
|
594 <tool file="emboss_5/emboss_banana.xml" />
|
|
|
595 <tool file="emboss_5/emboss_biosed.xml" />
|
|
|
596 <tool file="emboss_5/emboss_btwisted.xml" />
|
|
|
597 <tool file="emboss_5/emboss_cai_custom.xml" />
|
|
|
598 <tool file="emboss_5/emboss_cai.xml" />
|
|
|
599 <tool file="emboss_5/emboss_chaos.xml" />
|
|
|
600 <tool file="emboss_5/emboss_charge.xml" />
|
|
|
601 <tool file="emboss_5/emboss_checktrans.xml" />
|
|
|
602 <tool file="emboss_5/emboss_chips.xml" />
|
|
|
603 <tool file="emboss_5/emboss_cirdna.xml" />
|
|
|
604 <tool file="emboss_5/emboss_codcmp.xml" />
|
|
|
605 <tool file="emboss_5/emboss_coderet.xml" />
|
|
|
606 <tool file="emboss_5/emboss_compseq.xml" />
|
|
|
607 <tool file="emboss_5/emboss_cpgplot.xml" />
|
|
|
608 <tool file="emboss_5/emboss_cpgreport.xml" />
|
|
|
609 <tool file="emboss_5/emboss_cusp.xml" />
|
|
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610 <tool file="emboss_5/emboss_cutseq.xml" />
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611 <tool file="emboss_5/emboss_dan.xml" />
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612 <tool file="emboss_5/emboss_degapseq.xml" />
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613 <tool file="emboss_5/emboss_descseq.xml" />
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614 <tool file="emboss_5/emboss_diffseq.xml" />
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615 <tool file="emboss_5/emboss_digest.xml" />
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616 <tool file="emboss_5/emboss_dotmatcher.xml" />
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617 <tool file="emboss_5/emboss_dotpath.xml" />
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618 <tool file="emboss_5/emboss_dottup.xml" />
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619 <tool file="emboss_5/emboss_dreg.xml" />
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620 <tool file="emboss_5/emboss_einverted.xml" />
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621 <tool file="emboss_5/emboss_epestfind.xml" />
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622 <tool file="emboss_5/emboss_equicktandem.xml" />
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623 <tool file="emboss_5/emboss_est2genome.xml" />
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624 <tool file="emboss_5/emboss_etandem.xml" />
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625 <tool file="emboss_5/emboss_extractfeat.xml" />
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626 <tool file="emboss_5/emboss_extractseq.xml" />
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627 <tool file="emboss_5/emboss_freak.xml" />
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628 <tool file="emboss_5/emboss_fuzznuc.xml" />
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629 <tool file="emboss_5/emboss_fuzzpro.xml" />
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630 <tool file="emboss_5/emboss_fuzztran.xml" />
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631 <tool file="emboss_5/emboss_garnier.xml" />
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632 <tool file="emboss_5/emboss_geecee.xml" />
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633 <tool file="emboss_5/emboss_getorf.xml" />
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634 <tool file="emboss_5/emboss_helixturnhelix.xml" />
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635 <tool file="emboss_5/emboss_hmoment.xml" />
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636 <tool file="emboss_5/emboss_iep.xml" />
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637 <tool file="emboss_5/emboss_infoseq.xml" />
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638 <tool file="emboss_5/emboss_isochore.xml" />
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639 <tool file="emboss_5/emboss_lindna.xml" />
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640 <tool file="emboss_5/emboss_marscan.xml" />
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641 <tool file="emboss_5/emboss_maskfeat.xml" />
|
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642 <tool file="emboss_5/emboss_maskseq.xml" />
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643 <tool file="emboss_5/emboss_matcher.xml" />
|
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644 <tool file="emboss_5/emboss_megamerger.xml" />
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645 <tool file="emboss_5/emboss_merger.xml" />
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646 <tool file="emboss_5/emboss_msbar.xml" />
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647 <tool file="emboss_5/emboss_needle.xml" />
|
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|
648 <tool file="emboss_5/emboss_newcpgreport.xml" />
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649 <tool file="emboss_5/emboss_newcpgseek.xml" />
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650 <tool file="emboss_5/emboss_newseq.xml" />
|
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651 <tool file="emboss_5/emboss_noreturn.xml" />
|
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|
652 <tool file="emboss_5/emboss_notseq.xml" />
|
|
|
653 <tool file="emboss_5/emboss_nthseq.xml" />
|
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|
654 <tool file="emboss_5/emboss_octanol.xml" />
|
|
|
655 <tool file="emboss_5/emboss_oddcomp.xml" />
|
|
|
656 <tool file="emboss_5/emboss_palindrome.xml" />
|
|
|
657 <tool file="emboss_5/emboss_pasteseq.xml" />
|
|
|
658 <tool file="emboss_5/emboss_patmatdb.xml" />
|
|
|
659 <tool file="emboss_5/emboss_pepcoil.xml" />
|
|
|
660 <tool file="emboss_5/emboss_pepinfo.xml" />
|
|
|
661 <tool file="emboss_5/emboss_pepnet.xml" />
|
|
|
662 <tool file="emboss_5/emboss_pepstats.xml" />
|
|
|
663 <tool file="emboss_5/emboss_pepwheel.xml" />
|
|
|
664 <tool file="emboss_5/emboss_pepwindow.xml" />
|
|
|
665 <tool file="emboss_5/emboss_pepwindowall.xml" />
|
|
|
666 <tool file="emboss_5/emboss_plotcon.xml" />
|
|
|
667 <tool file="emboss_5/emboss_plotorf.xml" />
|
|
|
668 <tool file="emboss_5/emboss_polydot.xml" />
|
|
|
669 <tool file="emboss_5/emboss_preg.xml" />
|
|
|
670 <tool file="emboss_5/emboss_prettyplot.xml" />
|
|
|
671 <tool file="emboss_5/emboss_prettyseq.xml" />
|
|
|
672 <tool file="emboss_5/emboss_primersearch.xml" />
|
|
|
673 <tool file="emboss_5/emboss_revseq.xml" />
|
|
|
674 <tool file="emboss_5/emboss_seqmatchall.xml" />
|
|
|
675 <tool file="emboss_5/emboss_seqret.xml" />
|
|
|
676 <tool file="emboss_5/emboss_showfeat.xml" />
|
|
|
677 <tool file="emboss_5/emboss_shuffleseq.xml" />
|
|
|
678 <tool file="emboss_5/emboss_sigcleave.xml" />
|
|
|
679 <tool file="emboss_5/emboss_sirna.xml" />
|
|
|
680 <tool file="emboss_5/emboss_sixpack.xml" />
|
|
|
681 <tool file="emboss_5/emboss_skipseq.xml" />
|
|
|
682 <tool file="emboss_5/emboss_splitter.xml" />
|
|
|
683 <tool file="emboss_5/emboss_supermatcher.xml" />
|
|
|
684 <tool file="emboss_5/emboss_syco.xml" />
|
|
|
685 <tool file="emboss_5/emboss_tcode.xml" />
|
|
|
686 <tool file="emboss_5/emboss_textsearch.xml" />
|
|
|
687 <tool file="emboss_5/emboss_tmap.xml" />
|
|
|
688 <tool file="emboss_5/emboss_tranalign.xml" />
|
|
|
689 <tool file="emboss_5/emboss_transeq.xml" />
|
|
|
690 <tool file="emboss_5/emboss_trimest.xml" />
|
|
|
691 <tool file="emboss_5/emboss_trimseq.xml" />
|
|
|
692 <tool file="emboss_5/emboss_twofeat.xml" />
|
|
|
693 <tool file="emboss_5/emboss_union.xml" />
|
|
|
694 <tool file="emboss_5/emboss_vectorstrip.xml" />
|
|
|
695 <tool file="emboss_5/emboss_water.xml" />
|
|
|
696 <tool file="emboss_5/emboss_wobble.xml" />
|
|
|
697 <tool file="emboss_5/emboss_wordcount.xml" />
|
|
|
698 <tool file="emboss_5/emboss_wordmatch.xml" />
|
|
|
699 </section>
|
|
|
700 -->
|
|
|
701 </toolbox>
|
