Mercurial > repos > pjbriggs > weeder2
annotate weeder2_wrapper.xml @ 4:89315bdc1a8c draft default tip
Uploaded tool version 2.0.3.
| author | pjbriggs |
|---|---|
| date | Wed, 26 Sep 2018 10:12:56 -0400 |
| parents | f19e18ab01b1 |
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| rev | line source |
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| 4 | 1 <tool id="motiffinding_weeder2" name="Weeder2" version="2.0.3"> |
| 0 | 2 <description>Motif discovery in sequences from coregulated genes of a single species</description> |
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3 <requirements> |
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4 <requirement type="package" version="2.0">weeder</requirement> |
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5 </requirements> |
| 4 | 6 <command detect_errors="exit_code"><![CDATA[ |
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f19e18ab01b1
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7 bash $__tool_directory__/weeder2_wrapper.sh |
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8 $sequence_file $species_code ${species_code.fields.path} |
| 0 | 9 $output_motifs_file $output_matrix_file |
| 10 $strands | |
| 11 #if $chipseq.use_chipseq | |
| 12 -chipseq -top $chipseq.top | |
| 13 #end if | |
| 14 #if str( $advanced_options.advanced_options_selector ) == "on" | |
| 15 -maxm $advanced_options.n_motifs_report | |
| 16 -b $advanced_options.n_motifs_build | |
| 17 -sim $advanced_options.sim_threshold | |
| 18 -em $advanced_options.em_cycles | |
| 19 #end if | |
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f19e18ab01b1
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20 ]]></command> |
| 0 | 21 <inputs> |
| 22 <param name="sequence_file" type="data" format="fasta" label="Input sequence" /> | |
| 23 <param name="species_code" type="select" label="Species to use for background comparison"> | |
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24 <options from_data_table="weeder2"> |
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25 </options> |
| 0 | 26 </param> |
| 27 <param name="strands" label="Use both strands of sequence" type="boolean" | |
| 28 truevalue="" falsevalue="-ss" checked="True" | |
| 29 help="If not checked then use -ss option" /> | |
| 30 <conditional name="chipseq"> | |
| 31 <param name="use_chipseq" type="boolean" | |
| 32 label="Use the ChIP-seq heuristic" | |
| 33 help="Speeds up the computation (-chipseq)" | |
| 34 truevalue="yes" falsevalue="no" checked="on" /> | |
| 35 <when value="yes"> | |
| 36 <param name="top" type="integer" value="100" | |
| 37 label="Number of top input sequences with oligos to scan for" | |
| 38 help="Increase this value to improve the chance of finding motifs enriched only in a subset of your input sequences (-top)" /> | |
| 39 </when> | |
| 40 <when value="no"></when> | |
| 41 </conditional> | |
| 42 <conditional name="advanced_options"> | |
| 43 <param name="advanced_options_selector" type="select" | |
| 44 label="Display advanced options"> | |
| 45 <option value="off">Hide</option> | |
| 46 <option value="on">Display</option> | |
| 47 </param> | |
| 48 <when value="on"> | |
| 49 <param name="n_motifs_report" type="integer" value="25" | |
| 50 label="Number of discovered motifs to report" help="(-maxm)" /> | |
| 51 <param name="n_motifs_build" type="integer" value="50" | |
| 52 label="Number of top scoring motifs to build occurrences matrix profiles and outputs for" | |
| 53 help="(-b)" /> | |
| 54 <param name="sim_threshold" type="float" min="0.0" max="1.0" value="0.95" | |
| 55 label="Similarity threshold for the redundancy filter" | |
| 56 help="Remove motifs that are too similar, with lower values imposing a stricter filter. Must be between 0.0 and 1.0 (-sim)" /> | |
| 57 <param name="em_cycles" type="integer" min="0" max="100" value="1" | |
| 58 label="Number of expectation maximization (EM) cycles to perform" | |
| 59 help="Number of cycles must be between 0 and 100 (-em)" /> | |
| 60 </when> | |
| 61 <when value="off"> | |
| 62 </when> | |
| 63 </conditional> | |
| 64 </inputs> | |
| 65 <outputs> | |
| 66 <data name="output_motifs_file" format="txt" label="Weeder2 on ${on_string} (motifs)" /> | |
| 67 <data name="output_matrix_file" format="txt" label="Weeder2 on ${on_string} (matrix)" /> | |
| 68 </outputs> | |
| 69 <tests> | |
| 70 <test> | |
| 71 <param name="sequence_file" value="weeder_in.fa" ftype="fasta" /> | |
| 72 <param name="species_code" value="MM" /> | |
| 73 <output name="output_motifs_file" file="weeder2_motifs.out" lines_diff="2" /> | |
| 74 <output name="output_matrix_file" file="weeder2_matrix.out" /> | |
| 75 </test> | |
| 76 </tests> | |
| 77 <help> | |
| 78 | |
| 79 .. class:: infomark | |
| 80 | |
| 81 **What it does** | |
| 82 | |
| 83 Weeder2 is a program for finding novel motifs (transcription factor binding sites) | |
| 84 conserved in a set of regulatory regions of related genes. | |
| 85 | |
| 86 ------------- | |
| 87 | |
| 88 .. class:: infomark | |
| 89 | |
| 90 **Usage advice** | |
| 91 | |
| 92 Guidelines on how to use this tool can be seen in Zambelli et al. 2014 (see link | |
| 93 below), but the following is a brief guide. Please note that **motifs** are a model | |
| 94 or matrix that describes a set of sequences that may differ in the base composition. | |
| 95 **Oligos** are specific sequences found within the input sequences or genomic | |
| 96 background. | |
| 97 | |
| 98 **Input sequence** (in FASTA format) should be short (100-200bp) and be reasonably | |
| 99 expected to contain an enriched motif(s). This is not generally an issue with | |
| 100 transcription factor ChIP-seq derived sequences centred on the summit of binding | |
| 101 regions that are expected to contain a dominant motif and possibly secondary motifs. | |
| 102 | |
| 103 There is **no need to mask sequence for repetitive sequence** as factors may | |
| 104 legitimately bind repetitive sequence. | |
| 105 | |
| 106 **Use both strands of sequence** by default, unless there is a specific reason not | |
| 107 to do so. | |
| 108 | |
| 109 **Species to use for background comparison** should match the genome used to | |
| 110 generate the **input sequence**. The background genome motif frequencies are | |
| 111 generated from within the promoter regions of annotated genes and are shown to be a | |
| 112 good background for both promoter and other regulatory regions. | |
| 113 | |
| 114 **Use the ChIP-seq heuristic** (-chipseq) when there are a large number of | |
| 115 input sequences (hundreds or thousands). When -chipseq is used Weeder will use | |
| 116 only oligos from the first 100 sequences to build motifs with which it scans | |
| 117 all of the input sequences. This speeds up the computational time without too much | |
| 118 risk of losing important motifs. Even if not strictly necessary it's advisable to | |
| 119 order input sequences by their significance, e.g. fold enrichment or Pvalue. For | |
| 120 large data sets (-top) should be set to a number equating at least 10 to 20% of | |
| 121 input sequences (as recommended by the authors). | |
| 122 | |
| 123 **Number of discovered motifs to report** (-maxm) limits the number of reported | |
| 124 motifs even if there are more than -maxm. **Number of top scoring motifs to build | |
| 125 occurrences matrix profiles and outputs for** (-b) changes the number of top | |
| 126 scoring motifs of length 6, 8 and 10 for which the occurrence matrix is built. | |
| 127 Increasing -b may result in a larger number of reported motifs, but with potentially | |
| 128 more of low significance and increases the computational time. If increasing -b does | |
| 129 not result in more motifs in your results it means that the additional motifs are | |
| 130 filtered out by the redundancy filter or that the maximum number of reported motifs | |
| 131 set by -maxm has been reached. | |
| 132 | |
| 133 **Similarity threshold for the redundancy filter** (-sim) default setting is | |
| 134 recommended. | |
| 135 | |
| 136 **Number of expectation maximization (EM) cycles to perform** (-em) default is | |
| 137 recommended. The option is included to help "clean up" the resulting motif matrices. | |
| 138 In this version the number of EM steps can be increased, which can be useful for | |
| 139 motifs with highly redundant stretches of sequence. | |
| 140 | |
| 141 ------------- | |
| 142 | |
| 143 .. class:: infomark | |
| 144 | |
| 145 **A note on the results** | |
| 146 | |
| 147 The resulting matrices are the result of scanning (by default both strands) for | |
| 148 oligos of length 6, 8 and 8, allowing 1, 2 and 3 substitutions respectively. The | |
| 149 matrices within the matrix.w2 file can be input into other tools. The recommended | |
| 150 next step is to use **STAMP** (http://www.benoslab.pitt.edu/stamp/), which displays | |
| 151 the motifs as logos and identifies matches with libraries of known DNA binding | |
| 152 motifs, such as TRANSFAC or JASPAR. | |
| 153 | |
| 154 ------------- | |
| 155 | |
| 156 .. class:: infomark | |
| 157 | |
| 158 **Credits** | |
| 159 | |
| 160 This Galaxy tool has been developed by Peter Briggs and Ian Donaldson within the | |
| 161 Bioinformatics Core Facility at the University of Manchester, and runs the Weeder2 | |
| 162 motif discovery package: | |
| 163 | |
| 164 * Zambelli, F., Pesole, G. and Pavesi, G. 2014. Using Weeder, Pscan, and PscanChIP | |
| 165 for the Discovery of Enriched Transcription Factor Binding Site Motifs in | |
| 166 Nucleotide Sequences. Current Protocols in Bioinformatics. 47:2.11:2.11.1–2.11.31. | |
| 167 * http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi0211s47/full | |
| 168 | |
| 169 This tool is compatible with Weeder 2.0: | |
| 170 | |
| 171 * http://159.149.160.51/modtools/downloads/weeder2.html | |
| 172 | |
| 173 Please kindly acknowledge both this Galaxy tool, the Weeder package and the utility | |
| 174 scripts if you use it in your work. | |
| 175 </help> | |
| 1 | 176 <citations> |
| 177 <!-- | |
| 178 See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set | |
| 179 Can be either DOI or Bibtex | |
| 180 Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex | |
| 181 --> | |
| 182 <citation type="doi">10.1002/0471250953.bi0211s47</citation> | |
| 183 </citations> | |
| 0 | 184 </tool> |