Mercurial > repos > pjbriggs > weeder2
annotate weeder2_wrapper.xml @ 3:f19e18ab01b1 draft
Uploaded v2.0.2 (use conda for dependency resolution)
| author | pjbriggs |
|---|---|
| date | Mon, 05 Mar 2018 10:19:50 -0500 |
| parents | 3c5f10f7dd40 |
| children | 89315bdc1a8c |
| rev | line source |
|---|---|
|
3
f19e18ab01b1
Uploaded v2.0.2 (use conda for dependency resolution)
pjbriggs
parents:
2
diff
changeset
|
1 <tool id="motiffinding_weeder2" name="Weeder2" version="2.0.2"> |
| 0 | 2 <description>Motif discovery in sequences from coregulated genes of a single species</description> |
|
3
f19e18ab01b1
Uploaded v2.0.2 (use conda for dependency resolution)
pjbriggs
parents:
2
diff
changeset
|
3 <macros> |
|
f19e18ab01b1
Uploaded v2.0.2 (use conda for dependency resolution)
pjbriggs
parents:
2
diff
changeset
|
4 <import>weeder2_macros.xml</import> |
|
f19e18ab01b1
Uploaded v2.0.2 (use conda for dependency resolution)
pjbriggs
parents:
2
diff
changeset
|
5 </macros> |
|
2
3c5f10f7dd40
Updated to tool version 2.0.1 (use data table to locate freqfiles).
pjbriggs
parents:
1
diff
changeset
|
6 <requirements> |
|
3c5f10f7dd40
Updated to tool version 2.0.1 (use data table to locate freqfiles).
pjbriggs
parents:
1
diff
changeset
|
7 <requirement type="package" version="2.0">weeder</requirement> |
|
3c5f10f7dd40
Updated to tool version 2.0.1 (use data table to locate freqfiles).
pjbriggs
parents:
1
diff
changeset
|
8 </requirements> |
|
3
f19e18ab01b1
Uploaded v2.0.2 (use conda for dependency resolution)
pjbriggs
parents:
2
diff
changeset
|
9 <command><![CDATA[ |
|
f19e18ab01b1
Uploaded v2.0.2 (use conda for dependency resolution)
pjbriggs
parents:
2
diff
changeset
|
10 @CONDA_WEEDER2_FREQFILES_PATH@ && |
|
f19e18ab01b1
Uploaded v2.0.2 (use conda for dependency resolution)
pjbriggs
parents:
2
diff
changeset
|
11 bash $__tool_directory__/weeder2_wrapper.sh |
|
2
3c5f10f7dd40
Updated to tool version 2.0.1 (use data table to locate freqfiles).
pjbriggs
parents:
1
diff
changeset
|
12 $sequence_file $species_code ${species_code.fields.path} |
| 0 | 13 $output_motifs_file $output_matrix_file |
| 14 $strands | |
| 15 #if $chipseq.use_chipseq | |
| 16 -chipseq -top $chipseq.top | |
| 17 #end if | |
| 18 #if str( $advanced_options.advanced_options_selector ) == "on" | |
| 19 -maxm $advanced_options.n_motifs_report | |
| 20 -b $advanced_options.n_motifs_build | |
| 21 -sim $advanced_options.sim_threshold | |
| 22 -em $advanced_options.em_cycles | |
| 23 #end if | |
|
3
f19e18ab01b1
Uploaded v2.0.2 (use conda for dependency resolution)
pjbriggs
parents:
2
diff
changeset
|
24 ]]></command> |
| 0 | 25 <inputs> |
| 26 <param name="sequence_file" type="data" format="fasta" label="Input sequence" /> | |
| 27 <param name="species_code" type="select" label="Species to use for background comparison"> | |
|
2
3c5f10f7dd40
Updated to tool version 2.0.1 (use data table to locate freqfiles).
pjbriggs
parents:
1
diff
changeset
|
28 <options from_data_table="weeder2"> |
|
3c5f10f7dd40
Updated to tool version 2.0.1 (use data table to locate freqfiles).
pjbriggs
parents:
1
diff
changeset
|
29 </options> |
| 0 | 30 </param> |
| 31 <param name="strands" label="Use both strands of sequence" type="boolean" | |
| 32 truevalue="" falsevalue="-ss" checked="True" | |
| 33 help="If not checked then use -ss option" /> | |
| 34 <conditional name="chipseq"> | |
| 35 <param name="use_chipseq" type="boolean" | |
| 36 label="Use the ChIP-seq heuristic" | |
| 37 help="Speeds up the computation (-chipseq)" | |
| 38 truevalue="yes" falsevalue="no" checked="on" /> | |
| 39 <when value="yes"> | |
| 40 <param name="top" type="integer" value="100" | |
| 41 label="Number of top input sequences with oligos to scan for" | |
| 42 help="Increase this value to improve the chance of finding motifs enriched only in a subset of your input sequences (-top)" /> | |
| 43 </when> | |
| 44 <when value="no"></when> | |
| 45 </conditional> | |
| 46 <conditional name="advanced_options"> | |
| 47 <param name="advanced_options_selector" type="select" | |
| 48 label="Display advanced options"> | |
| 49 <option value="off">Hide</option> | |
| 50 <option value="on">Display</option> | |
| 51 </param> | |
| 52 <when value="on"> | |
| 53 <param name="n_motifs_report" type="integer" value="25" | |
| 54 label="Number of discovered motifs to report" help="(-maxm)" /> | |
| 55 <param name="n_motifs_build" type="integer" value="50" | |
| 56 label="Number of top scoring motifs to build occurrences matrix profiles and outputs for" | |
| 57 help="(-b)" /> | |
| 58 <param name="sim_threshold" type="float" min="0.0" max="1.0" value="0.95" | |
| 59 label="Similarity threshold for the redundancy filter" | |
| 60 help="Remove motifs that are too similar, with lower values imposing a stricter filter. Must be between 0.0 and 1.0 (-sim)" /> | |
| 61 <param name="em_cycles" type="integer" min="0" max="100" value="1" | |
| 62 label="Number of expectation maximization (EM) cycles to perform" | |
| 63 help="Number of cycles must be between 0 and 100 (-em)" /> | |
| 64 </when> | |
| 65 <when value="off"> | |
| 66 </when> | |
| 67 </conditional> | |
| 68 </inputs> | |
| 69 <outputs> | |
| 70 <data name="output_motifs_file" format="txt" label="Weeder2 on ${on_string} (motifs)" /> | |
| 71 <data name="output_matrix_file" format="txt" label="Weeder2 on ${on_string} (matrix)" /> | |
| 72 </outputs> | |
| 73 <tests> | |
| 74 <test> | |
| 75 <param name="sequence_file" value="weeder_in.fa" ftype="fasta" /> | |
| 76 <param name="species_code" value="MM" /> | |
| 77 <output name="output_motifs_file" file="weeder2_motifs.out" lines_diff="2" /> | |
| 78 <output name="output_matrix_file" file="weeder2_matrix.out" /> | |
| 79 </test> | |
| 80 </tests> | |
| 81 <help> | |
| 82 | |
| 83 .. class:: infomark | |
| 84 | |
| 85 **What it does** | |
| 86 | |
| 87 Weeder2 is a program for finding novel motifs (transcription factor binding sites) | |
| 88 conserved in a set of regulatory regions of related genes. | |
| 89 | |
| 90 ------------- | |
| 91 | |
| 92 .. class:: infomark | |
| 93 | |
| 94 **Usage advice** | |
| 95 | |
| 96 Guidelines on how to use this tool can be seen in Zambelli et al. 2014 (see link | |
| 97 below), but the following is a brief guide. Please note that **motifs** are a model | |
| 98 or matrix that describes a set of sequences that may differ in the base composition. | |
| 99 **Oligos** are specific sequences found within the input sequences or genomic | |
| 100 background. | |
| 101 | |
| 102 **Input sequence** (in FASTA format) should be short (100-200bp) and be reasonably | |
| 103 expected to contain an enriched motif(s). This is not generally an issue with | |
| 104 transcription factor ChIP-seq derived sequences centred on the summit of binding | |
| 105 regions that are expected to contain a dominant motif and possibly secondary motifs. | |
| 106 | |
| 107 There is **no need to mask sequence for repetitive sequence** as factors may | |
| 108 legitimately bind repetitive sequence. | |
| 109 | |
| 110 **Use both strands of sequence** by default, unless there is a specific reason not | |
| 111 to do so. | |
| 112 | |
| 113 **Species to use for background comparison** should match the genome used to | |
| 114 generate the **input sequence**. The background genome motif frequencies are | |
| 115 generated from within the promoter regions of annotated genes and are shown to be a | |
| 116 good background for both promoter and other regulatory regions. | |
| 117 | |
| 118 **Use the ChIP-seq heuristic** (-chipseq) when there are a large number of | |
| 119 input sequences (hundreds or thousands). When -chipseq is used Weeder will use | |
| 120 only oligos from the first 100 sequences to build motifs with which it scans | |
| 121 all of the input sequences. This speeds up the computational time without too much | |
| 122 risk of losing important motifs. Even if not strictly necessary it's advisable to | |
| 123 order input sequences by their significance, e.g. fold enrichment or Pvalue. For | |
| 124 large data sets (-top) should be set to a number equating at least 10 to 20% of | |
| 125 input sequences (as recommended by the authors). | |
| 126 | |
| 127 **Number of discovered motifs to report** (-maxm) limits the number of reported | |
| 128 motifs even if there are more than -maxm. **Number of top scoring motifs to build | |
| 129 occurrences matrix profiles and outputs for** (-b) changes the number of top | |
| 130 scoring motifs of length 6, 8 and 10 for which the occurrence matrix is built. | |
| 131 Increasing -b may result in a larger number of reported motifs, but with potentially | |
| 132 more of low significance and increases the computational time. If increasing -b does | |
| 133 not result in more motifs in your results it means that the additional motifs are | |
| 134 filtered out by the redundancy filter or that the maximum number of reported motifs | |
| 135 set by -maxm has been reached. | |
| 136 | |
| 137 **Similarity threshold for the redundancy filter** (-sim) default setting is | |
| 138 recommended. | |
| 139 | |
| 140 **Number of expectation maximization (EM) cycles to perform** (-em) default is | |
| 141 recommended. The option is included to help "clean up" the resulting motif matrices. | |
| 142 In this version the number of EM steps can be increased, which can be useful for | |
| 143 motifs with highly redundant stretches of sequence. | |
| 144 | |
| 145 ------------- | |
| 146 | |
| 147 .. class:: infomark | |
| 148 | |
| 149 **A note on the results** | |
| 150 | |
| 151 The resulting matrices are the result of scanning (by default both strands) for | |
| 152 oligos of length 6, 8 and 8, allowing 1, 2 and 3 substitutions respectively. The | |
| 153 matrices within the matrix.w2 file can be input into other tools. The recommended | |
| 154 next step is to use **STAMP** (http://www.benoslab.pitt.edu/stamp/), which displays | |
| 155 the motifs as logos and identifies matches with libraries of known DNA binding | |
| 156 motifs, such as TRANSFAC or JASPAR. | |
| 157 | |
| 158 ------------- | |
| 159 | |
| 160 .. class:: infomark | |
| 161 | |
| 162 **Credits** | |
| 163 | |
| 164 This Galaxy tool has been developed by Peter Briggs and Ian Donaldson within the | |
| 165 Bioinformatics Core Facility at the University of Manchester, and runs the Weeder2 | |
| 166 motif discovery package: | |
| 167 | |
| 168 * Zambelli, F., Pesole, G. and Pavesi, G. 2014. Using Weeder, Pscan, and PscanChIP | |
| 169 for the Discovery of Enriched Transcription Factor Binding Site Motifs in | |
| 170 Nucleotide Sequences. Current Protocols in Bioinformatics. 47:2.11:2.11.1–2.11.31. | |
| 171 * http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi0211s47/full | |
| 172 | |
| 173 This tool is compatible with Weeder 2.0: | |
| 174 | |
| 175 * http://159.149.160.51/modtools/downloads/weeder2.html | |
| 176 | |
| 177 Please kindly acknowledge both this Galaxy tool, the Weeder package and the utility | |
| 178 scripts if you use it in your work. | |
| 179 </help> | |
| 1 | 180 <citations> |
| 181 <!-- | |
| 182 See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set | |
| 183 Can be either DOI or Bibtex | |
| 184 Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex | |
| 185 --> | |
| 186 <citation type="doi">10.1002/0471250953.bi0211s47</citation> | |
| 187 </citations> | |
| 0 | 188 </tool> |