Mercurial > repos > iuc > meme_chip
annotate meme_chip.xml @ 7:c321ab02c2a0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
| author | iuc |
|---|---|
| date | Fri, 20 Apr 2018 09:03:24 -0400 |
| parents | 444093446b0b |
| children | 81c0806236ef |
| rev | line source |
|---|---|
| 5 | 1 <tool id="meme_chip" name="MEME-ChIP" version="4.11.2"> |
| 0 | 2 <description>- motif discovery, enrichment analysis and clustering on large nucleotide datasets</description> |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 5 | 7 <code file="get_meme_motif_databases.py" /> |
| 0 | 8 <command detect_errors="exit_code"><![CDATA[ |
| 3 | 9 #import os |
| 10 #set primary_output = $os.path.join($output.files_path, "index.html") | |
| 5 | 11 meme-chip '$input' |
| 0 | 12 -noecho |
| 6 | 13 #if $control: |
| 3 | 14 -neg '$control' |
| 15 #end if | |
| 6 | 16 $sequence_alphabet |
| 0 | 17 -o '$output.files_path' |
|
7
c321ab02c2a0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
parents:
6
diff
changeset
|
18 #if str($options_type_cond.options_type)=='advanced': |
| 5 | 19 ## FIXME: CentriMo cannot be run, See the comments in the input section. |
| 20 ## #set run_centrimo = $options_type_cond.run_centrimo_cond.run_centrimo | |
| 3 | 21 ## #if str($run_centrimo) == "yes": |
| 22 ## -db $options_type_cond.run_centrimo_cond.meme_motif_databases.fields.path | |
| 6 | 23 ## #if $options_type_cond.run_centrimo_cond.centrimo_local: |
| 3 | 24 ## -centrimo-local |
| 25 ## #end if | |
| 6 | 26 ## #if $options_type_cond.run_centrimo_cond.centrimo_score: |
| 3 | 27 ## -centrimo-score $options_type_cond.run_centrimo_cond.centrimo_score |
| 28 ## #end if | |
| 6 | 29 ## #if $options_type_cond.run_centrimo_cond.centrimo_maxreg: |
| 3 | 30 ## -centrimo-maxreg $options_type_cond.run_centrimo_cond.centrimo_maxreg |
| 31 ## #end if | |
| 6 | 32 ## #if $options_type_cond.run_centrimo_cond.centrimo_ethresh: |
| 3 | 33 ## -centrimo-ethresh $options_type_cond.run_centrimo_cond.centrimo_ethresh |
| 34 ## #end if | |
| 6 | 35 ## #if $options_type_cond.run_centrimo_cond.centrimo_noseq: |
| 3 | 36 ## -centrimo-noseq |
| 37 ## #end if | |
| 6 | 38 ## #if $options_type_cond.run_centrimo_cond.centrimo_flip: |
| 3 | 39 ## -centrimo-flip |
| 40 ## #end if | |
| 41 ## #end if | |
|
7
c321ab02c2a0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
parents:
6
diff
changeset
|
42 $options_type_cond.search_given_strand |
| 0 | 43 -order $options_type_cond.background_model_order |
| 3 | 44 #if str($options_type_cond.subsampling_cond.subsampling) == "no": |
| 0 | 45 -norand |
|
7
c321ab02c2a0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
parents:
6
diff
changeset
|
46 #if $options_type_cond.subsampling_cond.subsampling.seed: |
| 0 | 47 -seed $options_type_cond.subsampling_cond.subsampling.seed |
| 48 #end if | |
| 49 #end if | |
| 6 | 50 #if $options_type_cond.nmeme: |
| 0 | 51 -nmeme $options_type_cond.nmeme |
| 52 #end if | |
| 6 | 53 #if $options_type_cond.ccut: |
| 0 | 54 -ccut $options_type_cond.ccut |
| 55 #end if | |
| 56 -group-thresh $options_type_cond.group_threash | |
|
7
c321ab02c2a0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
parents:
6
diff
changeset
|
57 #if str($options_type_cond.group_weak): |
| 0 | 58 -group-weak $options_type_cond.group_weak |
| 59 #end if | |
| 5 | 60 -filter-thresh $options_type_cond.filter_thresh |
|
7
c321ab02c2a0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
parents:
6
diff
changeset
|
61 $options_type_cond.old_clustering |
| 0 | 62 -meme-mod $options_type_cond.meme_mod |
| 6 | 63 #if $options_type_cond.meme_minw: |
| 0 | 64 -meme-minw $options_type_cond.meme_minw |
| 65 #end if | |
| 6 | 66 #if $options_type_cond.meme_maxw: |
| 0 | 67 -meme-maxw $options_type_cond.meme_maxw |
| 68 #end if | |
| 6 | 69 #if $options_type_cond.meme_nmotifs: |
| 0 | 70 -meme-nmotifs $options_type_cond.meme_nmotifs |
| 71 #end if | |
| 6 | 72 #if $options_type_cond.meme_minsites: |
| 0 | 73 -meme-minsites $options_type_cond.meme_minsites |
| 74 #end if | |
| 6 | 75 #if $options_type_cond.meme_maxsites: |
| 0 | 76 -meme-maxsites $options_type_cond.meme_maxsites |
| 77 #end if | |
|
7
c321ab02c2a0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
parents:
6
diff
changeset
|
78 $options_type_cond.meme_pal |
| 0 | 79 -dreme-e $options_type_cond.dreme_e |
| 80 -dreme-m $options_type_cond.dreme_m | |
| 81 -spamo-skip | |
| 82 -fimo-skip | |
| 83 #end if | |
| 3 | 84 && rm '$output' |
| 85 && ln -s $primary_output '$output' | |
| 86 ]]></command> | |
| 0 | 87 <inputs> |
| 88 <param name="input" type="data" format="fasta" label="Primary sequences" help="Nucleotide sequences must have equal length"/> | |
| 3 | 89 <param name="control" type="data" format="fasta" optional="true" label="Control sequences" help="If no selection, positive sequences in the input are shuffled to create the negative set"/> |
| 0 | 90 <param name="sequence_alphabet" type="select" label="Sequence alphabet"> |
| 5 | 91 <option value="-dna" selected="true">DNA</option> |
| 92 <option value="-rna">RNA</option> | |
| 0 | 93 </param> |
| 94 <conditional name="options_type_cond"> | |
| 95 <param name="options_type" type="select" label="Options Configuration"> | |
| 96 <option value="basic" selected="true">Basic</option> | |
| 97 <option value="advanced">Advanced</option> | |
| 98 </param> | |
| 99 <when value="basic"/> | |
| 100 <when value="advanced"> | |
| 3 | 101 <!-- |
| 102 FIXME: CentriMo cannot be run since the tool form cannot populate the mem_motif_database select list below. | |
| 103 <conditional name="run_centrimo_cond"> | |
| 104 <param name="run_centrimo" type="select" label="Run TOMTOM and CentriMo?"> | |
| 105 <option value="yes" selected="true">Yes</option> | |
| 106 <option value="no">No</option> | |
| 107 </param> | |
| 108 <when value="yes"> | |
| 109 | |
| 110 We have 2 dynamic select lists here. The first select list (meme_motif_database_dir) is populated from the meme_motif_databases | |
| 111 data table. The second select list (meme_motif_database) is dynamically re-rendered whenever the selection in the meme_motif_database_dir | |
| 112 select list is changed. This composition used to work (see Examples->Dynamic Options section of | |
| 113 https://docs.galaxyproject.org/en/latest/dev/schema.html) but no longer does. We'll have to figure out what is broken in | |
| 114 the dynamic options code in ~/parameters/basic.py in order to uncomment this block. | |
| 115 | |
| 116 <param name="meme_motif_database_dir" type="select" label="Select the motifs (DNA)" refresh_on_change="True"> | |
| 117 <options from_data_table="meme_motif_databases"> | |
| 118 <filter type="sort_by" column="1"/> | |
| 119 <validator type="no_options" message="No MEME motif databases are available for the selected input"/> | |
| 120 </options> | |
| 121 </param> | |
| 122 <param name="meme_motif_database" type="select" label="MEME motif database" dynamic_options="get_meme_motif_database_options(file_path=meme_motif_database_dir)"/> | |
| 123 <param name="centrimo_local" type="boolean" truevalue="true" falsevalue="" checked="False" label="Compute enrichment of all regions"/> | |
| 5 | 124 <param name="centrimo_score" type="integer" optional="true" value="0" min="0" label="Minimum allowed CentriMo match score"/> |
| 125 <param name="centrimo_maxreg" type="integer" optional="true" value="0" min="0" label="Maximum CentriMo region size to be considered"/> | |
| 126 <param name="centrimo_ethresh" type="integer" optional="true" value="0" min="0" label="CentriMo E-value threshold for reporting" /> | |
| 3 | 127 <param name="centrimo_noseq" type="boolean" truevalue="true" falsevalue="" checked="False" label="Store CentriMo sequence IDs in the output"/> |
| 128 <param name="centrimo_flip" type="boolean" truevalue="true" falsevalue="" checked="False" label="Reflect CentriMo matches on reverse strand around center"/> | |
| 129 </when> | |
| 130 <when value="no"/> | |
| 131 </conditional> | |
| 132 --> | |
| 0 | 133 <param name="background_model_order" type="select" label="Select the order of the Markov background model"> |
| 134 <option value="0">0-order model of sequences</option> | |
| 135 <option value="1" selected="True">1st order model of sequences</option> | |
| 136 <option value="2">2nd order model of sequences</option> | |
| 137 <option value="3">3rd order model of sequences</option> | |
| 138 <option value="4">4th order model of sequences</option> | |
| 139 </param> | |
|
7
c321ab02c2a0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
parents:
6
diff
changeset
|
140 <param name="nmeme" type="integer" optional="true" value="" min="1" label="Limit of sequences to pass to MEME"/> |
| 0 | 141 <conditional name="subsampling_cond"> |
| 142 <param name="subsampling" type="select" label="Should subsampling be random?" help="Select 'No' if your input sequences are sorted in order of confidence (best to worst)"> | |
| 143 <option value="yes" selected="true">Yes</option> | |
| 144 <option value="no">No</option> | |
| 145 </param> | |
| 146 <when value="yes"> | |
|
7
c321ab02c2a0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
parents:
6
diff
changeset
|
147 <param name="seed" type="integer" optional="true" value="" min="1" label="Seed for the randomized selection of sequences"/> |
| 0 | 148 </when> |
| 149 <when value="no"/> | |
| 150 </conditional> | |
| 5 | 151 <param name="ccut" type="integer" optional="true" value="100" min="0" label="maximum size of a sequence before it is cut down to a centered section" help="Zero value indicates the sequences should not be cut down"/> |
| 0 | 152 <param name="group_threash" type="float" value="0.05" min="0" label="Primary threshold for clustering motifs" /> |
| 5 | 153 <param name="group_weak" type="float" optional="true" value="0" min="0" label="Secondary threshold for clustering motifs" help="Zero value results in 2*primary threshold"/> |
| 0 | 154 <param name="filter_thresh" type="float" value="0.05" min="0" label="E-value threshold for including motifs"/> |
|
7
c321ab02c2a0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
parents:
6
diff
changeset
|
155 <param name="search_given_strand" type="boolean" truevalue="-norc" falsevalue="" checked="False" label="Search given strand only"/> |
|
c321ab02c2a0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
parents:
6
diff
changeset
|
156 <param argument="-old_clustering" type="boolean" truevalue="-old_clustering" falsevalue="" checked="False" label="Pick cluster seed motifs based only on significance"/> |
| 0 | 157 <param name="meme_mod" type="select" label="What is the expected motif site distribution?"> |
| 158 <option value="oops" selected="True">One occurance per sequence</option> | |
| 159 <option value="zoops">Zero or one occurances per sequence</option> | |
| 160 <option value="anr">Any number of repititions</option> | |
| 161 </param> | |
| 5 | 162 <param name="meme_minw" type="integer" optional="true" value="0" min="0" label="Minimum motif width"/> |
| 163 <param name="meme_maxw" type="integer" optional="true" value="0" min="0" label="Maximum motif width"/> | |
| 164 <param name="meme_nmotifs" type="integer" optional="true" value="0" min="0" label="Maximum number of motifs to find"/> | |
| 165 <param name="meme_minsites" type="integer" optional="true" value="0" min="0" label="Minimum number of sites per motif"/> | |
| 166 <param name="meme_maxsites" type="integer" optional="true" value="0" label="Maximum number of sites per motif"/> | |
|
7
c321ab02c2a0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
parents:
6
diff
changeset
|
167 <param argument="-meme_pal" type="boolean" truevalue="-meme-pal" falsevalue="" checked="False" label="Look for palindromes only"/> |
| 0 | 168 <param name="dreme_e" type="float" value="0.05" min="0" label="Stop DREME searching after reaching this E-value threshold"/> |
| 169 <param name="dreme_m" type="integer" value="10" min="1" label="Stop DREME searching after finding this many motifs" /> | |
| 170 </when> | |
| 171 </conditional> | |
| 172 <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False"> | |
| 173 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator> | |
| 174 </param> | |
| 175 </inputs> | |
| 176 <outputs> | |
| 177 <data name="output" format="html" label="${tool.name} (html) on ${on_string}"/> | |
| 178 </outputs> | |
| 179 <tests> | |
| 180 <test> | |
| 5 | 181 <param name="input" value="input1.fasta" ftype="fasta"/> |
| 182 <param name="non_commercial_use" value="True"/> | |
| 183 <output name="output" file="output1.html" ftype="html" compare="contains"/> | |
| 184 </test> | |
| 185 <test> | |
| 186 <param name="input" value="input1.fasta" ftype="fasta"/> | |
| 6 | 187 <param name="sequence_alphabet" value="-rna"/> |
| 5 | 188 <param name="options_type" value="advanced"/> |
| 189 <param name="background_model_order" value="0"/> | |
| 190 <param name="non_commercial_use" value="True"/> | |
| 191 <output name="output" file="output1.html" ftype="html" compare="contains"/> | |
| 0 | 192 </test> |
| 193 </tests> | |
| 194 <help> | |
| 195 .. class:: warningmark | |
| 196 | |
| 197 **WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted. | |
| 198 Before using, be sure to review, agree, and comply with the license.** | |
| 199 | |
| 200 MWMW-ChIP perform motif discovery, motif enrichment analysis and clustering on large nucleotide datasets. | |
| 201 | |
| 202 If you want to specify sequence weights, you must include them at the top of your input FASTA file. | |
| 203 | |
| 204 MEME discovers novel, ungapped motifs (recurring, fixed-length patterns) in your sequences (sample output from sequences). | |
| 205 MEME splits variable-length patterns into two or more separate motifs. A motif is a sequence pattern that occurs repeatedly | |
| 206 in a group of related sequences. MEME represents motifs as position-dependent letter-probability matrices which describe the | |
| 207 probability of each possible letter at each position in the pattern. Individual MEME motifs do not contain gaps. Patterns | |
| 208 with variable-length gaps are split by MEME into two or more separate motifs. MEME takes as input a group of sequences and | |
| 209 outputs as many motifs as requested. MEME uses statistical modeling techniques to automatically choose the best width, number | |
| 210 of occurrences, and description for each motif. | |
| 211 | |
| 212 .. class:: infomark | |
| 213 | |
| 214 For detailed information on MEME, click here_, or view the license_. | |
| 215 | |
| 216 .. _here: http://meme-suite.org/doc/meme.html?man_type=web | |
| 217 .. _license: http://meme-suite.org/doc/copyright.html?man_type=web | |
| 218 | |
| 219 </help> | |
| 220 <citations> | |
| 3 | 221 <citation type="doi">10.1093/bioinformatics/btr189</citation> |
| 0 | 222 </citations> |
| 223 </tool> | |
| 3 | 224 |