Mercurial > repos > iuc > meme_chip
annotate meme_chip.xml @ 8:81c0806236ef draft
Uploaded
| author | iuc |
|---|---|
| date | Thu, 12 Jul 2018 08:48:01 -0400 |
| parents | c321ab02c2a0 |
| children | 4fc125833bc2 |
| 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' |
|
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c321ab02c2a0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
parents:
6
diff
changeset
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18 #if str($options_type_cond.options_type)=='advanced': |
| 8 | 19 #if str($options_type_cond.run_centrimo_cond.run_centrimo) == "yes": |
| 20 -db $options_type_cond.run_centrimo_cond.meme_motif_databases.fields.path | |
| 21 #if $options_type_cond.run_centrimo_cond.centrimo_local: | |
| 22 -centrimo-local | |
| 23 #end if | |
| 24 #if $options_type_cond.run_centrimo_cond.centrimo_score: | |
| 25 -centrimo-score $options_type_cond.run_centrimo_cond.centrimo_score | |
| 26 #end if | |
| 27 #if $options_type_cond.run_centrimo_cond.centrimo_maxreg: | |
| 28 -centrimo-maxreg $options_type_cond.run_centrimo_cond.centrimo_maxreg | |
| 29 #end if | |
| 30 #if $options_type_cond.run_centrimo_cond.centrimo_ethresh: | |
| 31 -centrimo-ethresh $options_type_cond.run_centrimo_cond.centrimo_ethresh | |
| 32 #end if | |
| 33 #if $options_type_cond.run_centrimo_cond.centrimo_noseq: | |
| 34 -centrimo-noseq | |
| 35 #end if | |
| 36 #if $options_type_cond.run_centrimo_cond.centrimo_flip: | |
| 37 -centrimo-flip | |
| 38 #end if | |
| 39 #end if | |
|
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c321ab02c2a0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
parents:
6
diff
changeset
|
40 $options_type_cond.search_given_strand |
| 0 | 41 -order $options_type_cond.background_model_order |
| 3 | 42 #if str($options_type_cond.subsampling_cond.subsampling) == "no": |
| 0 | 43 -norand |
|
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c321ab02c2a0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
parents:
6
diff
changeset
|
44 #if $options_type_cond.subsampling_cond.subsampling.seed: |
| 0 | 45 -seed $options_type_cond.subsampling_cond.subsampling.seed |
| 46 #end if | |
| 47 #end if | |
| 6 | 48 #if $options_type_cond.nmeme: |
| 0 | 49 -nmeme $options_type_cond.nmeme |
| 50 #end if | |
| 6 | 51 #if $options_type_cond.ccut: |
| 0 | 52 -ccut $options_type_cond.ccut |
| 53 #end if | |
| 54 -group-thresh $options_type_cond.group_threash | |
|
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c321ab02c2a0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
parents:
6
diff
changeset
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55 #if str($options_type_cond.group_weak): |
| 0 | 56 -group-weak $options_type_cond.group_weak |
| 57 #end if | |
| 5 | 58 -filter-thresh $options_type_cond.filter_thresh |
|
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c321ab02c2a0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
parents:
6
diff
changeset
|
59 $options_type_cond.old_clustering |
| 0 | 60 -meme-mod $options_type_cond.meme_mod |
| 6 | 61 #if $options_type_cond.meme_minw: |
| 0 | 62 -meme-minw $options_type_cond.meme_minw |
| 63 #end if | |
| 6 | 64 #if $options_type_cond.meme_maxw: |
| 0 | 65 -meme-maxw $options_type_cond.meme_maxw |
| 66 #end if | |
| 6 | 67 #if $options_type_cond.meme_nmotifs: |
| 0 | 68 -meme-nmotifs $options_type_cond.meme_nmotifs |
| 69 #end if | |
| 6 | 70 #if $options_type_cond.meme_minsites: |
| 0 | 71 -meme-minsites $options_type_cond.meme_minsites |
| 72 #end if | |
| 6 | 73 #if $options_type_cond.meme_maxsites: |
| 0 | 74 -meme-maxsites $options_type_cond.meme_maxsites |
| 75 #end if | |
|
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c321ab02c2a0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742
iuc
parents:
6
diff
changeset
|
76 $options_type_cond.meme_pal |
| 0 | 77 -dreme-e $options_type_cond.dreme_e |
| 78 -dreme-m $options_type_cond.dreme_m | |
| 79 -spamo-skip | |
| 80 -fimo-skip | |
| 81 #end if | |
| 3 | 82 && rm '$output' |
| 83 && ln -s $primary_output '$output' | |
| 84 ]]></command> | |
| 0 | 85 <inputs> |
| 86 <param name="input" type="data" format="fasta" label="Primary sequences" help="Nucleotide sequences must have equal length"/> | |
| 3 | 87 <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 | 88 <param name="sequence_alphabet" type="select" label="Sequence alphabet"> |
| 5 | 89 <option value="-dna" selected="true">DNA</option> |
| 90 <option value="-rna">RNA</option> | |
| 0 | 91 </param> |
| 92 <conditional name="options_type_cond"> | |
| 93 <param name="options_type" type="select" label="Options Configuration"> | |
| 94 <option value="basic" selected="true">Basic</option> | |
| 95 <option value="advanced">Advanced</option> | |
| 96 </param> | |
| 97 <when value="basic"/> | |
| 98 <when value="advanced"> | |
| 3 | 99 <conditional name="run_centrimo_cond"> |
| 100 <param name="run_centrimo" type="select" label="Run TOMTOM and CentriMo?"> | |
| 101 <option value="yes" selected="true">Yes</option> | |
| 102 <option value="no">No</option> | |
| 103 </param> | |
| 104 <when value="yes"> | |
| 105 <param name="meme_motif_database_dir" type="select" label="Select the motifs (DNA)" refresh_on_change="True"> | |
| 106 <options from_data_table="meme_motif_databases"> | |
| 8 | 107 <column name="name" index="1"/> |
| 108 <column name="value" index="2"/> | |
| 3 | 109 <filter type="sort_by" column="1"/> |
| 110 <validator type="no_options" message="No MEME motif databases are available for the selected input"/> | |
| 111 </options> | |
| 112 </param> | |
| 113 <param name="meme_motif_database" type="select" label="MEME motif database" dynamic_options="get_meme_motif_database_options(file_path=meme_motif_database_dir)"/> | |
| 114 <param name="centrimo_local" type="boolean" truevalue="true" falsevalue="" checked="False" label="Compute enrichment of all regions"/> | |
| 5 | 115 <param name="centrimo_score" type="integer" optional="true" value="0" min="0" label="Minimum allowed CentriMo match score"/> |
| 116 <param name="centrimo_maxreg" type="integer" optional="true" value="0" min="0" label="Maximum CentriMo region size to be considered"/> | |
| 117 <param name="centrimo_ethresh" type="integer" optional="true" value="0" min="0" label="CentriMo E-value threshold for reporting" /> | |
| 3 | 118 <param name="centrimo_noseq" type="boolean" truevalue="true" falsevalue="" checked="False" label="Store CentriMo sequence IDs in the output"/> |
| 119 <param name="centrimo_flip" type="boolean" truevalue="true" falsevalue="" checked="False" label="Reflect CentriMo matches on reverse strand around center"/> | |
| 120 </when> | |
| 121 <when value="no"/> | |
| 122 </conditional> | |
| 0 | 123 <param name="background_model_order" type="select" label="Select the order of the Markov background model"> |
| 124 <option value="0">0-order model of sequences</option> | |
| 125 <option value="1" selected="True">1st order model of sequences</option> | |
| 126 <option value="2">2nd order model of sequences</option> | |
| 127 <option value="3">3rd order model of sequences</option> | |
| 128 <option value="4">4th order model of sequences</option> | |
| 129 </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
|
130 <param name="nmeme" type="integer" optional="true" value="" min="1" label="Limit of sequences to pass to MEME"/> |
| 0 | 131 <conditional name="subsampling_cond"> |
| 132 <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)"> | |
| 133 <option value="yes" selected="true">Yes</option> | |
| 134 <option value="no">No</option> | |
| 135 </param> | |
| 136 <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
|
137 <param name="seed" type="integer" optional="true" value="" min="1" label="Seed for the randomized selection of sequences"/> |
| 0 | 138 </when> |
| 139 <when value="no"/> | |
| 140 </conditional> | |
| 5 | 141 <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 | 142 <param name="group_threash" type="float" value="0.05" min="0" label="Primary threshold for clustering motifs" /> |
| 5 | 143 <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 | 144 <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
|
145 <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
|
146 <param argument="-old_clustering" type="boolean" truevalue="-old_clustering" falsevalue="" checked="False" label="Pick cluster seed motifs based only on significance"/> |
| 0 | 147 <param name="meme_mod" type="select" label="What is the expected motif site distribution?"> |
| 148 <option value="oops" selected="True">One occurance per sequence</option> | |
| 149 <option value="zoops">Zero or one occurances per sequence</option> | |
| 150 <option value="anr">Any number of repititions</option> | |
| 151 </param> | |
| 5 | 152 <param name="meme_minw" type="integer" optional="true" value="0" min="0" label="Minimum motif width"/> |
| 153 <param name="meme_maxw" type="integer" optional="true" value="0" min="0" label="Maximum motif width"/> | |
| 154 <param name="meme_nmotifs" type="integer" optional="true" value="0" min="0" label="Maximum number of motifs to find"/> | |
| 155 <param name="meme_minsites" type="integer" optional="true" value="0" min="0" label="Minimum number of sites per motif"/> | |
| 156 <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
|
157 <param argument="-meme_pal" type="boolean" truevalue="-meme-pal" falsevalue="" checked="False" label="Look for palindromes only"/> |
| 0 | 158 <param name="dreme_e" type="float" value="0.05" min="0" label="Stop DREME searching after reaching this E-value threshold"/> |
| 159 <param name="dreme_m" type="integer" value="10" min="1" label="Stop DREME searching after finding this many motifs" /> | |
| 160 </when> | |
| 161 </conditional> | |
| 162 <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"> | |
| 163 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator> | |
| 164 </param> | |
| 165 </inputs> | |
| 166 <outputs> | |
| 167 <data name="output" format="html" label="${tool.name} (html) on ${on_string}"/> | |
| 168 </outputs> | |
| 169 <tests> | |
| 170 <test> | |
| 5 | 171 <param name="input" value="input1.fasta" ftype="fasta"/> |
| 172 <param name="non_commercial_use" value="True"/> | |
| 173 <output name="output" file="output1.html" ftype="html" compare="contains"/> | |
| 174 </test> | |
| 175 <test> | |
| 176 <param name="input" value="input1.fasta" ftype="fasta"/> | |
| 6 | 177 <param name="sequence_alphabet" value="-rna"/> |
| 5 | 178 <param name="options_type" value="advanced"/> |
| 179 <param name="background_model_order" value="0"/> | |
| 180 <param name="non_commercial_use" value="True"/> | |
| 181 <output name="output" file="output1.html" ftype="html" compare="contains"/> | |
| 0 | 182 </test> |
| 183 </tests> | |
| 184 <help> | |
| 185 .. class:: warningmark | |
| 186 | |
| 187 **WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted. | |
| 188 Before using, be sure to review, agree, and comply with the license.** | |
| 189 | |
| 190 MWMW-ChIP perform motif discovery, motif enrichment analysis and clustering on large nucleotide datasets. | |
| 191 | |
| 192 If you want to specify sequence weights, you must include them at the top of your input FASTA file. | |
| 193 | |
| 194 MEME discovers novel, ungapped motifs (recurring, fixed-length patterns) in your sequences (sample output from sequences). | |
| 195 MEME splits variable-length patterns into two or more separate motifs. A motif is a sequence pattern that occurs repeatedly | |
| 196 in a group of related sequences. MEME represents motifs as position-dependent letter-probability matrices which describe the | |
| 197 probability of each possible letter at each position in the pattern. Individual MEME motifs do not contain gaps. Patterns | |
| 198 with variable-length gaps are split by MEME into two or more separate motifs. MEME takes as input a group of sequences and | |
| 199 outputs as many motifs as requested. MEME uses statistical modeling techniques to automatically choose the best width, number | |
| 200 of occurrences, and description for each motif. | |
| 201 | |
| 202 .. class:: infomark | |
| 203 | |
| 204 For detailed information on MEME, click here_, or view the license_. | |
| 205 | |
| 206 .. _here: http://meme-suite.org/doc/meme.html?man_type=web | |
| 207 .. _license: http://meme-suite.org/doc/copyright.html?man_type=web | |
| 208 | |
| 209 </help> | |
| 210 <citations> | |
| 3 | 211 <citation type="doi">10.1093/bioinformatics/btr189</citation> |
| 0 | 212 </citations> |
| 213 </tool> | |
| 3 | 214 |